/usr/share/R/doc/manual/R-admin.html is in r-doc-html 3.0.2-1ubuntu1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840 841 842 843 844 845 846 847 848 849 850 851 852 853 854 855 856 857 858 859 860 861 862 863 864 865 866 867 868 869 870 871 872 873 874 875 876 877 878 879 880 881 882 883 884 885 886 887 888 889 890 891 892 893 894 895 896 897 898 899 900 901 902 903 904 905 906 907 908 909 910 911 912 913 914 915 916 917 918 919 920 921 922 923 924 925 926 927 928 929 930 931 932 933 934 935 936 937 938 939 940 941 942 943 944 945 946 947 948 949 950 951 952 953 954 955 956 957 958 959 960 961 962 963 964 965 966 967 968 969 970 971 972 973 974 975 976 977 978 979 980 981 982 983 984 985 986 987 988 989 990 991 992 993 994 995 996 997 998 999 1000 1001 1002 1003 1004 1005 1006 1007 1008 1009 1010 1011 1012 1013 1014 1015 1016 1017 1018 1019 1020 1021 1022 1023 1024 1025 1026 1027 1028 1029 1030 1031 1032 1033 1034 1035 1036 1037 1038 1039 1040 1041 1042 1043 1044 1045 1046 1047 1048 1049 1050 1051 1052 1053 1054 1055 1056 1057 1058 1059 1060 1061 1062 1063 1064 1065 1066 1067 1068 1069 1070 1071 1072 1073 1074 1075 1076 1077 1078 1079 1080 1081 1082 1083 1084 1085 1086 1087 1088 1089 1090 1091 1092 1093 1094 1095 1096 1097 1098 1099 1100 1101 1102 1103 1104 1105 1106 1107 1108 1109 1110 1111 1112 1113 1114 1115 1116 1117 1118 1119 1120 1121 1122 1123 1124 1125 1126 1127 1128 1129 1130 1131 1132 1133 1134 1135 1136 1137 1138 1139 1140 1141 1142 1143 1144 1145 1146 1147 1148 1149 1150 1151 1152 1153 1154 1155 1156 1157 1158 1159 1160 1161 1162 1163 1164 1165 1166 1167 1168 1169 1170 1171 1172 1173 1174 1175 1176 1177 1178 1179 1180 1181 1182 1183 1184 1185 1186 1187 1188 1189 1190 1191 1192 1193 1194 1195 1196 1197 1198 1199 1200 1201 1202 1203 1204 1205 1206 1207 1208 1209 1210 1211 1212 1213 1214 1215 1216 1217 1218 1219 1220 1221 1222 1223 1224 1225 1226 1227 1228 1229 1230 1231 1232 1233 1234 1235 1236 1237 1238 1239 1240 1241 1242 1243 1244 1245 1246 1247 1248 1249 1250 1251 1252 1253 1254 1255 1256 1257 1258 1259 1260 1261 1262 1263 1264 1265 1266 1267 1268 1269 1270 1271 1272 1273 1274 1275 1276 1277 1278 1279 1280 1281 1282 1283 1284 1285 1286 1287 1288 1289 1290 1291 1292 1293 1294 1295 1296 1297 1298 1299 1300 1301 1302 1303 1304 1305 1306 1307 1308 1309 1310 1311 1312 1313 1314 1315 1316 1317 1318 1319 1320 1321 1322 1323 1324 1325 1326 1327 1328 1329 1330 1331 1332 1333 1334 1335 1336 1337 1338 1339 1340 1341 1342 1343 1344 1345 1346 1347 1348 1349 1350 1351 1352 1353 1354 1355 1356 1357 1358 1359 1360 1361 1362 1363 1364 1365 1366 1367 1368 1369 1370 1371 1372 1373 1374 1375 1376 1377 1378 1379 1380 1381 1382 1383 1384 1385 1386 1387 1388 1389 1390 1391 1392 1393 1394 1395 1396 1397 1398 1399 1400 1401 1402 1403 1404 1405 1406 1407 1408 1409 1410 1411 1412 1413 1414 1415 1416 1417 1418 1419 1420 1421 1422 1423 1424 1425 1426 1427 1428 1429 1430 1431 1432 1433 1434 1435 1436 1437 1438 1439 1440 1441 1442 1443 1444 1445 1446 1447 1448 1449 1450 1451 1452 1453 1454 1455 1456 1457 1458 1459 1460 1461 1462 1463 1464 1465 1466 1467 1468 1469 1470 1471 1472 1473 1474 1475 1476 1477 1478 1479 1480 1481 1482 1483 1484 1485 1486 1487 1488 1489 1490 1491 1492 1493 1494 1495 1496 1497 1498 1499 1500 1501 1502 1503 1504 1505 1506 1507 1508 1509 1510 1511 1512 1513 1514 1515 1516 1517 1518 1519 1520 1521 1522 1523 1524 1525 1526 1527 1528 1529 1530 1531 1532 1533 1534 1535 1536 1537 1538 1539 1540 1541 1542 1543 1544 1545 1546 1547 1548 1549 1550 1551 1552 1553 1554 1555 1556 1557 1558 1559 1560 1561 1562 1563 1564 1565 1566 1567 1568 1569 1570 1571 1572 1573 1574 1575 1576 1577 1578 1579 1580 1581 1582 1583 1584 1585 1586 1587 1588 1589 1590 1591 1592 1593 1594 1595 1596 1597 1598 1599 1600 1601 1602 1603 1604 1605 1606 1607 1608 1609 1610 1611 1612 1613 1614 1615 1616 1617 1618 1619 1620 1621 1622 1623 1624 1625 1626 1627 1628 1629 1630 1631 1632 1633 1634 1635 1636 1637 1638 1639 1640 1641 1642 1643 1644 1645 1646 1647 1648 1649 1650 1651 1652 1653 1654 1655 1656 1657 1658 1659 1660 1661 1662 1663 1664 1665 1666 1667 1668 1669 1670 1671 1672 1673 1674 1675 1676 1677 1678 1679 1680 1681 1682 1683 1684 1685 1686 1687 1688 1689 1690 1691 1692 1693 1694 1695 1696 1697 1698 1699 1700 1701 1702 1703 1704 1705 1706 1707 1708 1709 1710 1711 1712 1713 1714 1715 1716 1717 1718 1719 1720 1721 1722 1723 1724 1725 1726 1727 1728 1729 1730 1731 1732 1733 1734 1735 1736 1737 1738 1739 1740 1741 1742 1743 1744 1745 1746 1747 1748 1749 1750 1751 1752 1753 1754 1755 1756 1757 1758 1759 1760 1761 1762 1763 1764 1765 1766 1767 1768 1769 1770 1771 1772 1773 1774 1775 1776 1777 1778 1779 1780 1781 1782 1783 1784 1785 1786 1787 1788 1789 1790 1791 1792 1793 1794 1795 1796 1797 1798 1799 1800 1801 1802 1803 1804 1805 1806 1807 1808 1809 1810 1811 1812 1813 1814 1815 1816 1817 1818 1819 1820 1821 1822 1823 1824 1825 1826 1827 1828 1829 1830 1831 1832 1833 1834 1835 1836 1837 1838 1839 1840 1841 1842 1843 1844 1845 1846 1847 1848 1849 1850 1851 1852 1853 1854 1855 1856 1857 1858 1859 1860 1861 1862 1863 1864 1865 1866 1867 1868 1869 1870 1871 1872 1873 1874 1875 1876 1877 1878 1879 1880 1881 1882 1883 1884 1885 1886 1887 1888 1889 1890 1891 1892 1893 1894 1895 1896 1897 1898 1899 1900 1901 1902 1903 1904 1905 1906 1907 1908 1909 1910 1911 1912 1913 1914 1915 1916 1917 1918 1919 1920 1921 1922 1923 1924 1925 1926 1927 1928 1929 1930 1931 1932 1933 1934 1935 1936 1937 1938 1939 1940 1941 1942 1943 1944 1945 1946 1947 1948 1949 1950 1951 1952 1953 1954 1955 1956 1957 1958 1959 1960 1961 1962 1963 1964 1965 1966 1967 1968 1969 1970 1971 1972 1973 1974 1975 1976 1977 1978 1979 1980 1981 1982 1983 1984 1985 1986 1987 1988 1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 2017 2018 2019 2020 2021 2022 2023 2024 2025 2026 2027 2028 2029 2030 2031 2032 2033 2034 2035 2036 2037 2038 2039 2040 2041 2042 2043 2044 2045 2046 2047 2048 2049 2050 2051 2052 2053 2054 2055 2056 2057 2058 2059 2060 2061 2062 2063 2064 2065 2066 2067 2068 2069 2070 2071 2072 2073 2074 2075 2076 2077 2078 2079 2080 2081 2082 2083 2084 2085 2086 2087 2088 2089 2090 2091 2092 2093 2094 2095 2096 2097 2098 2099 2100 2101 2102 2103 2104 2105 2106 2107 2108 2109 2110 2111 2112 2113 2114 2115 2116 2117 2118 2119 2120 2121 2122 2123 2124 2125 2126 2127 2128 2129 2130 2131 2132 2133 2134 2135 2136 2137 2138 2139 2140 2141 2142 2143 2144 2145 2146 2147 2148 2149 2150 2151 2152 2153 2154 2155 2156 2157 2158 2159 2160 2161 2162 2163 2164 2165 2166 2167 2168 2169 2170 2171 2172 2173 2174 2175 2176 2177 2178 2179 2180 2181 2182 2183 2184 2185 2186 2187 2188 2189 2190 2191 2192 2193 2194 2195 2196 2197 2198 2199 2200 2201 2202 2203 2204 2205 2206 2207 2208 2209 2210 2211 2212 2213 2214 2215 2216 2217 2218 2219 2220 2221 2222 2223 2224 2225 2226 2227 2228 2229 2230 2231 2232 2233 2234 2235 2236 2237 2238 2239 2240 2241 2242 2243 2244 2245 2246 2247 2248 2249 2250 2251 2252 2253 2254 2255 2256 2257 2258 2259 2260 2261 2262 2263 2264 2265 2266 2267 2268 2269 2270 2271 2272 2273 2274 2275 2276 2277 2278 2279 2280 2281 2282 2283 2284 2285 2286 2287 2288 2289 2290 2291 2292 2293 2294 2295 2296 2297 2298 2299 2300 2301 2302 2303 2304 2305 2306 2307 2308 2309 2310 2311 2312 2313 2314 2315 2316 2317 2318 2319 2320 2321 2322 2323 2324 2325 2326 2327 2328 2329 2330 2331 2332 2333 2334 2335 2336 2337 2338 2339 2340 2341 2342 2343 2344 2345 2346 2347 2348 2349 2350 2351 2352 2353 2354 2355 2356 2357 2358 2359 2360 2361 2362 2363 2364 2365 2366 2367 2368 2369 2370 2371 2372 2373 2374 2375 2376 2377 2378 2379 2380 2381 2382 2383 2384 2385 2386 2387 2388 2389 2390 2391 2392 2393 2394 2395 2396 2397 2398 2399 2400 2401 2402 2403 2404 2405 2406 2407 2408 2409 2410 2411 2412 2413 2414 2415 2416 2417 2418 2419 2420 2421 2422 2423 2424 2425 2426 2427 2428 2429 2430 2431 2432 2433 2434 2435 2436 2437 2438 2439 2440 2441 2442 2443 2444 2445 2446 2447 2448 2449 2450 2451 2452 2453 2454 2455 2456 2457 2458 2459 2460 2461 2462 2463 2464 2465 2466 2467 2468 2469 2470 2471 2472 2473 2474 2475 2476 2477 2478 2479 2480 2481 2482 2483 2484 2485 2486 2487 2488 2489 2490 2491 2492 2493 2494 2495 2496 2497 2498 2499 2500 2501 2502 2503 2504 2505 2506 2507 2508 2509 2510 2511 2512 2513 2514 2515 2516 2517 2518 2519 2520 2521 2522 2523 2524 2525 2526 2527 2528 2529 2530 2531 2532 2533 2534 2535 2536 2537 2538 2539 2540 2541 2542 2543 2544 2545 2546 2547 2548 2549 2550 2551 2552 2553 2554 2555 2556 2557 2558 2559 2560 2561 2562 2563 2564 2565 2566 2567 2568 2569 2570 2571 2572 2573 2574 2575 2576 2577 2578 2579 2580 2581 2582 2583 2584 2585 2586 2587 2588 2589 2590 2591 2592 2593 2594 2595 2596 2597 2598 2599 2600 2601 2602 2603 2604 2605 2606 2607 2608 2609 2610 2611 2612 2613 2614 2615 2616 2617 2618 2619 2620 2621 2622 2623 2624 2625 2626 2627 2628 2629 2630 2631 2632 2633 2634 2635 2636 2637 2638 2639 2640 2641 2642 2643 2644 2645 2646 2647 2648 2649 2650 2651 2652 2653 2654 2655 2656 2657 2658 2659 2660 2661 2662 2663 2664 2665 2666 2667 2668 2669 2670 2671 2672 2673 2674 2675 2676 2677 2678 2679 2680 2681 2682 2683 2684 2685 2686 2687 2688 2689 2690 2691 2692 2693 2694 2695 2696 2697 2698 2699 2700 2701 2702 2703 2704 2705 2706 2707 2708 2709 2710 2711 2712 2713 2714 2715 2716 2717 2718 2719 2720 2721 2722 2723 2724 2725 2726 2727 2728 2729 2730 2731 2732 2733 2734 2735 2736 2737 2738 2739 2740 2741 2742 2743 2744 2745 2746 2747 2748 2749 2750 2751 2752 2753 2754 2755 2756 2757 2758 2759 2760 2761 2762 2763 2764 2765 2766 2767 2768 2769 2770 2771 2772 2773 2774 2775 2776 2777 2778 2779 2780 2781 2782 2783 2784 2785 2786 2787 2788 2789 2790 2791 2792 2793 2794 2795 2796 2797 2798 2799 2800 2801 2802 2803 2804 2805 2806 2807 2808 2809 2810 2811 2812 2813 2814 2815 2816 2817 2818 2819 2820 2821 2822 2823 2824 2825 2826 2827 2828 2829 2830 2831 2832 2833 2834 2835 2836 2837 2838 2839 2840 2841 2842 2843 2844 2845 2846 2847 2848 2849 2850 2851 2852 2853 2854 2855 2856 2857 2858 2859 2860 2861 2862 2863 2864 2865 2866 2867 2868 2869 2870 2871 2872 2873 2874 2875 2876 2877 2878 2879 2880 2881 2882 2883 2884 2885 2886 2887 2888 2889 2890 2891 2892 2893 2894 2895 2896 2897 2898 2899 2900 2901 2902 2903 2904 2905 2906 2907 2908 2909 2910 2911 2912 2913 2914 2915 2916 2917 2918 2919 2920 2921 2922 2923 2924 2925 2926 2927 2928 2929 2930 2931 2932 2933 2934 2935 2936 2937 2938 2939 2940 2941 2942 2943 2944 2945 2946 2947 2948 2949 2950 2951 2952 2953 2954 2955 2956 2957 2958 2959 2960 2961 2962 2963 2964 2965 2966 2967 2968 2969 2970 2971 2972 2973 2974 2975 2976 2977 2978 2979 2980 2981 2982 2983 2984 2985 2986 2987 2988 2989 2990 2991 2992 2993 2994 2995 2996 2997 2998 2999 3000 3001 3002 3003 3004 3005 3006 3007 3008 3009 3010 3011 3012 3013 3014 3015 3016 3017 3018 3019 3020 3021 3022 3023 3024 3025 3026 3027 3028 3029 3030 3031 3032 3033 3034 3035 3036 3037 3038 3039 3040 3041 3042 3043 3044 3045 3046 3047 3048 3049 3050 3051 3052 3053 3054 3055 3056 3057 3058 3059 3060 3061 3062 3063 3064 3065 3066 3067 3068 3069 3070 3071 3072 3073 3074 3075 3076 3077 3078 3079 3080 3081 3082 3083 3084 3085 3086 3087 3088 3089 3090 3091 3092 3093 3094 3095 3096 3097 3098 3099 3100 3101 3102 3103 3104 3105 3106 3107 3108 3109 3110 3111 3112 3113 3114 3115 3116 3117 3118 3119 3120 3121 3122 3123 3124 3125 3126 3127 3128 3129 3130 3131 3132 3133 3134 3135 3136 3137 3138 3139 3140 3141 3142 3143 3144 3145 3146 3147 3148 3149 3150 3151 3152 3153 3154 3155 3156 3157 3158 3159 3160 3161 3162 3163 3164 3165 3166 3167 3168 3169 3170 3171 3172 3173 3174 3175 3176 3177 3178 3179 3180 3181 3182 3183 3184 3185 3186 3187 3188 3189 3190 3191 3192 3193 3194 3195 3196 3197 3198 3199 3200 3201 3202 3203 3204 3205 3206 3207 3208 3209 3210 3211 3212 3213 3214 3215 3216 3217 3218 3219 3220 3221 3222 3223 3224 3225 3226 3227 3228 3229 3230 3231 3232 3233 3234 3235 3236 3237 3238 3239 3240 3241 3242 3243 3244 3245 3246 3247 3248 3249 3250 3251 3252 3253 3254 3255 3256 3257 3258 3259 3260 3261 3262 3263 3264 3265 3266 3267 3268 3269 3270 3271 3272 3273 3274 3275 3276 3277 3278 3279 3280 3281 3282 3283 3284 3285 3286 3287 3288 3289 3290 3291 3292 3293 3294 3295 3296 3297 3298 3299 3300 3301 3302 3303 3304 3305 3306 3307 3308 3309 3310 3311 3312 3313 3314 3315 3316 3317 3318 3319 3320 3321 3322 3323 3324 3325 3326 3327 3328 3329 3330 3331 3332 3333 3334 3335 3336 3337 3338 3339 3340 3341 3342 3343 3344 3345 3346 3347 3348 3349 3350 3351 3352 3353 3354 3355 3356 3357 3358 3359 3360 3361 3362 3363 3364 3365 3366 3367 3368 3369 3370 3371 3372 3373 3374 3375 3376 3377 3378 3379 3380 3381 3382 3383 3384 3385 3386 3387 3388 3389 3390 3391 3392 3393 3394 3395 3396 3397 3398 3399 3400 3401 3402 3403 3404 3405 3406 3407 3408 3409 3410 3411 3412 3413 3414 3415 3416 3417 3418 3419 3420 3421 3422 3423 3424 3425 3426 3427 3428 3429 3430 3431 3432 3433 3434 3435 3436 3437 3438 3439 3440 3441 3442 3443 3444 3445 3446 3447 3448 3449 3450 3451 3452 3453 3454 3455 3456 3457 3458 3459 3460 3461 3462 3463 3464 3465 3466 3467 3468 3469 3470 3471 3472 3473 3474 3475 3476 3477 3478 3479 3480 3481 3482 3483 3484 3485 3486 3487 3488 3489 3490 3491 3492 3493 3494 3495 3496 3497 3498 3499 3500 3501 3502 3503 3504 3505 3506 3507 3508 3509 3510 3511 3512 3513 3514 3515 3516 3517 3518 3519 3520 3521 3522 3523 3524 3525 3526 3527 3528 3529 3530 3531 3532 3533 3534 3535 3536 3537 3538 3539 3540 3541 3542 3543 3544 3545 3546 3547 3548 3549 3550 3551 3552 3553 3554 3555 3556 3557 3558 3559 3560 3561 3562 3563 3564 3565 3566 3567 3568 3569 3570 3571 3572 3573 3574 3575 3576 3577 3578 3579 3580 3581 3582 3583 3584 3585 3586 3587 3588 3589 3590 3591 3592 3593 3594 3595 3596 3597 3598 3599 3600 3601 3602 3603 3604 3605 3606 3607 3608 3609 3610 3611 3612 3613 3614 3615 3616 3617 3618 3619 3620 3621 3622 3623 3624 3625 3626 3627 3628 3629 3630 3631 3632 3633 3634 3635 3636 3637 3638 3639 3640 3641 3642 3643 3644 3645 3646 3647 3648 3649 3650 3651 3652 3653 3654 3655 3656 3657 3658 3659 3660 3661 3662 3663 3664 3665 3666 3667 3668 3669 3670 3671 3672 3673 3674 3675 3676 3677 3678 3679 3680 3681 3682 3683 3684 3685 3686 3687 3688 3689 3690 3691 3692 3693 3694 3695 3696 3697 3698 3699 3700 3701 3702 3703 3704 3705 3706 3707 3708 3709 3710 3711 3712 3713 3714 3715 3716 3717 3718 3719 3720 3721 3722 3723 3724 3725 3726 3727 3728 3729 3730 3731 3732 3733 3734 3735 3736 3737 3738 3739 3740 3741 3742 3743 3744 3745 3746 3747 3748 3749 3750 3751 3752 3753 3754 3755 3756 3757 3758 3759 3760 3761 3762 3763 3764 3765 3766 3767 3768 3769 3770 3771 3772 3773 3774 3775 3776 3777 3778 3779 3780 3781 3782 3783 3784 3785 3786 3787 3788 3789 3790 3791 3792 3793 3794 3795 3796 3797 3798 3799 3800 3801 3802 3803 3804 3805 3806 3807 3808 3809 3810 3811 3812 3813 3814 3815 3816 3817 3818 3819 3820 3821 3822 3823 3824 3825 3826 3827 3828 3829 3830 3831 3832 3833 3834 3835 3836 3837 3838 3839 3840 3841 3842 3843 3844 3845 3846 3847 3848 3849 3850 3851 3852 3853 3854 3855 3856 3857 3858 3859 3860 3861 3862 3863 3864 3865 3866 3867 3868 3869 3870 3871 3872 3873 3874 3875 3876 3877 3878 3879 3880 3881 3882 3883 3884 3885 3886 3887 3888 3889 3890 3891 3892 3893 3894 3895 3896 3897 3898 3899 3900 3901 3902 3903 3904 3905 3906 3907 3908 3909 3910 3911 3912 3913 3914 3915 3916 3917 3918 3919 3920 3921 3922 3923 3924 3925 3926 3927 3928 3929 3930 3931 3932 3933 3934 3935 3936 3937 3938 3939 3940 3941 3942 3943 3944 3945 3946 3947 3948 3949 3950 3951 3952 3953 3954 3955 3956 3957 3958 3959 3960 3961 3962 3963 3964 3965 3966 3967 3968 3969 3970 3971 3972 3973 3974 3975 3976 3977 3978 3979 3980 3981 3982 3983 3984 3985 3986 3987 3988 3989 3990 3991 3992 3993 3994 3995 3996 3997 3998 3999 4000 4001 4002 4003 4004 4005 4006 4007 4008 4009 4010 4011 4012 4013 4014 4015 4016 4017 4018 4019 4020 4021 4022 4023 4024 4025 4026 4027 4028 4029 4030 4031 4032 4033 4034 4035 4036 4037 4038 4039 4040 4041 4042 4043 4044 4045 4046 4047 4048 4049 4050 4051 4052 4053 4054 4055 4056 4057 4058 4059 4060 4061 4062 4063 4064 4065 4066 4067 4068 4069 4070 4071 4072 4073 4074 4075 4076 4077 4078 4079 4080 4081 4082 4083 4084 4085 4086 4087 4088 4089 4090 4091 4092 4093 4094 4095 4096 4097 4098 4099 4100 4101 4102 4103 4104 4105 4106 4107 4108 4109 4110 4111 4112 4113 4114 4115 4116 4117 4118 4119 4120 4121 4122 4123 4124 4125 4126 4127 4128 4129 4130 4131 4132 4133 4134 4135 4136 4137 4138 4139 4140 4141 4142 4143 4144 4145 4146 4147 4148 4149 4150 4151 4152 4153 4154 4155 4156 4157 4158 4159 4160 4161 4162 4163 4164 4165 4166 4167 4168 4169 4170 4171 4172 4173 4174 4175 4176 4177 4178 4179 4180 4181 4182 4183 4184 4185 4186 4187 4188 4189 4190 4191 4192 4193 4194 4195 4196 4197 4198 4199 4200 4201 4202 4203 4204 4205 4206 4207 4208 4209 4210 4211 4212 4213 4214 4215 4216 4217 4218 4219 4220 4221 4222 4223 4224 4225 4226 4227 4228 4229 4230 4231 4232 4233 4234 4235 4236 4237 4238 4239 4240 4241 4242 4243 4244 4245 4246 4247 4248 4249 4250 4251 4252 4253 4254 4255 4256 4257 4258 4259 4260 4261 4262 4263 4264 4265 4266 4267 4268 4269 4270 4271 4272 4273 4274 4275 4276 4277 4278 4279 4280 4281 4282 4283 4284 4285 4286 4287 4288 4289 4290 4291 4292 4293 4294 4295 4296 4297 4298 4299 4300 4301 4302 4303 4304 4305 4306 4307 4308 4309 4310 4311 4312 4313 4314 4315 4316 4317 4318 4319 4320 4321 4322 4323 4324 4325 4326 4327 4328 4329 4330 4331 4332 4333 4334 4335 4336 4337 4338 4339 4340 4341 4342 4343 4344 4345 4346 4347 4348 4349 4350 4351 4352 4353 4354 4355 4356 4357 4358 4359 4360 4361 4362 4363 4364 4365 4366 4367 4368 4369 4370 4371 4372 4373 4374 4375 4376 4377 4378 4379 4380 4381 4382 4383 4384 4385 4386 4387 4388 4389 4390 4391 4392 4393 4394 4395 4396 4397 4398 4399 4400 4401 4402 4403 4404 4405 4406 4407 4408 4409 4410 4411 4412 4413 4414 4415 4416 4417 4418 4419 4420 4421 4422 4423 4424 4425 4426 4427 4428 4429 4430 4431 4432 4433 4434 4435 4436 4437 4438 4439 4440 4441 4442 4443 4444 4445 4446 4447 4448 4449 4450 4451 4452 4453 4454 4455 4456 4457 4458 4459 4460 4461 4462 4463 4464 4465 4466 4467 4468 4469 4470 4471 4472 4473 4474 4475 4476 4477 4478 4479 4480 4481 4482 4483 4484 4485 4486 4487 4488 4489 4490 4491 4492 4493 4494 4495 4496 4497 4498 4499 4500 4501 4502 4503 4504 4505 4506 4507 4508 4509 4510 4511 4512 4513 4514 4515 4516 4517 4518 4519 4520 4521 4522 4523 4524 4525 4526 4527 4528 4529 4530 4531 4532 4533 4534 4535 4536 4537 4538 4539 4540 4541 4542 4543 4544 4545 4546 4547 4548 4549 4550 4551 4552 4553 4554 4555 4556 4557 4558 4559 4560 4561 4562 4563 4564 4565 4566 4567 4568 4569 4570 4571 4572 4573 4574 4575 4576 4577 4578 4579 4580 4581 4582 4583 4584 4585 4586 4587 4588 4589 4590 4591 4592 4593 4594 4595 4596 4597 4598 4599 4600 4601 4602 4603 4604 4605 4606 4607 4608 4609 4610 4611 4612 4613 4614 4615 4616 4617 4618 4619 4620 4621 4622 4623 4624 4625 4626 4627 4628 4629 4630 4631 4632 4633 4634 4635 4636 4637 4638 4639 4640 4641 4642 4643 4644 4645 4646 4647 4648 4649 4650 4651 4652 4653 4654 4655 4656 4657 4658 4659 4660 4661 4662 4663 4664 4665 4666 4667 4668 4669 4670 4671 4672 4673 4674 4675 4676 4677 4678 4679 4680 4681 4682 4683 4684 4685 4686 4687 4688 4689 4690 4691 4692 4693 4694 4695 4696 4697 4698 4699 4700 4701 4702 4703 4704 4705 4706 4707 4708 4709 4710 4711 4712 4713 4714 4715 4716 4717 4718 4719 4720 4721 4722 4723 4724 4725 4726 4727 4728 4729 4730 4731 4732 4733 4734 4735 4736 4737 4738 4739 4740 4741 4742 4743 4744 4745 4746 4747 4748 4749 4750 4751 4752 4753 4754 4755 4756 4757 4758 4759 4760 4761 4762 4763 4764 4765 4766 4767 4768 4769 4770 4771 4772 4773 4774 4775 4776 4777 4778 4779 4780 4781 4782 4783 4784 4785 4786 4787 4788 4789 4790 4791 4792 4793 4794 4795 4796 4797 4798 4799 4800 4801 4802 4803 4804 4805 4806 4807 4808 4809 4810 4811 4812 4813 4814 4815 4816 4817 4818 4819 4820 4821 4822 4823 4824 4825 4826 4827 4828 4829 4830 4831 4832 4833 4834 4835 4836 4837 4838 4839 4840 4841 4842 4843 4844 4845 4846 4847 4848 4849 4850 4851 4852 4853 4854 4855 4856 4857 4858 4859 4860 4861 4862 4863 4864 4865 4866 4867 4868 4869 4870 4871 4872 4873 4874 4875 4876 4877 4878 4879 4880 4881 4882 4883 4884 4885 4886 4887 4888 4889 4890 4891 4892 4893 4894 4895 4896 4897 4898 4899 4900 4901 4902 4903 4904 4905 4906 4907 4908 4909 4910 4911 4912 4913 4914 4915 4916 4917 4918 4919 4920 4921 4922 4923 4924 4925 4926 4927 4928 4929 4930 4931 4932 4933 4934 4935 4936 4937 4938 4939 4940 4941 4942 4943 4944 4945 4946 4947 4948 4949 4950 4951 4952 4953 4954 4955 4956 4957 4958 4959 4960 4961 4962 4963 4964 4965 4966 4967 4968 4969 4970 4971 4972 4973 4974 4975 4976 4977 4978 4979 4980 4981 4982 4983 4984 4985 4986 4987 4988 4989 4990 4991 4992 4993 4994 4995 4996 4997 4998 4999 5000 5001 5002 5003 5004 5005 5006 5007 5008 5009 5010 5011 5012 5013 5014 5015 5016 5017 5018 5019 5020 5021 5022 5023 5024 5025 5026 5027 5028 5029 5030 5031 5032 5033 5034 5035 5036 5037 5038 5039 5040 5041 5042 5043 5044 5045 5046 5047 5048 5049 5050 5051 5052 5053 5054 5055 5056 5057 5058 5059 5060 5061 5062 5063 5064 5065 5066 5067 5068 5069 5070 5071 5072 5073 5074 5075 5076 5077 5078 5079 5080 5081 5082 5083 5084 5085 5086 5087 5088 5089 5090 5091 5092 5093 5094 5095 5096 5097 5098 5099 5100 5101 5102 5103 5104 5105 5106 5107 5108 5109 5110 5111 5112 5113 5114 5115 5116 5117 5118 5119 5120 5121 5122 5123 5124 5125 5126 5127 5128 5129 5130 5131 5132 5133 5134 5135 5136 5137 5138 5139 5140 5141 5142 5143 5144 5145 5146 5147 5148 5149 5150 5151 5152 5153 5154 5155 5156 5157 5158 5159 5160 5161 5162 5163 5164 5165 5166 5167 5168 5169 5170 5171 5172 5173 5174 5175 5176 5177 5178 5179 5180 5181 5182 5183 5184 5185 5186 5187 5188 5189 5190 5191 5192 5193 5194 5195 5196 5197 5198 5199 5200 5201 5202 5203 5204 5205 5206 5207 5208 5209 5210 5211 5212 5213 5214 5215 5216 5217 5218 5219 5220 5221 5222 5223 5224 5225 5226 5227 5228 5229 5230 5231 5232 5233 5234 5235 5236 5237 5238 5239 5240 5241 5242 5243 5244 5245 5246 5247 5248 5249 5250 5251 5252 5253 5254 5255 5256 5257 5258 5259 5260 5261 5262 5263 5264 5265 5266 5267 5268 5269 5270 5271 5272 5273 5274 5275 5276 5277 5278 5279 5280 5281 5282 5283 5284 5285 5286 5287 5288 5289 5290 5291 5292 5293 5294 5295 5296 5297 5298 5299 5300 5301 5302 5303 5304 5305 5306 5307 5308 5309 5310 5311 5312 5313 5314 5315 5316 5317 5318 5319 5320 5321 5322 5323 5324 5325 5326 5327 5328 5329 5330 5331 5332 5333 5334 5335 5336 5337 5338 5339 5340 5341 5342 5343 5344 5345 5346 5347 5348 5349 5350 5351 5352 5353 5354 5355 5356 5357 5358 5359 5360 5361 5362 5363 5364 5365 5366 5367 5368 5369 5370 5371 5372 5373 5374 5375 5376 5377 5378 5379 5380 5381 5382 5383 5384 5385 5386 5387 5388 5389 5390 5391 5392 5393 5394 5395 5396 5397 5398 5399 5400 5401 5402 5403 5404 5405 5406 5407 5408 5409 5410 5411 5412 5413 5414 5415 5416 5417 5418 5419 5420 5421 5422 5423 5424 5425 5426 5427 5428 5429 5430 5431 5432 5433 5434 5435 5436 5437 5438 5439 5440 5441 5442 5443 5444 5445 5446 5447 5448 5449 5450 5451 5452 5453 5454 5455 5456 5457 5458 5459 5460 5461 5462 5463 5464 5465 5466 5467 5468 5469 5470 5471 5472 5473 5474 5475 5476 5477 5478 5479 5480 5481 5482 5483 5484 5485 5486 5487 5488 5489 5490 5491 5492 5493 5494 5495 5496 5497 5498 5499 5500 5501 5502 5503 5504 5505 5506 5507 5508 5509 5510 5511 5512 5513 5514 5515 5516 5517 5518 5519 5520 5521 5522 5523 5524 5525 5526 5527 5528 5529 5530 5531 5532 5533 5534 5535 5536 5537 5538 5539 5540 5541 5542 5543 5544 5545 5546 5547 5548 5549 5550 5551 5552 5553 5554 5555 5556 5557 5558 5559 5560 5561 5562 5563 5564 5565 5566 5567 5568 5569 5570 5571 5572 5573 5574 5575 5576 5577 5578 5579 5580 5581 5582 5583 5584 5585 5586 5587 5588 5589 5590 5591 5592 5593 5594 5595 5596 5597 5598 5599 5600 5601 5602 5603 5604 5605 5606 5607 5608 5609 5610 5611 5612 5613 5614 5615 5616 5617 5618 5619 5620 5621 5622 5623 5624 5625 5626 5627 5628 5629 5630 5631 5632 5633 5634 5635 5636 5637 5638 5639 5640 5641 5642 5643 5644 5645 5646 5647 5648 5649 5650 5651 5652 5653 5654 5655 5656 5657 5658 5659 5660 5661 5662 5663 5664 5665 5666 5667 5668 5669 5670 5671 5672 5673 5674 5675 5676 5677 5678 5679 5680 5681 5682 5683 5684 5685 5686 5687 5688 5689 5690 5691 5692 5693 5694 5695 5696 5697 5698 5699 5700 5701 5702 5703 5704 5705 5706 5707 5708 5709 5710 5711 5712 5713 5714 5715 5716 5717 5718 5719 5720 5721 5722 5723 5724 5725 5726 5727 5728 5729 5730 5731 5732 5733 5734 5735 5736 5737 5738 5739 5740 5741 5742 5743 5744 5745 5746 5747 5748 5749 5750 5751 5752 5753 5754 5755 5756 5757 5758 5759 5760 5761 5762 5763 5764 5765 5766 5767 5768 5769 5770 5771 5772 5773 5774 5775 5776 5777 5778 5779 5780 5781 5782 5783 5784 5785 5786 5787 5788 5789 5790 5791 5792 5793 5794 5795 5796 5797 5798 5799 5800 5801 5802 5803 5804 5805 5806 5807 5808 5809 5810 5811 5812 5813 5814 5815 5816 5817 5818 5819 5820 5821 5822 5823 5824 5825 5826 5827 5828 5829 5830 5831 5832 5833 5834 5835 5836 5837 5838 5839 5840 5841 5842 5843 5844 5845 5846 5847 5848 5849 5850 5851 5852 5853 5854 5855 5856 5857 5858 5859 5860 5861 5862 5863 5864 5865 5866 5867 5868 5869 5870 5871 5872 5873 5874 5875 5876 5877 5878 5879 5880 5881 5882 5883 5884 5885 5886 5887 5888 5889 5890 5891 5892 5893 5894 5895 5896 5897 5898 5899 5900 5901 5902 5903 5904 5905 5906 5907 5908 5909 5910 5911 5912 5913 5914 5915 5916 5917 5918 5919 5920 5921 5922 5923 5924 5925 5926 5927 5928 5929 5930 5931 5932 5933 5934 5935 5936 5937 5938 5939 5940 5941 5942 5943 5944 5945 5946 5947 5948 5949 5950 5951 5952 5953 5954 5955 5956 5957 5958 5959 5960 5961 5962 5963 5964 5965 5966 5967 5968 5969 5970 5971 5972 5973 5974 5975 5976 5977 5978 5979 5980 5981 5982 5983 5984 5985 5986 5987 5988 5989 5990 5991 5992 5993 5994 5995 5996 5997 5998 5999 6000 6001 6002 6003 6004 6005 6006 6007 6008 6009 6010 6011 6012 6013 6014 6015 6016 6017 6018 6019 6020 6021 6022 6023 6024 6025 6026 6027 6028 6029 6030 6031 6032 6033 6034 6035 6036 6037 6038 6039 6040 6041 6042 6043 6044 6045 6046 6047 6048 6049 6050 6051 6052 6053 6054 6055 6056 6057 6058 6059 6060 6061 6062 6063 6064 6065 6066 6067 6068 6069 6070 6071 6072 6073 6074 6075 6076 6077 6078 6079 6080 6081 6082 6083 6084 6085 6086 6087 6088 6089 6090 6091 6092 6093 6094 6095 6096 6097 6098 6099 6100 6101 6102 6103 6104 6105 6106 6107 6108 6109 6110 6111 6112 6113 6114 6115 6116 6117 6118 6119 6120 6121 6122 6123 6124 6125 6126 6127 6128 6129 6130 6131 6132 6133 6134 6135 6136 6137 6138 6139 6140 6141 6142 6143 6144 6145 6146 6147 6148 6149 6150 6151 6152 6153 6154 6155 6156 6157 6158 6159 6160 6161 6162 6163 6164 6165 6166 6167 6168 6169 6170 6171 6172 6173 6174 6175 6176 6177 6178 6179 6180 6181 6182 6183 6184 6185 6186 6187 6188 6189 6190 6191 6192 6193 6194 6195 6196 6197 6198 6199 6200 6201 6202 6203 6204 6205 6206 6207 6208 6209 6210 6211 6212 6213 6214 6215 6216 6217 6218 6219 6220 6221 6222 6223 6224 6225 6226 6227 6228 6229 6230 6231 6232 6233 6234 6235 6236 6237 6238 6239 6240 6241 6242 6243 6244 6245 6246 6247 6248 6249 6250 6251 6252 6253 6254 6255 6256 6257 6258 6259 6260 6261 6262 6263 6264 6265 6266 6267 6268 6269 6270 6271 6272 6273 6274 6275 6276 6277 6278 6279 6280 6281 6282 6283 6284 6285 6286 6287 6288 6289 6290 6291 6292 6293 6294 6295 6296 6297 6298 6299 6300 6301 6302 6303 6304 6305 6306 6307 6308 6309 6310 6311 6312 6313 6314 6315 6316 6317 6318 6319 6320 6321 6322 6323 6324 6325 6326 6327 6328 6329 6330 6331 6332 6333 6334 6335 6336 6337 6338 6339 6340 6341 6342 6343 6344 6345 6346 6347 6348 6349 6350 6351 6352 6353 6354 6355 6356 6357 6358 6359 6360 6361 6362 6363 6364 6365 6366 6367 6368 6369 6370 6371 6372 6373 6374 6375 6376 6377 6378 6379 6380 6381 6382 6383 6384 6385 6386 6387 6388 6389 6390 6391 6392 6393 6394 6395 6396 6397 6398 6399 6400 6401 6402 6403 6404 6405 6406 6407 6408 6409 6410 6411 6412 6413 6414 6415 6416 6417 6418 6419 6420 6421 6422 6423 6424 6425 6426 6427 6428 6429 6430 6431 6432 6433 6434 6435 6436 6437 6438 6439 6440 6441 6442 6443 6444 6445 6446 6447 6448 6449 6450 6451 6452 6453 6454 6455 6456 6457 6458 6459 6460 6461 6462 6463 6464 6465 6466 6467 6468 6469 6470 6471 6472 6473 6474 6475 6476 6477 6478 6479 6480 6481 6482 6483 6484 6485 6486 6487 6488 6489 6490 6491 6492 6493 6494 6495 6496 6497 6498 6499 6500 6501 6502 6503 6504 6505 6506 6507 6508 6509 6510 6511 6512 6513 6514 6515 6516 6517 6518 6519 6520 6521 6522 6523 6524 6525 6526 6527 6528 6529 6530 6531 6532 6533 6534 6535 6536 6537 6538 6539 6540 6541 6542 6543 6544 6545 6546 6547 6548 6549 6550 6551 6552 6553 6554 6555 6556 6557 6558 6559 6560 6561 6562 6563 6564 6565 6566 6567 6568 6569 6570 6571 6572 6573 6574 6575 6576 6577 6578 6579 6580 6581 6582 6583 6584 6585 6586 6587 6588 6589 6590 6591 6592 6593 6594 6595 6596 6597 6598 6599 6600 6601 6602 6603 6604 6605 6606 6607 6608 6609 6610 6611 6612 6613 6614 6615 6616 6617 6618 6619 6620 6621 6622 6623 6624 6625 6626 6627 6628 6629 6630 6631 6632 6633 6634 6635 6636 6637 6638 6639 6640 6641 6642 6643 6644 6645 6646 6647 6648 6649 6650 6651 6652 6653 6654 6655 6656 6657 6658 6659 6660 6661 6662 6663 6664 6665 6666 6667 6668 6669 6670 6671 6672 6673 6674 6675 6676 6677 6678 6679 6680 6681 6682 6683 6684 6685 6686 6687 6688 6689 6690 6691 6692 6693 6694 6695 6696 6697 6698 6699 6700 6701 6702 6703 6704 6705 6706 6707 6708 6709 6710 6711 6712 6713 6714 6715 6716 6717 6718 6719 6720 6721 6722 6723 6724 | <!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
<html>
<!-- This manual is for R, version 3.0.2 (2013-09-25).
Copyright (C) 2001-2013 R Core Team
Permission is granted to make and distribute verbatim copies of this
manual provided the copyright notice and this permission notice are
preserved on all copies.
Permission is granted to copy and distribute modified versions of this
manual under the conditions for verbatim copying, provided that the
entire resulting derived work is distributed under the terms of a
permission notice identical to this one.
Permission is granted to copy and distribute translations of this manual
into another language, under the above conditions for modified versions,
except that this permission notice may be stated in a translation
approved by the R Core Team. -->
<!-- Created by GNU Texinfo 5.1, http://www.gnu.org/software/texinfo/ -->
<head>
<title>R Installation and Administration</title>
<meta name="description" content="R Installation and Administration">
<meta name="keywords" content="R Installation and Administration">
<meta name="resource-type" content="document">
<meta name="distribution" content="global">
<meta name="Generator" content="makeinfo">
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
<link href="#Top" rel="start" title="Top">
<link href="#Function-and-variable-index" rel="index" title="Function and variable index">
<link href="#SEC_Contents" rel="contents" title="Table of Contents">
<link href="dir.html#Top" rel="up" title="(dir)">
<style type="text/css">
<!--
a.summary-letter {text-decoration: none}
blockquote.smallquotation {font-size: smaller}
div.display {margin-left: 3.2em}
div.example {margin-left: 3.2em}
div.indentedblock {margin-left: 3.2em}
div.lisp {margin-left: 3.2em}
div.smalldisplay {margin-left: 3.2em}
div.smallexample {margin-left: 3.2em}
div.smallindentedblock {margin-left: 3.2em; font-size: smaller}
div.smalllisp {margin-left: 3.2em}
kbd {font-style:oblique}
pre.display {font-family: inherit}
pre.format {font-family: inherit}
pre.menu-comment {font-family: serif}
pre.menu-preformatted {font-family: serif}
pre.smalldisplay {font-family: inherit; font-size: smaller}
pre.smallexample {font-size: smaller}
pre.smallformat {font-family: inherit; font-size: smaller}
pre.smalllisp {font-size: smaller}
span.nocodebreak {white-space:nowrap}
span.nolinebreak {white-space:nowrap}
span.roman {font-family:serif; font-weight:normal}
span.sansserif {font-family:sans-serif; font-weight:normal}
ul.no-bullet {list-style: none}
body {margin-left: 5%; margin-right: 5%;}
H1 {
background: white;
color: rgb(25%, 25%, 25%);
font-family: monospace;
font-size: xx-large;
text-align: center
}
H2 {
background: white;
color: rgb(40%, 40%, 40%);
font-family: monospace;
font-size: x-large;
text-align: center
}
H3 {
background: white;
color: rgb(40%, 40%, 40%);
font-family: monospace;
font-size: large
}
H4 {
background: white;
color: rgb(40%, 40%, 40%);
font-family: monospace
}
span.samp{font-family: monospace}
span.command{font-family: monospace}
span.option{font-family: monospace}
span.file{font-family: monospace}
span.env{font-family: monospace}
ul {
margin-top: 0.25ex;
margin-bottom: 0.25ex;
}
li {
margin-top: 0.25ex;
margin-bottom: 0.25ex;
}
p {
margin-top: 0.6ex;
margin-bottom: 1.2ex;
}
-->
</style>
</head>
<body lang="en" bgcolor="#FFFFFF" text="#000000" link="#0000FF" vlink="#800080" alink="#FF0000">
<h1 class="settitle" align="center">R Installation and Administration</h1>
<a name="SEC_Contents"></a>
<h2 class="contents-heading">Table of Contents</h2>
<div class="contents">
<ul class="no-bullet">
<li><a name="toc-Obtaining-R-1" href="#Obtaining-R">1 Obtaining R</a>
<ul class="no-bullet">
<li><a name="toc-Getting-and-unpacking-the-sources-1" href="#Getting-and-unpacking-the-sources">1.1 Getting and unpacking the sources</a></li>
<li><a name="toc-Getting-patched-and-development-versions-1" href="#Getting-patched-and-development-versions">1.2 Getting patched and development versions</a>
<ul class="no-bullet">
<li><a name="toc-Using-Subversion-and-rsync-1" href="#Using-Subversion-and-rsync">1.2.1 Using Subversion and rsync</a></li>
</ul></li>
</ul></li>
<li><a name="toc-Installing-R-under-Unix_002dalikes-1" href="#Installing-R-under-Unix_002dalikes">2 Installing R under Unix-alikes</a>
<ul class="no-bullet">
<li><a name="toc-Simple-compilation-1" href="#Simple-compilation">2.1 Simple compilation</a></li>
<li><a name="toc-Help-options-1" href="#Help-options">2.2 Help options</a></li>
<li><a name="toc-Making-the-manuals-1" href="#Making-the-manuals">2.3 Making the manuals</a></li>
<li><a name="toc-Installation-1" href="#Installation">2.4 Installation</a></li>
<li><a name="toc-Uninstallation-1" href="#Uninstallation">2.5 Uninstallation</a></li>
<li><a name="toc-Sub_002darchitectures-1" href="#Sub_002darchitectures">2.6 Sub-architectures</a>
<ul class="no-bullet">
<li><a name="toc-Multilib-1" href="#Multilib">2.6.1 Multilib</a></li>
</ul></li>
<li><a name="toc-Other-Options-1" href="#Other-Options">2.7 Other Options</a></li>
<li><a name="toc-Testing-an-Installation" href="#Testing-a-Unix_002dalike-Installation">2.8 Testing an Installation</a></li>
</ul></li>
<li><a name="toc-Installing-R-under-Windows-1" href="#Installing-R-under-Windows">3 Installing R under Windows</a>
<ul class="no-bullet">
<li><a name="toc-Building-from-source-1" href="#Building-from-source">3.1 Building from source</a>
<ul class="no-bullet">
<li><a name="toc-Getting-the-tools-1" href="#Getting-the-tools">3.1.1 Getting the tools</a></li>
<li><a name="toc-Getting-the-source-files-1" href="#Getting-the-source-files">3.1.2 Getting the source files</a></li>
<li><a name="toc-Building-the-core-files-1" href="#Building-the-core-files">3.1.3 Building the core files</a></li>
<li><a name="toc-Building-the-bitmap-files-1" href="#Building-the-bitmap-files">3.1.4 Building the bitmap files</a></li>
<li><a name="toc-Building-the-cairo-devices" href="#Building-the-cairo-devices-files">3.1.5 Building the cairo devices</a></li>
<li><a name="toc-Checking-the-build-1" href="#Checking-the-build">3.1.6 Checking the build</a></li>
<li><a name="toc-Building-the-manuals-1" href="#Building-the-manuals">3.1.7 Building the manuals</a></li>
<li><a name="toc-Building-the-Inno-Setup-installer-1" href="#Building-the-Inno-Setup-installer">3.1.8 Building the Inno Setup installer</a></li>
<li><a name="toc-Building-the-MSI-installer-1" href="#Building-the-MSI-installer">3.1.9 Building the MSI installer</a></li>
<li><a name="toc-64_002dbit-Windows-builds-1" href="#g_t64_002dbit-Windows-builds">3.1.10 64-bit Windows builds</a></li>
</ul></li>
<li><a name="toc-Testing-an-Installation-1" href="#Testing-a-Windows-Installation">3.2 Testing an Installation</a></li>
</ul></li>
<li><a name="toc-Installing-R-under-OS-X-1" href="#Installing-R-under-OS-X">4 Installing R under OS X</a>
<ul class="no-bullet">
<li><a name="toc-Running-R-under-OS-X-1" href="#Running-R-under-OS-X">4.1 Running R under OS X</a></li>
<li><a name="toc-Uninstalling-under-OS-X-1" href="#Uninstalling-under-OS-X">4.2 Uninstalling under OS X</a></li>
<li><a name="toc-Multiple-versions-1" href="#Multiple-versions">4.3 Multiple versions</a></li>
</ul></li>
<li><a name="toc-Running-R-1" href="#Running-R">5 Running R</a></li>
<li><a name="toc-Add_002don-packages-1" href="#Add_002don-packages">6 Add-on packages</a>
<ul class="no-bullet">
<li><a name="toc-Default-packages-1" href="#Default-packages">6.1 Default packages</a></li>
<li><a name="toc-Managing-libraries-1" href="#Managing-libraries">6.2 Managing libraries</a></li>
<li><a name="toc-Installing-packages-1" href="#Installing-packages">6.3 Installing packages</a>
<ul class="no-bullet">
<li><a name="toc-Windows" href="#Windows-packages">6.3.1 Windows</a></li>
<li><a name="toc-OS-X-1" href="#OS-X-packages">6.3.2 OS X</a></li>
<li><a name="toc-Customizing-package-compilation-1" href="#Customizing-package-compilation">6.3.3 Customizing package compilation</a></li>
<li><a name="toc-Multiple-sub_002darchitectures-1" href="#Multiple-sub_002darchitectures">6.3.4 Multiple sub-architectures</a></li>
<li><a name="toc-Byte_002dcompilation-1" href="#Byte_002dcompilation">6.3.5 Byte-compilation</a></li>
</ul></li>
<li><a name="toc-Updating-packages-1" href="#Updating-packages">6.4 Updating packages</a></li>
<li><a name="toc-Removing-packages-1" href="#Removing-packages">6.5 Removing packages</a></li>
<li><a name="toc-Setting-up-a-package-repository-1" href="#Setting-up-a-package-repository">6.6 Setting up a package repository</a></li>
<li><a name="toc-Checking-installed-source-packages-1" href="#Checking-installed-source-packages">6.7 Checking installed source packages</a></li>
</ul></li>
<li><a name="toc-Internationalization-and-Localization" href="#Internationalization">7 Internationalization and Localization</a>
<ul class="no-bullet">
<li><a name="toc-Locales-1" href="#Locales">7.1 Locales</a>
<ul class="no-bullet">
<li><a name="toc-Locales-under-Unix_002dalikes-1" href="#Locales-under-Unix_002dalikes">7.1.1 Locales under Unix-alikes</a></li>
<li><a name="toc-Locales-under-Windows-1" href="#Locales-under-Windows">7.1.2 Locales under Windows</a></li>
<li><a name="toc-Locales-under-OS-X-1" href="#Locales-under-OS-X">7.1.3 Locales under OS X</a></li>
</ul></li>
<li><a name="toc-Localization-of-messages-1" href="#Localization-of-messages">7.2 Localization of messages</a></li>
</ul></li>
<li><a name="toc-Choosing-between-32_002d-and-64_002dbit-builds-1" href="#Choosing-between-32_002d-and-64_002dbit-builds">8 Choosing between 32- and 64-bit builds</a></li>
<li><a name="toc-The-standalone-Rmath-library-1" href="#The-standalone-Rmath-library">9 The standalone Rmath library</a>
<ul class="no-bullet">
<li><a name="toc-Unix_002dalikes" href="#Unix_002dalike-standalone">9.1 Unix-alikes</a></li>
<li><a name="toc-Windows-1" href="#Windows-standalone">9.2 Windows</a></li>
</ul></li>
<li><a name="toc-Essential-and-useful-other-programs-under-a-Unix_002dalike-1" href="#Essential-and-useful-other-programs-under-a-Unix_002dalike">Appendix A Essential and useful other programs under a Unix-alike</a>
<ul class="no-bullet">
<li><a name="toc-Essential-programs-and-libraries-1" href="#Essential-programs-and-libraries">A.1 Essential programs and libraries</a></li>
<li><a name="toc-Useful-libraries-and-programs-1" href="#Useful-libraries-and-programs">A.2 Useful libraries and programs</a>
<ul class="no-bullet">
<li><a name="toc-Tcl_002fTk-1" href="#Tcl_002fTk">A.2.1 Tcl/Tk</a></li>
<li><a name="toc-Java-support-1" href="#Java-support">A.2.2 Java support</a></li>
</ul></li>
<li><a name="toc-Linear-algebra-1" href="#Linear-algebra">A.3 Linear algebra</a>
<ul class="no-bullet">
<li><a name="toc-BLAS-1" href="#BLAS">A.3.1 BLAS</a>
<ul class="no-bullet">
<li><a name="toc-ATLAS-1" href="#ATLAS">A.3.1.1 ATLAS</a></li>
<li><a name="toc-ACML-1" href="#ACML">A.3.1.2 ACML</a></li>
<li><a name="toc-Goto-and-OpenBLAS-1" href="#Goto-and-OpenBLAS">A.3.1.3 Goto and OpenBLAS</a></li>
<li><a name="toc-Intel-MKL" href="#MKL">A.3.1.4 Intel MKL</a></li>
<li><a name="toc-Shared-BLAS-1" href="#Shared-BLAS">A.3.1.5 Shared BLAS</a></li>
</ul></li>
<li><a name="toc-LAPACK-1" href="#LAPACK">A.3.2 LAPACK</a></li>
<li><a name="toc-Caveats-1" href="#Caveats">A.3.3 Caveats</a></li>
</ul></li>
</ul></li>
<li><a name="toc-Configuration-on-a-Unix_002dalike-1" href="#Configuration-on-a-Unix_002dalike">Appendix B Configuration on a Unix-alike</a>
<ul class="no-bullet">
<li><a name="toc-Configuration-options-1" href="#Configuration-options">B.1 Configuration options</a></li>
<li><a name="toc-Internationalization-support-1" href="#Internationalization-support">B.2 Internationalization support</a></li>
<li><a name="toc-Configuration-variables-1" href="#Configuration-variables">B.3 Configuration variables</a>
<ul class="no-bullet">
<li><a name="toc-Setting-paper-size-1" href="#Setting-paper-size">B.3.1 Setting paper size</a></li>
<li><a name="toc-Setting-the-browsers-1" href="#Setting-the-browsers">B.3.2 Setting the browsers</a></li>
<li><a name="toc-Compilation-flags-1" href="#Compilation-flags">B.3.3 Compilation flags</a></li>
<li><a name="toc-Making-manuals-1" href="#Making-manuals">B.3.4 Making manuals</a></li>
</ul></li>
<li><a name="toc-Setting-the-shell-1" href="#Setting-the-shell">B.4 Setting the shell</a></li>
<li><a name="toc-Using-make-1" href="#Using-make">B.5 Using make</a></li>
<li><a name="toc-Using-FORTRAN-1" href="#Using-FORTRAN">B.6 Using FORTRAN</a>
<ul class="no-bullet">
<li><a name="toc-Using-gfortran-1" href="#Using-gfortran">B.6.1 Using gfortran</a></li>
</ul></li>
<li><a name="toc-Compile-and-load-flags-1" href="#Compile-and-load-flags">B.7 Compile and load flags</a></li>
</ul></li>
<li><a name="toc-Platform-notes-1" href="#Platform-notes">Appendix C Platform notes</a>
<ul class="no-bullet">
<li><a name="toc-X11-issues-1" href="#X11-issues">C.1 X11 issues</a></li>
<li><a name="toc-Linux-1" href="#Linux">C.2 Linux</a>
<ul class="no-bullet">
<li><a name="toc-Clang-1" href="#Clang">C.2.1 Clang</a></li>
<li><a name="toc-Intel-compilers-1" href="#Intel-compilers">C.2.2 Intel compilers</a></li>
<li><a name="toc-Oracle-Solaris-Studio-compilers-1" href="#Oracle-Solaris-Studio-compilers">C.2.3 Oracle Solaris Studio compilers</a></li>
</ul></li>
<li><a name="toc-OS-X-2" href="#OS-X">C.3 OS X</a>
<ul class="no-bullet">
<li><a name="toc-Snow-Leopard-1" href="#Snow-Leopard">C.3.1 Snow Leopard</a></li>
<li><a name="toc-Lion-1" href="#Lion">C.3.2 Lion</a></li>
<li><a name="toc-Mountain-Lion-1" href="#Mountain-Lion">C.3.3 Mountain Lion</a></li>
<li><a name="toc-Mavericks-1" href="#Mavericks">C.3.4 Mavericks</a></li>
<li><a name="toc-Tcl_002fTk-headers-and-libraries-1" href="#Tcl_002fTk-headers-and-libraries">C.3.5 Tcl/Tk headers and libraries</a></li>
<li><a name="toc-Java" href="#Java-_0028OS-X_0029">C.3.6 Java</a></li>
<li><a name="toc-Frameworks-1" href="#Frameworks">C.3.7 Frameworks</a></li>
<li><a name="toc-Building-R_002eapp-1" href="#Building-R_002eapp">C.3.8 Building R.app</a></li>
</ul></li>
<li><a name="toc-Solaris-1" href="#Solaris">C.4 Solaris</a>
<ul class="no-bullet">
<li><a name="toc-Using-gcc-1" href="#Using-gcc">C.4.1 Using gcc</a></li>
</ul></li>
<li><a name="toc-AIX-1" href="#AIX">C.5 AIX</a></li>
<li><a name="toc-FreeBSD-1" href="#FreeBSD">C.6 FreeBSD</a></li>
<li><a name="toc-Cygwin-1" href="#Cygwin">C.7 Cygwin</a></li>
<li><a name="toc-New-platforms-1" href="#New-platforms">C.8 New platforms</a></li>
</ul></li>
<li><a name="toc-The-Windows-toolset-1" href="#The-Windows-toolset">Appendix D The Windows toolset</a>
<ul class="no-bullet">
<li><a name="toc-LaTeX-1" href="#LaTeX">D.1 LaTeX</a></li>
<li><a name="toc-The-Inno-Setup-installer-1" href="#The-Inno-Setup-installer">D.2 The Inno Setup installer</a></li>
<li><a name="toc-The-command-line-tools-1" href="#The-command-line-tools">D.3 The command line tools</a></li>
<li><a name="toc-The-MinGW_002dw64-toolchain-1" href="#The-MinGW_002dw64-toolchain">D.4 The MinGW-w64 toolchain</a></li>
<li><a name="toc-Useful-additional-programs-1" href="#Useful-additional-programs">D.5 Useful additional programs</a></li>
</ul></li>
<li><a name="toc-Function-and-variable-index-1" href="#Function-and-variable-index">Function and variable index</a></li>
<li><a name="toc-Concept-index-1" href="#Concept-index">Concept index</a></li>
<li><a name="toc-Environment-variable-index-1" href="#Environment-variable-index">Environment variable index</a></li>
</ul>
</div>
<a name="Top"></a>
<div class="header">
<p>
Next: <a href="#Obtaining-R" accesskey="n" rel="next">Obtaining R</a>, Previous: <a href="dir.html#Top" accesskey="p" rel="previous">(dir)</a>, Up: <a href="dir.html#Top" accesskey="u" rel="up">(dir)</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="R-Installation-and-Administration"></a>
<h1 class="top">R Installation and Administration</h1>
<p>This is a guide to installation and administration for R.
</p>
<p>This manual is for R, version 3.0.2 (2013-09-25).
</p>
<p>Copyright © 2001–2013 R Core Team
</p>
<blockquote>
<p>Permission is granted to make and distribute verbatim copies of this
manual provided the copyright notice and this permission notice are
preserved on all copies.
</p>
<p>Permission is granted to copy and distribute modified versions of this
manual under the conditions for verbatim copying, provided that the
entire resulting derived work is distributed under the terms of a
permission notice identical to this one.
</p>
<p>Permission is granted to copy and distribute translations of this manual
into another language, under the above conditions for modified versions,
except that this permission notice may be stated in a translation
approved by the R Core Team.
</p></blockquote>
<table class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">• <a href="#Obtaining-R" accesskey="1">Obtaining R</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Installing-R-under-Unix_002dalikes" accesskey="2">Installing R under Unix-alikes</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Installing-R-under-Windows" accesskey="3">Installing R under Windows</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Installing-R-under-OS-X" accesskey="4">Installing R under OS X</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Running-R" accesskey="5">Running R</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Add_002don-packages" accesskey="6">Add-on packages</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Internationalization" accesskey="7">Internationalization</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Choosing-between-32_002d-and-64_002dbit-builds" accesskey="8">Choosing between 32- and 64-bit builds</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#The-standalone-Rmath-library" accesskey="9">The standalone Rmath library</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Essential-and-useful-other-programs-under-a-Unix_002dalike">Essential and useful other programs under a Unix-alike</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Configuration-on-a-Unix_002dalike">Configuration on a Unix-alike</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Platform-notes">Platform notes</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#The-Windows-toolset">The Windows toolset</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Function-and-variable-index">Function and variable index</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Concept-index">Concept index</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Environment-variable-index">Environment variable index</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
</table>
<hr>
<a name="Obtaining-R"></a>
<div class="header">
<p>
Next: <a href="#Installing-R-under-Unix_002dalikes" accesskey="n" rel="next">Installing R under Unix-alikes</a>, Previous: <a href="#Top" accesskey="p" rel="previous">Top</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Obtaining-R-1"></a>
<h2 class="chapter">1 Obtaining R</h2>
<a name="index-Obtaining-R"></a>
<p>Sources, binaries and documentation for R can be obtained via
<acronym>CRAN</acronym>, the “Comprehensive R Archive Network” whose current
members are listed at <a href="http://CRAN.R-project.org/mirrors.html">http://CRAN.R-project.org/mirrors.html</a>.
</p>
<table class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">• <a href="#Getting-and-unpacking-the-sources" accesskey="1">Getting and unpacking the sources</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Getting-patched-and-development-versions" accesskey="2">Getting patched and development versions</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
</table>
<hr>
<a name="Getting-and-unpacking-the-sources"></a>
<div class="header">
<p>
Next: <a href="#Getting-patched-and-development-versions" accesskey="n" rel="next">Getting patched and development versions</a>, Previous: <a href="#Obtaining-R" accesskey="p" rel="previous">Obtaining R</a>, Up: <a href="#Obtaining-R" accesskey="u" rel="up">Obtaining R</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Getting-and-unpacking-the-sources-1"></a>
<h3 class="section">1.1 Getting and unpacking the sources</h3>
<a name="index-Sources-for-R"></a>
<p>The simplest way is to download the most recent
<samp>R-<var>x</var>.<var>y</var>.<var>z</var>.tar.gz</samp> file, and unpack it with
</p>
<div class="example">
<pre class="example">tar -xf R-<var>x</var>.<var>y</var>.<var>z</var>.tar.gz
</pre></div>
<p>on systems that have a suitable<a name="DOCF1" href="#FOOT1"><sup>1</sup></a>
<code>tar</code> installed. On other systems you need to have the
<code>gzip</code> program installed, when you can use
</p>
<div class="example">
<pre class="example">gzip -dc R-<var>x</var>.<var>y</var>.<var>z</var>.tar.gz | tar -xf -
</pre></div>
<p>The pathname of the directory into which the sources are unpacked should
not contain spaces, as most <code>make</code> programs (and specifically
<acronym>GNU</acronym> <code>make</code>) do not expect spaces.
</p>
<p>If you want the build to be usable by a group of users, set <code>umask</code>
before unpacking so that the files will be readable by the target group
(e.g., <code>umask 022</code> to be usable by all users). Keep this
setting of <code>umask</code> whilst building and installing.
</p>
<p>If you use a recent GNU version of <code>tar</code> and do this as a root
account (which on Windows includes accounts with administrator
privileges) you may see many warnings about changing ownership. In
which case you can use
</p>
<div class="example">
<pre class="example">tar --no-same-owner -xf R-<var>x</var>.<var>y</var>.<var>z</var>.tar.gz
</pre></div>
<p>and perhaps also include the option <samp>--no-same-permissions</samp>.
<a name="index-TAR_005fOPTIONS"></a>
(These options can also be set in the <code>TAR_OPTIONS</code> environment
variable: if more than one option is included they should be separated
by spaces.)
</p>
<hr>
<a name="Getting-patched-and-development-versions"></a>
<div class="header">
<p>
Previous: <a href="#Getting-and-unpacking-the-sources" accesskey="p" rel="previous">Getting and unpacking the sources</a>, Up: <a href="#Obtaining-R" accesskey="u" rel="up">Obtaining R</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Getting-patched-and-development-versions-1"></a>
<h3 class="section">1.2 Getting patched and development versions</h3>
<p>A patched version of the current release, ‘<samp>r-patched</samp>’, and the
current development version, ‘<samp>r-devel</samp>’, are available as daily
tarballs and via access to the R Subversion repository. (For the two
weeks prior to the release of a minor (3.x.0) version, ‘<samp>r-patched</samp>’
tarballs may refer to beta/release candidates of the upcoming release,
the patched version of the current release being available via
Subversion.)
</p>
<p>The tarballs are available from
<a href="ftp://ftp.stat.math.ethz.ch/pub/Software/R/">ftp://ftp.stat.math.ethz.ch/pub/Software/R/</a>. Download
<samp>R-patched.tar.gz</samp> or <samp>R-devel.tar.gz</samp> (or the <samp>.tar.bz2</samp>
versions) and unpack as described in the previous section. They are
built in exactly the same way as distributions of R releases.
</p>
<table class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">• <a href="#Using-Subversion-and-rsync" accesskey="1">Using Subversion and rsync</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
</table>
<hr>
<a name="Using-Subversion-and-rsync"></a>
<div class="header">
<p>
Previous: <a href="#Getting-patched-and-development-versions" accesskey="p" rel="previous">Getting patched and development versions</a>, Up: <a href="#Getting-patched-and-development-versions" accesskey="u" rel="up">Getting patched and development versions</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Using-Subversion-and-rsync-1"></a>
<h4 class="subsection">1.2.1 Using Subversion and rsync</h4>
<a name="index-Subversion"></a>
<p>Sources are also available via <a href="https://svn.R-project.org/R/">https://svn.R-project.org/R/</a>, the
R Subversion repository. If you have a Subversion client (see
<a href="http://subversion.apache.org/">http://subversion.apache.org/</a>), you can check out and update the
current ‘<samp>r-devel</samp>’ from
<a href="https://svn.r-project.org/R/trunk/">https://svn.r-project.org/R/trunk/</a> and the current
‘<samp>r-patched</samp>’ from
‘<samp>https://svn.r-project.org/R/branches/R-<var>x</var>-<var>y</var>-branch/</samp>’
(where <var>x</var> and <var>y</var> are the major and minor number of the current
released version of R). E.g., use
</p>
<div class="example">
<pre class="example">svn checkout https://svn.r-project.org/R/trunk/ <var>path</var>
</pre></div>
<p>to check out ‘<samp>r-devel</samp>’ into directory <var>path</var> (which will be
created if necessary). The alpha, beta and RC versions of an upcoming
<var>x.y.0</var> release are available from
‘<samp>https://svn.r-project.org/R/branches/R-<var>x</var>-<var>y</var>-branch/</samp>’ in
the four-week period prior to the release.
</p>
<p>Note that ‘<samp>https:</samp>’ is required<a name="DOCF2" href="#FOOT2"><sup>2</sup></a>,
and that the SSL certificate for the Subversion server of the R project
should be recognized as from a trusted source.
</p>
<p>Note that retrieving the sources by e.g. <code>wget -r</code> or
<code>svn export</code> from that URL will not work (and will give a error
early in the <code>make</code> process): the Subversion information is
needed to build R.
</p>
<p>The Subversion repository does not contain the current sources for the
recommended packages, which can be obtained by <code>rsync</code> or
downloaded from <acronym>CRAN</acronym>. To use <code>rsync</code> to install the
appropriate sources for the recommended packages, run
<code>./tools/rsync-recommended</code> from the top-level directory of the
R sources.
</p>
<p>If downloading manually from <acronym>CRAN</acronym>, do ensure that you have the
correct versions of the recommended packages: if the number in the file
<samp>VERSION</samp> is ‘<samp><var>x</var>.<var>y</var>.<var>z</var></samp>’ you need to download
the contents of ‘<samp>http://CRAN.R-project.org/src/contrib/<var>dir</var></samp>’,
where <var>dir</var> is ‘<samp><var>x</var>.<var>y</var>.<var>z</var>/Recommended</samp>’ for
r-devel or <samp><var>x</var>.<var>y</var>-patched/Recommended</samp> for r-patched,
respectively, to directory <samp>src/library/Recommended</samp> in the sources
you have unpacked. After downloading manually you need to execute
<code>tools/link-recommended</code> from the top level of the sources to
make the requisite links in <samp>src/library/Recommended</samp>. A suitable
incantation from the top level of the R sources using <code>wget</code>
might be (for the correct value of <samp><var>dir</var></samp>)
</p>
<div class="example">
<pre class="example">wget -r -l1 --no-parent -A\*.gz -nd -P src/library/Recommended \
http://CRAN.R-project.org/src/contrib/<var>dir</var>
./tools/link-recommended
</pre></div>
<hr>
<a name="Installing-R-under-Unix_002dalikes"></a>
<div class="header">
<p>
Next: <a href="#Installing-R-under-Windows" accesskey="n" rel="next">Installing R under Windows</a>, Previous: <a href="#Obtaining-R" accesskey="p" rel="previous">Obtaining R</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Installing-R-under-Unix_002dalikes-1"></a>
<h2 class="chapter">2 Installing R under Unix-alikes</h2>
<a name="index-Installing-under-Unix_002dalikes"></a>
<p>R will configure and build under most common Unix and Unix-alike
platforms including ‘<samp><var>cpu</var>-*-linux-gnu</samp>’ for the
‘<samp>alpha</samp>’, ‘<samp>arm</samp>’, ‘<samp>hppa</samp>’, ‘<samp>ix86</samp>’,
‘<samp>ia64</samp>’, ‘<samp>m68k</samp>’, ‘<samp>mips</samp>’, ‘<samp>mipsel</samp>’,
‘<samp>powerpc</samp>’, ‘<samp>s390</samp>’, ‘<samp>sparc</samp>’, and ‘<samp>x86_64</samp>’
<acronym>CPU</acronym>s,
‘<samp>x86_64-apple-darwin</samp>’, ‘<samp>i386-sun-solaris</samp>’ and
‘<samp>sparc-sun-solaris</samp>’ as well as
perhaps (it is tested less frequently on these platforms)
‘<samp>i386-apple-darwin</samp>’, ‘<samp>i386-*-freebsd</samp>’, ‘<samp>x86_64-*-freebsd</samp>’,
‘<samp>i386-*-netbsd</samp>’, ‘<samp>i386-*-openbsd</samp>’ and
‘<samp>powerpc-ibm-aix6*</samp>’
</p>
<a name="index-Linux"></a>
<a name="index-OS-X"></a>
<p>In addition, binary distributions are available for some common Linux
distributions and for OS X (formerly Mac OS). See the <acronym>FAQ</acronym> for
current details. These are installed in platform-specific ways, so for
the rest of this chapter we consider only building from the sources.
</p>
<table class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">• <a href="#Simple-compilation" accesskey="1">Simple compilation</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Help-options" accesskey="2">Help options</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Making-the-manuals" accesskey="3">Making the manuals</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Installation" accesskey="4">Installation</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Uninstallation" accesskey="5">Uninstallation</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Sub_002darchitectures" accesskey="6">Sub-architectures</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Other-Options" accesskey="7">Other Options</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Testing-a-Unix_002dalike-Installation" accesskey="8">Testing a Unix-alike Installation</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
</table>
<hr>
<a name="Simple-compilation"></a>
<div class="header">
<p>
Next: <a href="#Help-options" accesskey="n" rel="next">Help options</a>, Previous: <a href="#Installing-R-under-Unix_002dalikes" accesskey="p" rel="previous">Installing R under Unix-alikes</a>, Up: <a href="#Installing-R-under-Unix_002dalikes" accesskey="u" rel="up">Installing R under Unix-alikes</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Simple-compilation-1"></a>
<h3 class="section">2.1 Simple compilation</h3>
<p>First review the essential and useful tools and libraries in
<a href="#Essential-and-useful-other-programs-under-a-Unix_002dalike">Essential and useful other programs under a Unix-alike</a>, and install
those you
<a name="index-TMPDIR"></a>
want or need. Ensure that the environment variable <code>TMPDIR</code> is
either unset (and <samp>/tmp</samp> exists and can be written in and scripts
can be executed from) or points to a valid temporary directory (one from
which execution of scripts is allowed) whose path does not contain
spaces.<a name="DOCF3" href="#FOOT3"><sup>3</sup></a>
</p>
<a name="index-R_005fHOME"></a>
<p>Choose a directory to install the R tree (R is not just a binary, but
has additional data sets, help files, font metrics etc). Let us call
this place <var>R_HOME</var>. Untar the source code. This should create
directories <samp>src</samp>, <samp>doc</samp>, and several more under a top-level
directory: change to that top-level directory (At this point North
American readers should consult <a href="#Setting-paper-size">Setting paper size</a>.) Issue the
following commands:
</p>
<a name="index-configure"></a>
<div class="example">
<pre class="example">./configure
make
</pre></div>
<p>(See <a href="#Using-make">Using make</a> if your make is not called ‘<samp>make</samp>’.) Users of
Debian-based 64-bit systems<a name="DOCF4" href="#FOOT4"><sup>4</sup></a> may need
</p>
<div class="example">
<pre class="example">./configure LIBnn=lib
make
</pre></div>
<p>Then check the built system works correctly by
</p>
<div class="example">
<pre class="example">make check
</pre></div>
<p>Failures are not necessarily problems as they might be caused by missing
functionality,<a name="DOCF5" href="#FOOT5"><sup>5</sup></a> but you should look carefully at any
reported discrepancies. (Some non-fatal errors are expected in locales
that do not support Latin-1, in particular in true <code>C</code> locales and
non-UTF-8 non-Western-European locales.) A failure in
<samp>tests/ok-errors.R</samp> may indicate inadequate resource limits
(see <a href="#Running-R">Running R</a>).
</p>
<p>More comprehensive testing can be done by
</p>
<div class="example">
<pre class="example">make check-devel
</pre></div>
<p>or
</p>
<div class="example">
<pre class="example">make check-all
</pre></div>
<p>see file <samp>tests/README</samp>.
</p>
<p>If the command <code>configure</code> and <code>make</code> commands execute
successfully, a shell-script front-end called <samp>R</samp> will be created
and copied to <samp><var>R_HOME</var>/bin</samp>. You can link or copy this script
to a place where users can invoke it, for example to
<samp>/usr/local/bin/R</samp>. You could also copy the man page <samp>R.1</samp> to
a place where your <code>man</code> reader finds it, such as
<samp>/usr/local/man/man1</samp>. If you want to install the complete R
tree to, e.g., <samp>/usr/local/lib/R</samp>, see <a href="#Installation">Installation</a>. Note:
you do not <em>need</em> to install R: you can run it from where it was
built.
</p>
<p>You do not necessarily have to build R in the top-level source
directory (say, <samp><var>TOP_SRCDIR</var></samp>). To build in
<samp><var>BUILDDIR</var></samp>, run
</p>
<a name="index-configure-1"></a>
<div class="example">
<pre class="example">cd <var>BUILDDIR</var>
<var>TOP_SRCDIR</var>/configure
make
</pre></div>
<p>and so on, as described further below. This has the advantage of always
keeping your source tree clean and is particularly recommended when you
work with a version of R from Subversion. (You may need
<acronym>GNU</acronym> <code>make</code> to allow this, and you will need no spaces
in the path to the build directory.)
</p>
<p>Now <code>rehash</code> if necessary, type <kbd>R</kbd>, and read the R manuals
and the R <acronym>FAQ</acronym> (files <samp>FAQ</samp> or
<samp>doc/manual/R-FAQ.html</samp>, or
<a href="http://CRAN.R-project.org/doc/FAQ/R-FAQ.html">http://CRAN.R-project.org/doc/FAQ/R-FAQ.html</a> which always
has the version for the latest release of R).
</p>
<hr>
<a name="Help-options"></a>
<div class="header">
<p>
Next: <a href="#Making-the-manuals" accesskey="n" rel="next">Making the manuals</a>, Previous: <a href="#Simple-compilation" accesskey="p" rel="previous">Simple compilation</a>, Up: <a href="#Installing-R-under-Unix_002dalikes" accesskey="u" rel="up">Installing R under Unix-alikes</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Help-options-1"></a>
<h3 class="section">2.2 Help options</h3>
<p>By default <acronym>HTML</acronym> help pages are created when needed rather than being
built at install time.
</p>
<p>If you need to disable the server and want <acronym>HTML</acronym> help, there is the
option to build <acronym>HTML</acronym> pages when packages are installed
(including those installed with R). This is enabled by the
<code>configure</code> option <samp>--enable-prebuilt-html</samp>. Whether
<code>R CMD INSTALL</code> (and hence <code>install.packages</code>) pre-builds
<acronym>HTML</acronym> pages is determined by looking at the R installation and is
reported by <code>R CMD INSTALL --help</code>: it can be overridden by
specifying one of the <code>INSTALL</code> options <samp>--html</samp> or
<samp>--no-html</samp>.
</p>
<p>The server is disabled by setting the environment variable
<a name="index-R_005fDISABLE_005fHTTPD"></a>
<code>R_DISABLE_HTTPD</code> to a non-empty value, either before R is
started or within the R session before <acronym>HTML</acronym> help (including
<code>help.start</code>) is used. It is also possible that system security
measures will prevent the server from being started, for example if the
loopback interface has been disabled. See
<code>?tools::startDynamicHelp</code> for more details.
</p>
<hr>
<a name="Making-the-manuals"></a>
<div class="header">
<p>
Next: <a href="#Installation" accesskey="n" rel="next">Installation</a>, Previous: <a href="#Help-options" accesskey="p" rel="previous">Help options</a>, Up: <a href="#Installing-R-under-Unix_002dalikes" accesskey="u" rel="up">Installing R under Unix-alikes</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Making-the-manuals-1"></a>
<h3 class="section">2.3 Making the manuals</h3>
<a name="index-Manuals"></a>
<p>There is a set of manuals that can be built from the sources,
</p>
<dl compact="compact">
<dt>‘<samp>fullrefman</samp>’</dt>
<dd><p>Printed versions of all the help pages for base and recommended packages
(over 3300 pages).
</p></dd>
<dt>‘<samp>refman</samp>’</dt>
<dd><p>Printed versions of the help pages for selected base packages (over 1900 pages)
</p></dd>
<dt>‘<samp>R-FAQ</samp>’</dt>
<dd><p>R <acronym>FAQ</acronym>
</p></dd>
<dt>‘<samp>R-intro</samp>’</dt>
<dd><p>“An Introduction to R”.
</p></dd>
<dt>‘<samp>R-data</samp>’</dt>
<dd><p>“R Data Import/Export”.
</p></dd>
<dt>‘<samp>R-admin</samp>’</dt>
<dd><p>“R Installation and Administration”, this manual.
</p></dd>
<dt>‘<samp>R-exts</samp>’</dt>
<dd><p>“Writing R Extensions”.
</p></dd>
<dt>‘<samp>R-lang</samp>’</dt>
<dd><p>“The R Language Definition”.
</p></dd>
</dl>
<p>To make these (with ‘<samp>fullrefman</samp>’ rather than ‘<samp>refman</samp>’), use
</p>
<div class="example">
<pre class="example">make pdf <span class="roman">to create PDF versions</span>
make info <span class="roman">to create info files (not ‘<samp>refman</samp>’ nor ‘<samp>fullrefman</samp>’).</span>
</pre></div>
<p>You will not be able to build any of these unless you have
<code>makeinfo</code> version 4.7 or later installed, and for PDF you must
have <code>texi2dvi</code> and <samp>texinfo.tex</samp> installed (which are part
of the <acronym>GNU</acronym> <strong>texinfo</strong> distribution but are, especially
<samp>texinfo.tex</samp>, often made part of the TeX package in
re-distributions).
</p>
<p>The PDF versions can be viewed using any recent PDF viewer: they have
hyperlinks that can be followed. The info files are suitable for
reading online with Emacs or the standalone <acronym>GNU</acronym> <code>info</code>
program. The PDF versions will be created using the paper size selected
at configuration (default ISO a4): this can be overridden by setting
<code>R_PAPERSIZE</code>
<a name="index-R_005fPAPERSIZE"></a>
on the <code>make</code> command line, or setting <code>R_PAPERSIZE</code> in the
environment and using <code>make -e</code>. (If re-making the manuals for
a different paper size, you should first delete the file
<samp>doc/manual/version.texi</samp>. The usual value for North America would
be ‘<samp>letter</samp>’.)
</p>
<p>There are some issues with making the PDF reference manual,
<samp>fullrefman.pdf</samp> or <samp>refman.pdf</samp>. The help files contain both
ISO Latin1 characters (e.g. in <samp>text.Rd</samp>) and upright quotes,
neither of which are contained in the standard LaTeX Computer Modern
fonts. We have provided four alternatives:
</p>
<dl compact="compact">
<dt><code>times</code></dt>
<dd><p>(The default.) Using standard PostScript fonts, Times Roman, Helvetica
and Courier. This works well both for on-screen viewing and for
printing. One disadvantage is that the Usage and Examples sections may
come out rather wide: this can be overcome by using <em>in addition</em>
either of the options <code>inconsolata</code>, on a Unix-alike only if found
by <code>configure</code>) or <code>beramono</code>, which replace the Courier
monospaced font by Inconsolata or Bera Sans mono respectively. (You
will need a recent version of the appropriate LaTeX package
<strong>inconsolata</strong> or <strong>bera</strong> installed.)
</p>
<p>Note that in most LaTeX installations this will not actually use the
standard fonts for PDF, but rather embed the URW clones NimbusRom,
NimbusSans and (for Courier, if used) NimbusMon.
</p>
</dd>
<dt><code>lm</code></dt>
<dd><p>Using the <em>Latin Modern</em> fonts. These are not often installed as
part of a TeX distribution, but can obtained from
<a href="http://www.ctan.org/tex-archive/fonts/ps-type1/lm/">http://www.ctan.org/tex-archive/fonts/ps-type1/lm/</a> and
mirrors. This uses fonts rather similar to Computer Modern, but is not
so good on-screen as <code>times</code>.
</p>
</dd>
<dt><code>cm-super</code></dt>
<dd><p>Using type-1 versions of the Computer Modern fonts by Vladimir Volovich.
This is a large installation, obtainable from
<a href="http://www.ctan.org/tex-archive/fonts/ps-type1/cm-super/">http://www.ctan.org/tex-archive/fonts/ps-type1/cm-super/</a>
and its mirrors. These type-1 fonts have poor hinting and so are
nowhere near as readable on-screen as the other three options.
</p>
</dd>
<dt><code>ae</code></dt>
<dd><p>A package to use composites of Computer Modern fonts. This works well
most of the time, and its PDF is more readable on-screen than the
previous two options. There are three fonts for which it will need to
use bitmapped fonts, <samp>tctt0900.600pk</samp>, <samp>tctt1000.600pk</samp> and
<samp>tcrm1000.600pk</samp>. Unfortunately, if those files are not available,
Acrobat Reader will substitute completely incorrect glyphs so you need
to examine the logs carefully.
</p></dd>
</dl>
<p>The default can be overridden by setting the environment variable
<a name="index-R_005fRD4PDF"></a>
<code>R_RD4PDF</code>. (On Unix-alikes, this will be picked up at install time
and stored in <samp>etc/Renviron</samp>, but can still be overridden when the
manuals are built, using <code>make -e</code>.) The usual <a name="DOCF6" href="#FOOT6"><sup>6</sup></a> default value for <code>R_RD4PDF</code> is
‘<samp>times,inconsolata,hyper</samp>’: omit ‘<samp>hyper</samp>’ if you do not want
hyperlinks (e.g. for printing the manual) or do not have LaTeX
package <strong>hyperref</strong>, and omit ‘<samp>inconsolata</samp>’ if you do not have
LaTeX package <strong>inconsolata</strong> installed.
</p>
<hr>
<a name="Installation"></a>
<div class="header">
<p>
Next: <a href="#Uninstallation" accesskey="n" rel="next">Uninstallation</a>, Previous: <a href="#Making-the-manuals" accesskey="p" rel="previous">Making the manuals</a>, Up: <a href="#Installing-R-under-Unix_002dalikes" accesskey="u" rel="up">Installing R under Unix-alikes</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Installation-1"></a>
<h3 class="section">2.4 Installation</h3>
<a name="index-Installation"></a>
<p>To ensure that the installed tree is usable by the right group of users,
set <code>umask</code> appropriately (perhaps to ‘<samp>022</samp>’) before unpacking
the sources and throughout the build process.
</p>
<p>After
</p>
<a name="index-configure-2"></a>
<div class="example">
<pre class="example">./configure
make
make check
</pre></div>
<p>(or, when building outside the source,
<code><var>TOP_SRCDIR</var>/configure</code>, etc) have been completed
successfully, you can install the complete R tree to your system by
typing
</p>
<div class="example">
<pre class="example">make install
</pre></div>
<p>A parallel make can be used (but run <code>make</code> before <code>make
install</code>): however it is not recommended for <code>make check</code> as the
output from different checks will interleaved and hard to decipher.
</p>
<p>This will install to the following directories:
</p>
<dl compact="compact">
<dt><samp><var>prefix</var>/bin</samp> or <samp><var>bindir</var></samp></dt>
<dd><p>the front-end shell script and other scripts and executables
</p></dd>
<dt><samp><var>prefix</var>/man/man1</samp> or <samp><var>mandir</var>/man1</samp></dt>
<dd><p>the man page
</p></dd>
<dt><samp><var>prefix</var>/<var>LIBnn</var>/R</samp> or <samp><var>libdir</var>/R</samp></dt>
<dd><p>all the rest (libraries, on-line help system, …). Here
<var>LIBnn</var> is usually ‘<samp>lib</samp>’, but may be ‘<samp>lib64</samp>’ on some
64-bit Linux systems. This is known as the R home directory.
</p></dd>
</dl>
<p>where <var>prefix</var> is determined during configuration (typically
<samp>/usr/local</samp>) and can be set by running <code>configure</code> with
the option <samp>--prefix</samp>, as in
</p>
<a name="index-configure-3"></a>
<div class="example">
<pre class="example">./configure --prefix=/where/you/want/R/to/go
</pre></div>
<p>This causes <code>make install</code> to install the R script to
<samp>/where/you/want/R/to/go/bin</samp>, and so on. The prefix of the
installation directories can be seen in the status message that is
displayed at the end of <code>configure</code>. You can install into
another directory tree by using
</p>
<div class="example">
<pre class="example">make prefix=/path/to/here install
</pre></div>
<p>at least with <acronym>GNU</acronym> <code>make</code> (and current Solaris and
FreeBSD <code>make</code>, but not some older Unix makes).
</p>
<p>More precise control is available at configure time via options: see
<code>configure --help</code> for details. (However, most of the ‘Fine
tuning of the installation directories’ options are not used by R.)
</p>
<p>Configure options <samp>--bindir</samp> and <samp>--mandir</samp> are supported
and govern where a copy of the <code>R</code> script and the <code>man</code>
page are installed.
</p>
<p>The configure option <samp>--libdir</samp> controls where the main R
files are installed: the default is ‘<samp><var>eprefix</var>/<var>LIBnn</var></samp>’,
where <var>eprefix</var> is the prefix used for installing
architecture-dependent files, defaults to <var>prefix</var>, and can be set
via the configure option <samp>--exec-prefix</samp>.
</p>
<p>Each of <code>bindir</code>, <code>mandir</code> and <code>libdir</code> can also be
specified on the <code>make install</code> command line (at least for
<acronym>GNU</acronym> <code>make</code>).
</p>
<p>The <code>configure</code> or <code>make</code> variables <code>rdocdir</code> and
<code>rsharedir</code> can be used to install the system-independent
<samp>doc</samp> and <samp>share</samp> directories to somewhere other than
<code>libdir</code>. The C header files can be installed to the value of
<code>rincludedir</code>: note that as the headers are not installed into a
subdirectory you probably want something like
<code>rincludedir=/usr/local/include/R-3.0.2</code>.
</p>
<p>If you want the R home to be something other than
<samp><var>libdir</var>/R</samp>, use <samp>rhome</samp>: for example
</p>
<div class="example">
<pre class="example">make install rhome=/usr/local/lib64/R-3.0.2
</pre></div>
<p>will use a version-specific R home on a non-Debian Linux 64-bit
system.
</p>
<p>If you have made R as a shared/dynamic library you can install it in
your system’s library directory by
</p>
<div class="example">
<pre class="example">make prefix=/path/to/here install-libR
</pre></div>
<p>where <code>prefix</code> is optional, and <code>libdir</code> will give more
precise control.
</p>
<div class="example">
<pre class="example">make install-strip
</pre></div>
<p>will install stripped executables, and on platforms where this is
supported, stripped libraries in directories <samp>lib</samp> and
<samp>modules</samp> and in the standard packages.
</p>
<p>Note that installing R into a directory whose path contains spaces is
not supported, and at least some aspects (such as installing source
packages) will not work.
</p>
<a name="index-Manuals_002c-installing"></a>
<p>To install info and PDF versions of the manuals, use one or both of
</p>
<div class="example">
<pre class="example">make install-info
make install-pdf
</pre></div>
<p>Once again, it is optional to specify <code>prefix</code>, <code>libdir</code> or
<code>rhome</code> (the PDF manuals are installed under the R home
directory). (<code>make install-info</code> needs Perl installed if there
is no command <code>install-info</code> on the system.)
</p>
<p>More precise control is possible. For info, the setting used is that of
<code>infodir</code> (default <samp><var>prefix</var>/info</samp>, set by configure
option <samp>--infodir</samp>). The PDF files are installed into the R
<samp>doc</samp> tree, set by the <code>make</code> variable <code>rdocdir</code>.
</p>
<p>A staged installation is possible, that it is installing R into a
temporary directory in order to move the installed tree to its final
destination. In this case <code>prefix</code> (and so on) should reflect the
<a name="index-DESTDIR"></a>
final destination, and <code>DESTDIR</code> should be used: see
<a href="http://www.gnu.org/prep/standards/html_node/DESTDIR.html">http://www.gnu.org/prep/standards/html_node/DESTDIR.html</a>.
</p>
<p>You can optionally install the run-time tests that are part of
<code>make check-all</code> by
</p>
<div class="example">
<pre class="example">make install-tests
</pre></div>
<p>which populates a <samp>tests</samp> directory in the installation.
</p>
<hr>
<a name="Uninstallation"></a>
<div class="header">
<p>
Next: <a href="#Sub_002darchitectures" accesskey="n" rel="next">Sub-architectures</a>, Previous: <a href="#Installation" accesskey="p" rel="previous">Installation</a>, Up: <a href="#Installing-R-under-Unix_002dalikes" accesskey="u" rel="up">Installing R under Unix-alikes</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Uninstallation-1"></a>
<h3 class="section">2.5 Uninstallation</h3>
<p>You can uninstall R by
</p>
<div class="example">
<pre class="example">make uninstall
</pre></div>
<p>optionally specifying <code>prefix</code> etc in the same way as specified for
installation.
</p>
<p>This will also uninstall any installed manuals. There are specific
targets to uninstall info and PDF manuals in file
<samp>doc/manual/Makefile</samp>.
</p>
<p>Target <code>uninstall-tests</code> will uninstall any installed tests, as
well as removing the directory <samp>tests</samp> containing the test results.
</p>
<hr>
<a name="Sub_002darchitectures"></a>
<div class="header">
<p>
Next: <a href="#Other-Options" accesskey="n" rel="next">Other Options</a>, Previous: <a href="#Uninstallation" accesskey="p" rel="previous">Uninstallation</a>, Up: <a href="#Installing-R-under-Unix_002dalikes" accesskey="u" rel="up">Installing R under Unix-alikes</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Sub_002darchitectures-1"></a>
<h3 class="section">2.6 Sub-architectures</h3>
<p>Some platforms can support closely related builds of R which can
share all but the executables and dynamic objects. Examples include
builds under Linux and Solaris for different <acronym>CPU</acronym>s or 32- and
64-bit builds.
</p>
<p>R supports the idea of architecture-specific builds, specified by
adding ‘<samp>r_arch=<var>name</var></samp>’ to the <code>configure</code> line. Here
<var>name</var> can be anything non-empty, and is used to name subdirectories
of <samp>lib</samp>, <samp>etc</samp>, <samp>include</samp> and the package <samp>libs</samp>
subdirectories. Example names from other software are the use of
<samp>sparcv9</samp> on Sparc Solaris and <samp>32</samp> by <code>gcc</code> on
‘<samp>x86_64</samp>’ Linux.
</p>
<p>If you have two or more such builds you can install them over each other
(and for 32/64-bit builds on one architecture, one build can be done
without ‘<samp>r_arch</samp>’). The space savings can be considerable: on
‘<samp>x86_64</samp>’ Linux a basic install (without debugging symbols) took
63Mb, and adding a 32-bit build added 6Mb. If you have installed
multiple builds you can select which build to run by
</p>
<div class="example">
<pre class="example">R --arch=<var>name</var>
</pre></div>
<p>and just running ‘<samp>R</samp>’ will run the last build that was installed.
</p>
<p><code>R CMD INSTALL</code> will detect if more than one build is installed and
try to install packages with the appropriate library objects for each.
This will not be done if the package has an executable <code>configure</code>
script or a <samp>src/Makefile</samp> file. In such cases you can install for
extra builds by
</p>
<div class="example">
<pre class="example">R --arch=<var>name</var> CMD INSTALL --libs-only <var>pkg1</var> <var>pkg2</var> …
</pre></div>
<p>If you want to mix sub-architectures compiled on different platforms
(for example ‘<samp>x86_64</samp>’ Linux and ‘<samp>i686</samp>’ Linux), it is
wise to use explicit names for each, and you may also need to set
<samp>libdir</samp> to ensure that they install into the same place.
</p>
<p>When sub-architectures are used the version of <code>Rscript</code> in
e.g. <samp>/usr/bin</samp> will be the last installed, but
architecture-specific versions will be available in e.g.
<samp>/usr/lib64/R/bin/exec${<var>R_ARCH</var>}</samp>. Normally all installed
architectures will run on the platform so the architecture of
<code>Rscript</code> itself does not matter. The executable
<code>Rscript</code> will run the <code>R</code> script, and at that time the
<a name="index-R_005fARCH"></a>
setting of the <code>R_ARCH</code> environment variable determines the
architecture which is run.
</p>
<p>When running post-install tests with sub-architectures, use
</p>
<div class="example">
<pre class="example">R --arch=<var>name</var> CMD make check[-devel|all]
</pre></div>
<p>to select a sub-architecture to check.
</p>
<p>Sub-architectures are also used on Windows, but by selecting executables
within the appropriate <samp>bin</samp> directory,
<samp><var>R_HOME</var>/bin/i386</samp> or <samp><var>R_HOME</var>/bin/x64</samp>. For
backwards compatibility with R < 2.12.0, there are executables
<samp><var>R_HOME</var>/bin/R.exe</samp> or <samp><var>R_HOME</var>/bin/Rscript.exe</samp>:
these will run an executable from one of the subdirectories, which one
being taken first from the
<a name="index-R_005fARCH-1"></a>
<code>R_ARCH</code> environment variable, then from the
<samp>--arch</samp> command-line option<a name="DOCF7" href="#FOOT7"><sup>7</sup></a> and finally from the
installation default (which is 32-bit for a combined 32/64 bit R
installation).
</p>
<table class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">• <a href="#Multilib" accesskey="1">Multilib</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
</table>
<hr>
<a name="Multilib"></a>
<div class="header">
<p>
Previous: <a href="#Sub_002darchitectures" accesskey="p" rel="previous">Sub-architectures</a>, Up: <a href="#Sub_002darchitectures" accesskey="u" rel="up">Sub-architectures</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Multilib-1"></a>
<h4 class="subsection">2.6.1 Multilib</h4>
<p>On Linux<a name="DOCF8" href="#FOOT8"><sup>8</sup></a>, there is an alternative mechanism for mixing 32-bit and 64-bit
libraries known as <em>multilib</em>. If a Linux distribution supports
multilib, then parallel builds of R may be installed in the
sub-directories <samp>lib</samp> (32-bit) and <samp>lib64</samp> (64-bit). The
build to be run may then be selected using the <code>setarch</code>
command. For example, a 32-bit build may be run by
</p>
<div class="example">
<pre class="example">setarch i686 R
</pre></div>
<p>The <code>setarch</code> command is only operational if both 32-bit and
64-bit builds are installed. If there is only one installation of R,
then this will always be run regardless of the architecture specified
by the <code>setarch</code> command.
</p>
<p>There can be problems with installing packages on the non-native
architecture. It is a good idea to run e.g. <code>setarch i686 R</code> for
sessions in which packages are to be installed, even if that is the only
version of R installed (since this tells the package installation
code the architecture needed).
</p>
<p>At present there is a potential problem with packages using Java, as
the post-install for a ‘<samp>i386</samp>’ RPM on ‘<samp>x86_64</samp>’ Linux
reconfigures Java and will find the ‘<samp>x86_64</samp>’ Java. If you know
where a 32-bit Java is installed you may be able to run (as root)
</p>
<div class="example">
<pre class="example">export JAVA_HOME=<path to jre directory of 32-bit Java>
setarch i686 R CMD javareconf
</pre></div>
<p>to get a suitable setting.
</p>
<p>When this mechanism is used, the version of <code>Rscript</code> in
e.g. <samp>/usr/bin</samp> will be the last installed, but an
architecture-specific version will be available in
e.g. <samp>/usr/lib64/R/bin</samp>. Normally all installed architectures
will run on the platform so the architecture of <code>Rscript</code> does
not matter.
</p>
<hr>
<a name="Other-Options"></a>
<div class="header">
<p>
Next: <a href="#Testing-a-Unix_002dalike-Installation" accesskey="n" rel="next">Testing a Unix-alike Installation</a>, Previous: <a href="#Sub_002darchitectures" accesskey="p" rel="previous">Sub-architectures</a>, Up: <a href="#Installing-R-under-Unix_002dalikes" accesskey="u" rel="up">Installing R under Unix-alikes</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Other-Options-1"></a>
<h3 class="section">2.7 Other Options</h3>
<p>There are many other installation options, most of which are listed by
<code>configure --help</code>. Almost all of those not listed elsewhere in
this manual are either standard <code>autoconf</code> options not relevant
to R or intended for specialist uses by the R developers.
</p>
<p>One that may be useful when working on R itself is the option
<samp>--disable-byte-compiled-packages</samp>, which ensures that the base
and recommended packages are lazyloaded but not byte-compiled.
(Alternatively the (make or environment) variable
<code>R_NO_BASE_COMPILE</code> can be set to a non-empty value for the duration
of the build.)
</p>
<hr>
<a name="Testing-a-Unix_002dalike-Installation"></a>
<div class="header">
<p>
Previous: <a href="#Other-Options" accesskey="p" rel="previous">Other Options</a>, Up: <a href="#Installing-R-under-Unix_002dalikes" accesskey="u" rel="up">Installing R under Unix-alikes</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Testing-an-Installation"></a>
<h3 class="section">2.8 Testing an Installation</h3>
<p>Full testing is possible only if the test files have been installed with
</p>
<div class="example">
<pre class="example">make install-tests
</pre></div>
<p>which populates a <samp>tests</samp> directory in the installation.
</p>
<p>If this has been done, two testing routes are available.
The first is to move to the home directory of the R installation
(as given by <code>R.home()</code>) and run
</p>
<div class="example">
<pre class="example">cd tests
## followed by one of
../bin/R CMD make check
../bin/R CMD make check-devel
../bin/R CMD make check-all
</pre></div>
<p>and other useful targets are <code>test-BasePackages</code> and
<code>test-Recommended</code> to the run tests of the standard and
recommended packages (if installed) respectively.
</p>
<p>This re-runs all the tests relevant to the installed R (including for
example code in the package vignettes), but not for example the ones
checking the example code in the manuals nor making the standalone Rmath
library. This can occasionally be useful when the operating environment
has been changed, for example by OS updates or by substituting the
<acronym>BLAS</acronym> (see <a href="#Shared-BLAS">Shared BLAS</a>).
</p>
<p>Alternatively, the installed R can be run, preferably with
<samp>--vanilla</samp>. Then
<a name="index-LC_005fCOLLATE"></a>
</p>
<div class="example">
<pre class="example">Sys.setenv(LC_COLLATE = "C", LANGUAGE = "en")
library("tools")
testInstalledBasic("both")
testInstalledPackages(scope = "base")
testInstalledPackages(scope = "recommended")
</pre></div>
<p>runs the basic tests and then all the tests on the standard and
recommended packages. These tests can be run from anywhere: the basic
tests write their results in the <samp>tests</samp> folder of the R home
directory and run slightly fewer tests than the first approach: in
particular they do not test Internet access.
</p>
<p>These tests work best if <code>diff</code> (in <samp>Rtools*.exe</samp> for
Windows users) is in the path.
</p>
<p>It is possible to test the installed packages (but not the
package-specific tests) by <code>testInstalledPackages</code> even if
<code>make install-tests</code> was not run.
</p>
<p>Note that the results may depend on the language set for times and
messages: for maximal similarity to reference results you may want to
try setting
</p>
<div class="example">
<pre class="example">LANGUAGE=en LC_TIME=C LC_COLLATE=C
</pre></div>
<p>but use a UTF-8 or Latin-1 locale.
</p>
<hr>
<a name="Installing-R-under-Windows"></a>
<div class="header">
<p>
Next: <a href="#Installing-R-under-OS-X" accesskey="n" rel="next">Installing R under OS X</a>, Previous: <a href="#Installing-R-under-Unix_002dalikes" accesskey="p" rel="previous">Installing R under Unix-alikes</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Installing-R-under-Windows-1"></a>
<h2 class="chapter">3 Installing R under Windows</h2>
<a name="index-Installing-under-Windows"></a>
<p>The <samp>bin/windows</samp> directory of a <acronym>CRAN</acronym> site contains
binaries for a base distribution and a large number of add-on packages
from <acronym>CRAN</acronym> to run on Windows XP or later on ix86 <acronym>CPU</acronym>s
(including AMD64/Intel64 cpus and Windows x64).
</p>
<p>Your file system must allow long file names (as is likely except
perhaps for some network-mounted systems).
</p>
<p>Installation is <em>via</em> the installer
<samp>R-3.0.2-win.exe</samp>. Just double-click on the icon and
follow the instructions. When installing on a 64-bit version of Windows
the options will include 32- or 64-bit versions of R (and the default is
to install both). You can uninstall R from the Control Panel.
</p>
<p>Note that you will be asked to choose a language for installation, and
that choice applies to both installation and un-installation but not to
running R itself.
</p>
<p>See the <a href="http://CRAN.R-project.org/bin/windows/base/rw-FAQ.html">R
Windows <acronym>FAQ</acronym></a> for more details on the binary installer.
</p>
<table class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">• <a href="#Building-from-source" accesskey="1">Building from source</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Testing-a-Windows-Installation" accesskey="2">Testing a Windows Installation</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
</table>
<hr>
<a name="Building-from-source"></a>
<div class="header">
<p>
Next: <a href="#Testing-a-Windows-Installation" accesskey="n" rel="next">Testing a Windows Installation</a>, Previous: <a href="#Installing-R-under-Windows" accesskey="p" rel="previous">Installing R under Windows</a>, Up: <a href="#Installing-R-under-Windows" accesskey="u" rel="up">Installing R under Windows</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Building-from-source-1"></a>
<h3 class="section">3.1 Building from source</h3>
<p>R can be built as either a 32-bit or 64-bit application on Windows:
to build the 64-bit application you need a 64-bit edition of Windows:
such an OS can also be used to build 32-bit R.
</p>
<p>The standard installer combines 32-bit and 64-bit builds into a single
executable which can then be installed into the same location and share
all the files except the <samp>.exe</samp> and <samp>.dll</samp> files and some
configuration files in the <samp>etc</samp> directory.
</p>
<table class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">• <a href="#Getting-the-tools" accesskey="1">Getting the tools</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Getting-the-source-files" accesskey="2">Getting the source files</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Building-the-core-files" accesskey="3">Building the core files</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Building-the-bitmap-files" accesskey="4">Building the bitmap files</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Building-the-cairo-devices-files" accesskey="5">Building the cairo devices files</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Checking-the-build" accesskey="6">Checking the build</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Building-the-manuals" accesskey="7">Building the manuals</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Building-the-Inno-Setup-installer" accesskey="8">Building the Inno Setup installer</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Building-the-MSI-installer" accesskey="9">Building the MSI installer</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#g_t64_002dbit-Windows-builds">64-bit Windows builds</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
</table>
<hr>
<a name="Getting-the-tools"></a>
<div class="header">
<p>
Next: <a href="#Getting-the-source-files" accesskey="n" rel="next">Getting the source files</a>, Previous: <a href="#Building-from-source" accesskey="p" rel="previous">Building from source</a>, Up: <a href="#Building-from-source" accesskey="u" rel="up">Building from source</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Getting-the-tools-1"></a>
<h4 class="subsection">3.1.1 Getting the tools</h4>
<p>If you want to build R from the sources, you will first need to
collect, install and test an extensive set of tools. See <a href="#The-Windows-toolset">The Windows toolset</a> (and perhaps updates in
<a href="http://CRAN.R-project.org/bin/windows/Rtools/">http://CRAN.R-project.org/bin/windows/Rtools/</a>) for details.
</p>
<p>The <samp>Rtools*.exe</samp> executable installer described in <a href="#The-Windows-toolset">The Windows toolset</a> also includes some source files in addition to the R
source as noted below. You should run it first, to obtain a working
<code>tar</code> and other necessities. Choose a “Full installation”, and
install the extra files into your intended R source directory, e.g.
<samp>C:/R</samp>. The directory name <em>should not contain spaces</em>. We
will call this directory <samp><var>R_HOME</var></samp> below.
</p>
<hr>
<a name="Getting-the-source-files"></a>
<div class="header">
<p>
Next: <a href="#Building-the-core-files" accesskey="n" rel="next">Building the core files</a>, Previous: <a href="#Getting-the-tools" accesskey="p" rel="previous">Getting the tools</a>, Up: <a href="#Building-from-source" accesskey="u" rel="up">Building from source</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Getting-the-source-files-1"></a>
<h4 class="subsection">3.1.2 Getting the source files</h4>
<p>You need to collect the following sets of files:
</p><ul>
<li> Get the R source code tarball <samp>R-3.0.2.tar.gz</samp> from
<acronym>CRAN</acronym>. Open a command window (or another shell) at directory
<var>R_HOME</var>, and run
<div class="example">
<pre class="example">tar -xf R-3.0.2.tar.gz
</pre></div>
<p>to create the source tree in <var>R_HOME</var>. <strong>Beware</strong>: do use
<code>tar</code> to extract the sources rather than tools such as WinZip.
If you are using an account with administrative privileges you may get a
lot of messages which can be suppressed by
</p>
<div class="example">
<pre class="example">tar --no-same-owner -xf R-3.0.2.tar.gz
</pre></div>
<a name="index-TAR_005fOPTIONS-1"></a>
<p>or perhaps better, set the environment variable <code>TAR_OPTIONS</code> to the
value ‘<samp>--no-same-owner --no-same-permissions</samp>’.
</p>
<p>It is also possible to obtain the source code using Subversion; see
<a href="#Obtaining-R">Obtaining R</a> for details.
</p>
</li><li> If you are not using a tarball you need to obtain copies of the
recommended packages from <acronym>CRAN</acronym>. Put the <samp>.tar.gz</samp> files
in <samp><var>R_HOME</var>/src/library/Recommended</samp> and run <code>make
link-recommended</code>. If you have an Internet connection, you can do this
automatically by running in <samp><var>R_HOME</var>/src/gnuwin32</samp>
<div class="example">
<pre class="example">make rsync-recommended
</pre></div>
</li></ul>
<p>The following additional items are normally installed by
<samp>Rtools30.exe</samp>. If instead you choose to do a completely manual
build you will also need
</p>
<ul>
<li> The Tcl/Tk support files are contained in <samp>Rtools30.exe</samp> and
available as <samp>.zip</samp> files from
<a href="http://www.stats.ox.ac.uk/pub/Rtools">http://www.stats.ox.ac.uk/pub/Rtools</a>. Please make sure you
install the right version: there is a 32-bit version and a 64-bit
version. They should be installed to <samp><var>R_HOME</var></samp>, creating
directory <samp>Tcl</samp> there.
</li><li> You need <code>libpng</code>, <code>jpeg</code> and <code>libtiff</code> sources
(available, e.g., from <a href="http://www.libpng.org/">http://www.libpng.org/</a>,
<a href="http://www.ijg.org">http://www.ijg.org</a> and
<a href="http://download.osgeo.org/libtiff/">http://download.osgeo.org/libtiff/</a>); current versions are
recommended and 7 or later is required. It is also possible to use
‘<samp>libjpeg-turbo</samp>’ from
<a href="http://sourceforge.net/projects/libjpeg-turbo/files/">http://sourceforge.net/projects/libjpeg-turbo/files/</a>.
<p>Working in the directory <samp><var>R_HOME</var>/src/gnuwin32/bitmap</samp>,
install the <code>libpng</code> and <code>jpeg</code> sources in sub-directories.
The <code>jpeg</code> sub-directory for version 9 is named <samp>jpeg-9</samp>; if
you use a different version (e.g. <samp>jpeg-8d</samp> or
<samp>libjpeg-turbo</samp>), copy file <samp>src/gnuwin32/MkRules.dist</samp> to
<samp>src/gnuwin32/MkRules.local</samp> and edit the definition of
<code>JPEGDIR</code>: the names of the <samp>libpng</samp> and <samp>libtiff</samp>
directories can also be set there.
</p>
<p>Example:
</p>
<div class="example">
<pre class="example">> tar -zxf libpng-1.6.2.tar.gz
> mv libpng-1.6.2 libpng
> tar -zxf jpegsrc.v9.tar.gz
> tar -zxf tiff-4.0.3.tar.gz
> mv tiff-4.0.3/libtiff .
> rm -rf tiff-4.0.3
</pre></div>
<p>(and see the comment above about <samp>--no-same-owner</samp>).
</p>
</li></ul>
<hr>
<a name="Building-the-core-files"></a>
<div class="header">
<p>
Next: <a href="#Building-the-bitmap-files" accesskey="n" rel="next">Building the bitmap files</a>, Previous: <a href="#Getting-the-source-files" accesskey="p" rel="previous">Getting the source files</a>, Up: <a href="#Building-from-source" accesskey="u" rel="up">Building from source</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Building-the-core-files-1"></a>
<h4 class="subsection">3.1.3 Building the core files</h4>
<a name="index-TMPDIR-1"></a>
<p>Set the environment variable <code>TMPDIR</code> to point to a writable
directory, with a path specified with forward slashes and no spaces.
(The default is <samp>/tmp</samp>, which may not be useful on Windows.)
</p>
<p>You may need to compile under a case-honouring file system: we found
that a <code>samba</code>-mounted file system (which maps all file names to
lower case) did not work.
</p>
<p>Open a command window at <samp><var>R_HOME</var>/src/gnuwin32</samp>. Look at
<samp>MkRules.dist</samp> and if settings need to be altered, copy it to
<samp>MkRules.local</samp> and edit the settings there. In particular, this
is where a 64-bit build is selected. Then run
</p>
<div class="example">
<pre class="example">make all recommended
</pre></div>
<p>and sit back and wait while the basic compile takes place.
</p>
<p>Notes:
</p><ul>
<li> We have had reports that earlier versions of anti-virus software locking
up the machine, but not for several years. However, aggressive
anti-virus checking such as the on-access scanning of Sophos can slow
the build down several-fold.
</li><li> By default Doug Lea’s <code>malloc</code> in the file
<samp><var>R_HOME</var>/src/gnuwin32/malloc.c</samp> is used for R’s internal
memory allocations. You can opt out of this by setting
<code>LEA_MALLOC=NO</code> in <samp>MkRules.dist</samp>, in which case the <code>malloc</code>
in <samp>msvcrt.dll</samp> is used. This does impose a considerable
performance penalty and has not been tested recently.
</li><li> You can run a parallel make by e.g.
<div class="example">
<pre class="example">make -j4 all
make -j4 recommended
</pre></div>
<p>but this is only likely to be worthwhile on a multi-core machine with
ample memory, and is not 100% reliable.
</p>
</li><li> It is possible (mainly for those working on R itself) to set the
(make or environment) variable <code>R_NO_BASE_COMPILE</code> to a non-empty
value, which inhibits the byte-compilation of the base and recommended
packages.
</li></ul>
<hr>
<a name="Building-the-bitmap-files"></a>
<div class="header">
<p>
Next: <a href="#Building-the-cairo-devices-files" accesskey="n" rel="next">Building the cairo devices files</a>, Previous: <a href="#Building-the-core-files" accesskey="p" rel="previous">Building the core files</a>, Up: <a href="#Building-from-source" accesskey="u" rel="up">Building from source</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Building-the-bitmap-files-1"></a>
<h4 class="subsection">3.1.4 Building the bitmap files</h4>
<a name="index-Rbitmap_002edll"></a>
<p>The file
<samp><var>R_HOME</var>/library/grDevices/libs/{i386,x64}Rbitmap.dll</samp> is
not built automatically.
</p>
<p>Running <code>make</code> in <samp><var>R_HOME</var>/src/gnuwin32/bitmap</samp> or
<code>make bitmapdll</code> in <samp><var>R_HOME</var>/src/gnuwin32</samp> should build
<samp>Rbitmap.dll</samp> and install it under
<samp><var>R_HOME</var>/library/grDevices/libs</samp>.
</p>
<hr>
<a name="Building-the-cairo-devices-files"></a>
<div class="header">
<p>
Next: <a href="#Checking-the-build" accesskey="n" rel="next">Checking the build</a>, Previous: <a href="#Building-the-bitmap-files" accesskey="p" rel="previous">Building the bitmap files</a>, Up: <a href="#Building-from-source" accesskey="u" rel="up">Building from source</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Building-the-cairo-devices"></a>
<h4 class="subsection">3.1.5 Building the cairo devices</h4>
<a name="index-winCairo_002edll"></a>
<p>The devices based on cairographics (<code>svg</code>, <code>cairo_pdf</code>,
<code>cairo_ps</code> and the <code>type = "cairo"</code> versions of <code>png</code>,
<code>jpeg</code>, <code>tiff</code> and <code>bmp</code>) are implemented in a separate
DLL <samp>winCairo.dll</samp> which is loaded when one of these devices is
first used. It is not built by default, and needs to be built after
<samp>Rbitmap.dll</samp>, by <code>make cairodevices</code>.
</p>
<p>To enable the building of these devices you need to install the static
cairographics libraries built by Simon Urbanek at
<a href="http://www.rforge.net/Cairo/files/cairo-current-win.tar.gz">http://www.rforge.net/Cairo/files/cairo-current-win.tar.gz</a>. Set
the macro ‘<samp>CAIRO_HOME</samp>’ in <samp>MkRules.local</samp>. (Note that this
tarball unpacks with a top-level directory <samp>src/</samp>:
‘<samp>CAIRO_HOME</samp>’ needs to include that directory in its path.)
</p>
<hr>
<a name="Checking-the-build"></a>
<div class="header">
<p>
Next: <a href="#Building-the-manuals" accesskey="n" rel="next">Building the manuals</a>, Previous: <a href="#Building-the-cairo-devices-files" accesskey="p" rel="previous">Building the cairo devices files</a>, Up: <a href="#Building-from-source" accesskey="u" rel="up">Building from source</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Checking-the-build-1"></a>
<h4 class="subsection">3.1.6 Checking the build</h4>
<p>You can test a build by running
</p>
<div class="example">
<pre class="example">make check
</pre></div>
<p>The recommended packages can be checked by
</p>
<div class="example">
<pre class="example">make check-recommended
</pre></div>
<p>Other levels of checking are
</p>
<div class="example">
<pre class="example">make check-devel
</pre></div>
<p>for a more thorough check of the R functionality, and
</p>
<div class="example">
<pre class="example">make check-all
</pre></div>
<p>for <code>check-devel</code> and <code>check-recommended</code>.
</p>
<p>If a test fails, there will almost always be a <samp>.Rout.fail</samp> file in
the directory being checked (often <samp>tests/Examples</samp> or
<samp>tests</samp>): examine the file to help pinpoint the problem.
</p>
<hr>
<a name="Building-the-manuals"></a>
<div class="header">
<p>
Next: <a href="#Building-the-Inno-Setup-installer" accesskey="n" rel="next">Building the Inno Setup installer</a>, Previous: <a href="#Checking-the-build" accesskey="p" rel="previous">Checking the build</a>, Up: <a href="#Building-from-source" accesskey="u" rel="up">Building from source</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Building-the-manuals-1"></a>
<h4 class="subsection">3.1.7 Building the manuals</h4>
<p>The PDF manuals can be made by
</p>
<div class="example">
<pre class="example">make manuals
</pre></div>
<p>If you want to make the info versions (not including the Reference
Manual), use
</p>
<div class="example">
<pre class="example">cd ../../doc/manual
make -f Makefile.win info
</pre></div>
<p>(all assuming you have <code>pdftex</code>/<code>pdflatex</code> installed and
in your path).
</p>
<p>See the <a href="#Making-the-manuals">Making the manuals</a> section in the Unix-alike section for setting
options such as the paper size and the fonts used.
</p>
<hr>
<a name="Building-the-Inno-Setup-installer"></a>
<div class="header">
<p>
Next: <a href="#Building-the-MSI-installer" accesskey="n" rel="next">Building the MSI installer</a>, Previous: <a href="#Building-the-manuals" accesskey="p" rel="previous">Building the manuals</a>, Up: <a href="#Building-from-source" accesskey="u" rel="up">Building from source</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Building-the-Inno-Setup-installer-1"></a>
<h4 class="subsection">3.1.8 Building the Inno Setup installer</h4>
<p>You need to have the files for a complete R build, including bitmap and
Tcl/Tk support and the manuals, as well as the recommended packages and
Inno Setup (see <a href="#The-Inno-Setup-installer">The Inno Setup installer</a>).
</p>
<p>Once everything is set up
</p>
<div class="example">
<pre class="example">make distribution
make check-all
</pre></div>
<p>will make all the pieces and the installers and put them in the
<samp>gnuwin32/cran</samp> subdirectory, then check the build. This works by
building all the parts in the sequence:
</p>
<div class="example">
<pre class="example">rbuild <span class="roman">(the executables, the <acronym>FAQ</acronym> docs etc.)</span>
rpackages <span class="roman">(the base packages)</span>
htmldocs <span class="roman">(the HTML documentation)</span>
bitmapdll <span class="roman">(the bitmap support files)</span>
cairodevices <span class="roman">(the cairo-based graphics devices)</span>
recommended <span class="roman">(the recommended packages)</span>
vignettes <span class="roman">(the vignettes in base packages:</span>
<span class="roman"> only needed if building from an svn checkout)</span>
manuals <span class="roman">(the PDF manuals)</span>
rinstaller <span class="roman">(the install program)</span>
crandir <span class="roman">(the <acronym>CRAN</acronym> distribution directory, only for 64-bit builds)</span>
</pre></div>
<p>The parts can be made individually if a full build is not needed, but
earlier parts must be built before later ones. (The <samp>Makefile</samp>
doesn’t enforce this dependency—some build targets force a lot of
computation even if all files are up to date.) The first four targets
are the default build if just <code>make</code> (or <code>make all</code>) is
run.
</p>
<p>Parallel make is not supported and likely to fail.
</p>
<p>If you want to customize the installation by adding extra packages,
replace <code>make rinstaller</code> by something like
</p>
<div class="example">
<pre class="example">make rinstaller EXTRA_PKGS='pkg1 pkg2 pkg3'
</pre></div>
<p>An alternative way to customize the installer starting with a binary
distribution is to first make an installation of R from the standard
installer, then add packages and make other customizations to that
installation. Then (after having customized file <samp>MkRules</samp>,
possibly <em>via</em> <samp>MkRules.local</samp>, and having made R in the
source tree) in <samp>src/gnuwin32/installer</samp> run
</p>
<div class="example">
<pre class="example">make myR IMAGEDIR=rootdir
</pre></div>
<p>where <samp>rootdir</samp> is the path to the root of the customized
installation (in double quotes if it contains spaces or backslashes).
</p>
<p>Both methods create an executable with a standard name such as
<samp>R-3.0.2-win.exe</samp>, so please rename it to indicate that
it is customized. If you intend to <em>distribute</em> a customized
installer please do check that license requirements are met – note that
the installer will state that the contents are distributed under GPL-2
and this has a requirement for <em>you</em> to supply the complete sources
(including the R sources even if you started with a binary distribution
of R, and also the sources of any extra packages (including their
external software) which are included).
</p>
<p>The defaults for the startup parameters may also be customized. For example
</p>
<div class="example">
<pre class="example">make myR IMAGEDIR=rootdir MDISDI=1
</pre></div>
<p>will create an installer that defaults to installing R to run in SDI
mode. See <samp>src/gnuwin32/installer/Makefile</samp> for the names and
values that can be set.
</p>
<p>The standard <acronym>CRAN</acronym> distribution of a 32/64-bit installer is
made by first building 32-bit R (just
</p>
<div class="example">
<pre class="example">make 32-bit
</pre></div>
<p>is needed), and then building 64-bit R with the macro <code>HOME32</code> set
in file <samp>MkRules.local</samp> to the top-level directory of the 32-bit
build. Then the <code>make rinstaller</code> step copies the files that
differ between architectures from the 32-bit build as it builds the
installer image.
</p>
<hr>
<a name="Building-the-MSI-installer"></a>
<div class="header">
<p>
Next: <a href="#g_t64_002dbit-Windows-builds" accesskey="n" rel="next">64-bit Windows builds</a>, Previous: <a href="#Building-the-Inno-Setup-installer" accesskey="p" rel="previous">Building the Inno Setup installer</a>, Up: <a href="#Building-from-source" accesskey="u" rel="up">Building from source</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Building-the-MSI-installer-1"></a>
<h4 class="subsection">3.1.9 Building the MSI installer</h4>
<p>It is also possible to build an installer for use with Microsoft
Installer. This is intended for use by sysadmins doing automated
installs, and is not recommended for casual use.
</p>
<p>It makes use of the Windows Installer XML (WiX) toolkit <em>version
3.5</em> (or perhaps later, untested) available from
<a href="http://wix.sourceforge.net/">http://wix.sourceforge.net/</a> or <a href="http://wixtoolset.org/">http://wixtoolset.org/</a>.
Once WiX is installed, set the path to its home directory in
<samp>MkRules.local</samp>.
</p>
<p>You need to have the files for a complete R build, including bitmap and
Tcl/Tk support and the manuals, as well as the recommended packages.
There is no option in the installer to customize startup options, so
edit <samp>etc/Rconsole</samp> and <samp>etc/Rprofile.site</samp> to set these as
required. Then
</p>
<div class="example">
<pre class="example">cd installer
make msi
</pre></div>
<p>which will result in a file with a name like
<samp>R-3.0.2-win32.msi</samp>. This can be double-clicked to be
installed, but those who need it will know what to do with it (usually
by running <code>msiexec /i</code> with additional options). Properties
that users might want to set from the <code>msiexec</code> command line
include ‘<samp>ALLUSERS</samp>’, ‘<samp>INSTALLDIR</samp>’ (something like
<samp>c:\Program Files\R\R-3.0.2</samp>) and ‘<samp>RMENU</samp>’ (the path
to the ‘<samp>R</samp>’ folder on the start menu) and ‘<samp>STARTDIR</samp>’ (the
starting directory for R shortcuts, defaulting to something like
<samp>c:\Users\name\Documents\R</samp>).
</p>
<p>The MSI installer can be built both from a 32-bit build of R
(<samp>R-3.0.2-win32.msi</samp>) and from a 64-bit build of R
(<samp>R-3.0.2-win64.msi</samp>, optionally including 32-bit files
by setting the macro <code>HOME32</code>, when the name is
<samp>R-3.0.2-win.msi</samp>). Unlike the main installer, a 64-bit
MSI installer can only be run on 64-bit Windows.
</p>
<p>Thanks to David del Campo (Dept of Statistics, University of Oxford)
for suggesting WiX and building a prototype installer.
</p>
<hr>
<a name="g_t64_002dbit-Windows-builds"></a>
<div class="header">
<p>
Previous: <a href="#Building-the-MSI-installer" accesskey="p" rel="previous">Building the MSI installer</a>, Up: <a href="#Building-from-source" accesskey="u" rel="up">Building from source</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="g_t64_002dbit-Windows-builds-1"></a>
<h4 class="subsection">3.1.10 64-bit Windows builds</h4>
<p>To build a 64-bit version of R you need a 64-bit toolchain: the only one
discussed here is based on the work of the MinGW-w64 project
(<a href="http://sourceforge.net/projects/mingw-w64/">http://sourceforge.net/projects/mingw-w64/</a>, but commercial
compilers such as those from Intel and PGI could be used (and have been
by R redistributors).
</p>
<p>Support for MinGW-w64 was developed in the R sources over the period
2008–10 and was first released as part of R 2.11.0. The assistance
of Yu Gong at a crucial step in porting R to MinGW-w64 is gratefully
acknowledged, as well as help from Kai Tietz, the lead developer of the
MinGW-w64 project.
</p>
<p>Windows 64-bit is now completely integrated into the R and package
build systems.
</p>
<hr>
<a name="Testing-a-Windows-Installation"></a>
<div class="header">
<p>
Previous: <a href="#Building-from-source" accesskey="p" rel="previous">Building from source</a>, Up: <a href="#Installing-R-under-Windows" accesskey="u" rel="up">Installing R under Windows</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Testing-an-Installation-1"></a>
<h3 class="section">3.2 Testing an Installation</h3>
<p>The Windows installer contains a set of test files used when building
R.
</p>
<p>The <code>Rtools</code> are not needed to run these tests. but more
comprehensive analysis of errors will be given if <code>diff</code> is in
the path (and <code>errorsAreFatal = FALSE</code> is then not needed below).
</p>
<p>Launch either <code>Rgui</code> or <code>Rterm</code>, preferably with
<samp>--vanilla</samp>. Then run
</p>
<div class="example">
<pre class="example">Sys.setenv(LC_COLLATE = "C", LANGUAGE = "en")
library("tools")
testInstalledBasic("both")
testInstalledPackages(scope = "base", errorsAreFatal = FALSE)
testInstalledPackages(scope = "recommended", errorsAreFatal = FALSE)
</pre></div>
<p>runs the basic tests and then all the tests on the standard and
recommended packages. These tests can be run from anywhere: they write
some of their results in the <samp>tests</samp> folder of the R home
directory (as given by <code>R.home()</code>), and hence may need to be run
under the account used to install R.
</p>
<p>The results of <code>example(md5sums)</code> when testing <strong>tools</strong> will
differ from the reference output as some files are installed with
Windows’ CRLF line endings.
</p>
<hr>
<a name="Installing-R-under-OS-X"></a>
<div class="header">
<p>
Next: <a href="#Running-R" accesskey="n" rel="next">Running R</a>, Previous: <a href="#Installing-R-under-Windows" accesskey="p" rel="previous">Installing R under Windows</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Installing-R-under-OS-X-1"></a>
<h2 class="chapter">4 Installing R under OS X</h2>
<a name="index-OS-X-1"></a>
<p>The front page of a <acronym>CRAN</acronym> site has a link ‘Download R for OS
X’. Click on that, then download the file <samp>R-3.0.2.pkg</samp>
and install it. This runs on OS X 10.6 and later (Snow Leopard, Lion,
Mountain Lion, Mavericks, …); it is a 64-bit (‘<samp>x86_64</samp>’)
build which should run on all Macs from mid-2008 on. For older Intel
Macs and some older versions of the OS you can install R from the
sources.
</p>
<p>It is important that is you use the binary package that your OS is fully
updated: run ‘Software Update’ from the Apple menu to be sure.
</p>
<p>To install, just double-click on the icon of the file you downloaded.
At the ‘Installation Type’ stage, note the option to ‘Customize’. This
currently shows three components (‘Package Name’). Everyone will need
the ‘R Framework’ component: the ‘R GUI’ and ‘Tcl/Tk’ components are
optional (the latter being needed to use package <strong>tcltk</strong>).
</p>
<p>This is an Apple Installer package. If you encounter any problem during
the installation, please check the Installer log by clicking on the
“Window” menu and item “Installer Log”. The full output (select
“Show All Log”) is useful for tracking down problems.
</p>
<p>On Mountain Lion and later with ‘GateKeeper’ active you will need to
right/control-click on any unsigned packages and select ‘<samp>Open</samp>’:
recent <acronym>CRAN</acronym> packages are signed.
</p>
<p>For building R from source, see <a href="#OS-X">OS X</a>.
</p>
<table class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">• <a href="#Running-R-under-OS-X" accesskey="1">Running R under OS X</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Uninstalling-under-OS-X" accesskey="2">Uninstalling under OS X</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Multiple-versions" accesskey="3">Multiple versions</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
</table>
<hr>
<a name="Running-R-under-OS-X"></a>
<div class="header">
<p>
Next: <a href="#Uninstalling-under-OS-X" accesskey="n" rel="next">Uninstalling under OS X</a>, Previous: <a href="#Installing-R-under-OS-X" accesskey="p" rel="previous">Installing R under OS X</a>, Up: <a href="#Installing-R-under-OS-X" accesskey="u" rel="up">Installing R under OS X</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Running-R-under-OS-X-1"></a>
<h3 class="section">4.1 Running R under OS X</h3>
<p>There are two ways to run R on OS X from the <acronym>CRAN</acronym> binary
distribution.
</p>
<p>There is a GUI console normally installed with the R icon in
<samp>/Applications</samp> which you can run by double-clicking (e.g. from
Launchpad or Finder). This is usually referred to as <small>R.APP</small> to
distinguish it from command-line R: its user manual is currently part
of the OS X FAQ at
<a href="http://cran.r-project.org/bin/macosx/RMacOSX-FAQ.html">http://cran.r-project.org/bin/macosx/RMacOSX-FAQ.html</a>
</p>
<p>You can run command-line R from a Terminal like any other Unix-alike:
see the next chapter of this manual. There are some small differences
which may surprise users of R on other platforms, notably the default
personal library directory (under <samp>~/Library/R</samp>,
e.g. <samp>~/Library/R/3.0/library</samp>), and that warnings, messages and
other output to <samp>stderr</samp> are highlighted in bold.
</p>
<hr>
<a name="Uninstalling-under-OS-X"></a>
<div class="header">
<p>
Next: <a href="#Multiple-versions" accesskey="n" rel="next">Multiple versions</a>, Previous: <a href="#Running-R-under-OS-X" accesskey="p" rel="previous">Running R under OS X</a>, Up: <a href="#Installing-R-under-OS-X" accesskey="u" rel="up">Installing R under OS X</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Uninstalling-under-OS-X-1"></a>
<h3 class="section">4.2 Uninstalling under OS X</h3>
<p>R for OS X consists of two parts: the GUI (<small>R.APP</small>) and the R
framework. The un-installation is as simple as removing those folders
(e.g. by dragging them into the Trash). The typical installation will
install the GUI into the <samp>/Applications/R.app</samp> folder and the R
framework into the <samp>/Library/Frameworks/R.frameweork</samp> folder. This
does leave some links in <samp>/usr/bin</samp>.
</p>
<p>If you want to get rid of R more completely using a Terminal, simply
run (prepend <code>sudo</code> if needed):
</p>
<div class="example">
<pre class="example">rm -rf /Library/Frameworks/R.framework /Applications/R.app \
/usr/bin/R /usr/bin/Rscript
</pre></div>
<p>The installation consisted of three Apple packages:
<code>org.r-project.R.Leopard.fw.pkg</code>,
<code>org.r-project.R.Leopard.GUI.pkg</code> and
<code>org.r-project.x86_64.tcltk.x11</code> (not all of which need be
installed). You can use <code>pkgutil --unlink</code> (not supported by Lion
or later) to remove their files or <code>pkgutil --forget</code> if you want
the Apple Installer to forget about the package without deleting its
files (useful for the R framework when installing multiple R versions
in parallel), or after you have deleted the files.
</p>
<p>Uninstalling the Tcl/Tk component (which is installed under
<samp>/usr/local</samp>) is not simple. You can list the files it installed
in a Terminal by
</p>
<div class="example">
<pre class="example">pkgutil --files org.r-project.x86_64.tcltk.x11
</pre></div>
<p>Note that some but not all of these files replace those in the Tcl/Tk 8.5.5
installation used for R 2.x, so care is needed if removing either.
</p>
<hr>
<a name="Multiple-versions"></a>
<div class="header">
<p>
Previous: <a href="#Uninstalling-under-OS-X" accesskey="p" rel="previous">Uninstalling under OS X</a>, Up: <a href="#Installing-R-under-OS-X" accesskey="u" rel="up">Installing R under OS X</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Multiple-versions-1"></a>
<h3 class="section">4.3 Multiple versions</h3>
<p>The installer will remove any previous version of the R framework
which it finds installed. This can be avoided by using <code>pkgutil
--forget</code> (see the previous section). However, note that different
versions are installed under
<samp>/Library/Frameworks/R.framework/Versions</samp> as <samp>2.15</samp>,
<samp>3.0</samp> and so on, so it is not possible to have different
‘<samp>3.x.y</samp>’ versions installed for the same ‘<samp>x</samp>’.
</p>
<p>A version of R can be run directly from the command-line as e.g.
</p><div class="example">
<pre class="example">/Library/Frameworks/R.framework/Versions/3.0/Resources/bin/R
</pre></div>
<p>However, <small>R.APP</small> will always run the ‘current’ version, that is the last
installed version. A small utility, <code>Rswitch.app</code> (available at
<a href="http://r.research.att.com/#other">http://r.research.att.com/#other</a>), can be used to change the
‘current’ version. However, this is of limited use as <small>R.APP</small> is
compiled against a particular version of R and will likely crash if
switched to an earlier version. This may allow you to install a
development version of R (de-selecting <small>R.APP</small>) and then switch back
to the release version.
</p>
<hr>
<a name="Running-R"></a>
<div class="header">
<p>
Next: <a href="#Add_002don-packages" accesskey="n" rel="next">Add-on packages</a>, Previous: <a href="#Installing-R-under-OS-X" accesskey="p" rel="previous">Installing R under OS X</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Running-R-1"></a>
<h2 class="chapter">5 Running R</h2>
<p>How to start R and what command-line options are available is discussed
in <a href="http://cran.r-project.org/doc/manuals//R-intro.html#Invoking-R">Invoking R</a> in <cite>An Introduction to R</cite>.
</p>
<p>You should ensure that the shell has set adequate resource limits: R
expects a stack size of at least 8MB and to be able to open at least 256
file descriptors. (Any modern OS will have default limits at least as
large as these, but apparently NetBSD does not. Use the shell command
<code>ulimit</code> (<code>sh</code>/<code>bash</code>) or <code>limit</code>
(<code>csh</code>/<code>tcsh</code>) to check.)
</p>
<p>R makes use of a number of environment variables, the default values
of many of which are set in file <samp><var>R_HOME</var>/etc/Renviron</samp> (there
are none set by default on Windows and hence no such file). These are
set at <code>configure</code> time, and you would not normally want to
<a name="index-R_005fPAPERSIZE-1"></a>
change them – a possible exception is <code>R_PAPERSIZE</code> (see <a href="#Setting-paper-size">Setting paper size</a>). The paper size will be deduced from the ‘<samp>LC_PAPER</samp>’
locale category if it exists and <code>R_PAPERSIZE</code> is unset, and this
will normally produce the right choice from ‘<samp>a4</samp>’ and ‘<samp>letter</samp>’
on modern Unix-alikes (but can always be overridden by setting
<code>R_PAPERSIZE</code>).
</p>
<p>Various environment variables can be set to determine where R creates
its per-session temporary directory. The environment variables
<a name="index-TMPDIR-2"></a>
<a name="index-TMP"></a>
<a name="index-TEMP"></a>
<code>TMPDIR</code>, <code>TMP</code> and <code>TEMP</code> are searched in turn and the
first one which is set and points to a writable area is used. If none
do, the final default is <samp>/tmp</samp> on Unix-alikes and the value of
<a name="index-R_005fUSER"></a>
<code>R_USER</code> on Windows. The path should not contain spaces.
</p>
<p>Some Unix-alike systems are set up to remove files and directories
periodically from <samp>/tmp</samp>, for example by a <code>cron</code> job
<a name="index-TMPDIR-3"></a>
running <code>tmpwatch</code>. Set <code>TMPDIR</code> to another directory
before starting long-running jobs on such a system.
</p>
<p>Note that <code>TMPDIR</code> will be used to execute <code>configure</code>
scripts when installing packages, so if <samp>/tmp</samp> has been mounted as
‘<samp>noexec</samp>’, <code>TMPDIR</code> needs to be set to a directory from which
execution is allowed.
</p>
<hr>
<a name="Add_002don-packages"></a>
<div class="header">
<p>
Next: <a href="#Internationalization" accesskey="n" rel="next">Internationalization</a>, Previous: <a href="#Running-R" accesskey="p" rel="previous">Running R</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Add_002don-packages-1"></a>
<h2 class="chapter">6 Add-on packages</h2>
<a name="index-Packages"></a>
<a name="index-Libraries"></a>
<table class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">• <a href="#Default-packages" accesskey="1">Default packages</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Managing-libraries" accesskey="2">Managing libraries</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Installing-packages" accesskey="3">Installing packages</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Updating-packages" accesskey="4">Updating packages</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Removing-packages" accesskey="5">Removing packages</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Setting-up-a-package-repository" accesskey="6">Setting up a package repository</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Checking-installed-source-packages" accesskey="7">Checking installed source packages</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
</table>
<p>It is helpful to use the correct terminology. A <em>package</em> is
loaded from a <em>library</em> by the function <code>library()</code>. Thus a
library is a directory containing installed packages; the main library
is <samp><var>R_HOME</var>/library</samp>, but others can be used, for example by
<a name="index-R_005fLIBS"></a>
setting the environment variable <code>R_LIBS</code> or using the R function
<code>.libPaths()</code>.
</p>
<hr>
<a name="Default-packages"></a>
<div class="header">
<p>
Next: <a href="#Managing-libraries" accesskey="n" rel="next">Managing libraries</a>, Previous: <a href="#Add_002don-packages" accesskey="p" rel="previous">Add-on packages</a>, Up: <a href="#Add_002don-packages" accesskey="u" rel="up">Add-on packages</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Default-packages-1"></a>
<h3 class="section">6.1 Default packages</h3>
<a name="index-Packages_002c-default"></a>
<p>The set of packages loaded on startup is by default
</p>
<div class="example">
<pre class="example">> getOption("defaultPackages")
[1] "datasets" "utils" "grDevices" "graphics" "stats" "methods"
</pre></div>
<p>(plus, of course, <strong>base</strong>) and this can be changed by setting the
option in startup code (e.g. in <samp>~/.Rprofile</samp>). It is initially
<a name="index-R_005fDEFAULT_005fPACKAGES"></a>
set to the value of the environment variable <code>R_DEFAULT_PACKAGES</code> if
set (as a comma-separated list). Setting <code>R_DEFAULT_PACKAGES=NULL</code>
ensures that only package <strong>base</strong> is loaded.
</p>
<p>Changing the set of default packages is normally used to reduce the set
for speed when scripting: in particular not using <strong>methods</strong> will
reduce the start-up time by a factor of up to two (and this is done by
<code>Rscript</code>). But it can also be used to customize R, e.g.
for class use.
</p>
<hr>
<a name="Managing-libraries"></a>
<div class="header">
<p>
Next: <a href="#Installing-packages" accesskey="n" rel="next">Installing packages</a>, Previous: <a href="#Default-packages" accesskey="p" rel="previous">Default packages</a>, Up: <a href="#Add_002don-packages" accesskey="u" rel="up">Add-on packages</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Managing-libraries-1"></a>
<h3 class="section">6.2 Managing libraries</h3>
<a name="index-Libraries_002c-managing"></a>
<p>R packages are installed into <em>libraries</em>, which are
directories in the file system containing a subdirectory for each
package installed there.
</p>
<p>R comes with a single library, <samp><var>R_HOME</var>/library</samp> which is
the value of the R object ‘<samp>.Library</samp>’ containing the standard and
recommended<a name="DOCF9" href="#FOOT9"><sup>9</sup></a> packages.
Both sites and users can create others and make use of them (or not) in
an R session. At the lowest level ‘<samp>.libPaths()</samp>’ can be used to
add paths to the collection of libraries or to report the current
collection.
</p>
<a name="index-Libraries_002c-site"></a>
<a name="index-Site-libraries"></a>
<p>R will automatically make use of a site-specific library
<samp><var>R_HOME</var>/site-library</samp> if this exists (it does not in a
vanilla R installation). This location can be overridden by
setting<a name="DOCF10" href="#FOOT10"><sup>10</sup></a> ‘<samp>.Library.site</samp>’ in
<samp><var>R_HOME</var>/etc/Rprofile.site</samp>, or (not recommended) by setting
the
<a name="index-R_005fLIBS_005fSITE"></a>
environment variable <code>R_LIBS_SITE</code>. Like ‘<samp>.Library</samp>’, the
site libraries are always included by ‘<samp>.libPaths()</samp>’.
</p>
<a name="index-Libraries_002c-user"></a>
<a name="index-User-libraries"></a>
<a name="index-R_005fLIBS_005fUSER"></a>
<p>Users can have one or more libraries, normally specified by the
environment variable <code>R_LIBS_USER</code>. This has a default value (to
see it, use ‘<samp>Sys.getenv("R_LIBS_USER")</samp>’ within an R session),
but that is only used if the corresponding directory actually exists
(which by default it will not).
</p>
<p>Both <code>R_LIBS_USER</code> and <code>R_LIBS_SITE</code> can specify multiple
library paths, separated by colons (semicolons on Windows).
</p>
<hr>
<a name="Installing-packages"></a>
<div class="header">
<p>
Next: <a href="#Updating-packages" accesskey="n" rel="next">Updating packages</a>, Previous: <a href="#Managing-libraries" accesskey="p" rel="previous">Managing libraries</a>, Up: <a href="#Add_002don-packages" accesskey="u" rel="up">Add-on packages</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Installing-packages-1"></a>
<h3 class="section">6.3 Installing packages</h3>
<a name="index-Packages_002c-installing"></a>
<table class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">• <a href="#Windows-packages" accesskey="1">Windows packages</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#OS-X-packages" accesskey="2">OS X packages</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Customizing-package-compilation" accesskey="3">Customizing package compilation</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Multiple-sub_002darchitectures" accesskey="4">Multiple sub-architectures</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Byte_002dcompilation" accesskey="5">Byte-compilation</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
</table>
<p>Packages may be distributed in source form or compiled binary form.
Installing source packages which contain C/C++/Fortran code requires
that compilers and related tools be installed. Binary packages are
platform-specific and generally need no special tools to install, but
see the documentation for your platform for details.
</p>
<p>Note that you may need to specify implicitly or explicitly the library to
which the package is to be installed. This is only an issue if you have
more than one library, of course.
</p>
<a name="index-TMPDIR-4"></a>
<p>Ensure that the environment variable <code>TMPDIR</code> is either unset (and
<samp>/tmp</samp> exists and can be written in and executed from) or points to
a valid temporary directory with a path not containing spaces.
</p>
<p>For most users it suffices to call
‘<samp>install.packages(<var>pkgname</var>)</samp>’ or its GUI equivalent if the
intention is to install a <acronym>CRAN</acronym> package and internet access is
available.<a name="DOCF11" href="#FOOT11"><sup>11</sup></a> On most systems ‘<samp>install.packages()</samp>’
will allow packages to be selected from a list box (typically with
several thousand items).
</p>
<p>To install packages from source on a Unix-alike use
</p>
<div class="example">
<pre class="example">R CMD INSTALL -l /path/to/library <var>pkg1</var> <var>pkg2</var> …
</pre></div>
<p>The part ‘<samp>-l /path/to/library</samp>’ can be omitted, in which case the
first library of a normal R session is used (that shown by
<code>.libPaths()[1]</code>).
</p>
<p>There are a number of options available: use <code>R CMD INSTALL --help</code>
to see the current list.
</p>
<a name="index-install_002epackages"></a>
<p>Alternatively, packages can be downloaded and installed from within
R. First set the option <code>CRAN</code> to your nearest <acronym>CRAN</acronym>
mirror using <code>chooseCRANmirror()</code>. Then download
and install packages <strong>pkg1</strong> and <strong>pkg2</strong> by
</p>
<div class="example">
<pre class="example">> install.packages(c("pkg1", "pkg2"))
</pre></div>
<p>The essential dependencies of the specified packages will also be fetched.
Unless the library is specified (argument <code>lib</code>) the first library
in the library search path is used: if this is not writable, R will
ask the user (in an interactive session) if the default personal library
should be created, and if allowed to will install the packages there.
</p>
<p>If you want to fetch a package and all those it depends on (in any way)
that are not already installed, use e.g.
</p>
<div class="example">
<pre class="example">> install.packages("Rcmdr", dependencies = TRUE)
</pre></div>
<p><code>install.packages</code> can install a source package from a local
<samp>.tar.gz</samp> file by setting argument <code>repos</code> to <code>NULL</code>:
this will be selected automatically if the name given is a single
<samp>.tar.gz</samp> file.
</p>
<p><code>install.packages</code> can look in several repositories, specified as a
character vector by the argument <code>repos</code>: these can include a
<acronym>CRAN</acronym> mirror, Bioconductor, Omegahat, R-forge, rforge.net,
local archives, local files, …). Function
<code>setRepositories()</code> can select amongst those repositories that the
R installation is aware of.
</p>
<p>Naive users sometimes forget that as well as installing a package, they
have to use <code>library</code> to make its functionality available.
</p>
<hr>
<a name="Windows-packages"></a>
<div class="header">
<p>
Next: <a href="#OS-X-packages" accesskey="n" rel="next">OS X packages</a>, Previous: <a href="#Installing-packages" accesskey="p" rel="previous">Installing packages</a>, Up: <a href="#Installing-packages" accesskey="u" rel="up">Installing packages</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Windows"></a>
<h4 class="subsection">6.3.1 Windows</h4>
<p>What <code>install.packages</code> does by default is different on Unix-alikes
(except OS X) and Windows. On Unix-alikes it consults the list of
available <em>source</em> packages on <acronym>CRAN</acronym> (or other
repository/ies), downloads the latest version of the package sources,
and installs them (via <code>R CMD INSTALL</code>). On Windows it looks (by
default) at the list of <em>binary</em> versions of packages available for
your version of R and downloads the latest versions (if any),
although optionally it will also download and install a source package
by setting the <code>type</code> argument.
</p>
<p>On Windows <code>install.packages</code> can also install a binary package
from a local <samp>zip</samp> file by setting argument <code>repos</code> to
<code>NULL</code>. <code>Rgui.exe</code> has a menu <code>Packages</code> with a GUI
interface to <code>install.packages</code>, <code>update.packages</code> and
<code>library</code>.
</p>
<p>Windows binary packages for R are distributed as a single binary
containing either or both architectures.
</p>
<p>A few of the binary packages need other software to be installed on your
system: see for example
<a href="http://CRAN.R-project.org/bin/windows/contrib/3.0/@ReadMe">http://CRAN.R-project.org/bin/windows/contrib/3.0/@ReadMe</a>.
For 64-bit builds, packages using Gtk+ (<a href="http://CRAN.R-project.org/package=Cairo"><strong>Cairo</strong></a>,
<a href="http://CRAN.R-project.org/package=RGtk2"><strong>RGtk2</strong></a>, <a href="http://CRAN.R-project.org/package=cairoDevice"><strong>cairoDevice</strong></a> and those that depend on them)
need the <samp>bin</samp> directory of a bundled distribution from
<a href="http://www.gtk.org/download-windows-64bit.html">http://www.gtk.org/download-windows-64bit.html</a> in the path: it
should work to have both 32- and 64-bit Gtk+ <samp>bin</samp> directories in
the path on a 64-bit version of R.
</p>
<p><code>R CMD INSTALL</code> works in Windows to install source packages. No
additional tools are needed if the package does not contain compiled
code, and <code>install.packages(type="source")</code> will work for such
packages (and for those with compiled code if the tools (see <a href="#The-Windows-toolset">The Windows toolset</a>) are in the path). We have seen occasional permission
problems after unpacking source packages on some Vista/Windows 7/Server
2008 systems: these have been circumvented by setting the environment
variable <code>R_INSTALL_TAR</code> to ‘<samp>tar.exe</samp>’.
<a name="index-R_005fINSTALL_005fTAR"></a>
</p>
<p>If you have only a source package that is known to work with current
R and just want a binary Windows build of it, you could make use of
the building service offered at
<a href="http://win-builder.r-project.org/">http://win-builder.r-project.org/</a>.
</p>
<p>For almost all packages <code>R CMD INSTALL</code> will attempt to install
both 32- and 64-bit builds of a package if run from a 32/64-bit install
of R. It will report success if the installation of the architecture
of the running <code>R</code> succeeded, whether or not the other
architecture was successfully installed. The exceptions are packages
with a non-empty <samp>configure.win</samp> script or which make use of
<samp>src/Makefile.win</samp>. If <samp>configure.win</samp> does something
appropriate to both architectures use<a name="DOCF12" href="#FOOT12"><sup>12</sup></a> option
<samp>--force-biarch</samp>: otherwise <code>R CMD INSTALL
--merge-multiarch</code> can be applied to a source tarball to merge separate
32- and 64-bit installs. (This can only be applied to a tarball, and
will only succeed if both installs succeed.)
</p>
<p>If you have a package without compiled code and no Windows-specific
help, you can zip up an installation on another OS and install from the
that zip file on Windows. However, such a package can be installed from
the sources on Windows without any additional tools.
</p>
<a name="index-LOCAL_005fSOFT"></a>
<p>There is provision to make use of a system-wide library of installed
external software by setting the <code>make</code> variable
<code>LOCAL_SOFT</code>, to give an equivalent of <samp>/usr/local</samp> on a
Unix-alike. This can be set in <samp>src/gnuwin/MkRules.local</samp> when
R is built from sources (see the comments in
<samp>src/gnuwin/MkRules.dist</samp>), or in file<a name="DOCF13" href="#FOOT13"><sup>13</sup></a> <samp>etc/i386/Makeconf</samp> or <samp>etc/x64/Makeconf</samp> for an
installed version of R. The version used by <acronym>CRAN</acronym> can be
downloaded from <a href="http://www.stats.ox.ac.uk/pub/Rtools/libs.html">http://www.stats.ox.ac.uk/pub/Rtools/libs.html</a>.
</p>
<hr>
<a name="OS-X-packages"></a>
<div class="header">
<p>
Next: <a href="#Customizing-package-compilation" accesskey="n" rel="next">Customizing package compilation</a>, Previous: <a href="#Windows-packages" accesskey="p" rel="previous">Windows packages</a>, Up: <a href="#Installing-packages" accesskey="u" rel="up">Installing packages</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="OS-X-1"></a>
<h4 class="subsection">6.3.2 OS X</h4>
<p>On OS X <code>install.packages</code> works as it does on other Unix-alike
systems, but there is an additional type <code>mac.binary</code> (the default
in the <acronym>CRAN</acronym> distribution but not when compiling from source)
that can be passed to <code>install.packages</code> in order to download and
install binary packages from a suitable repository. These OS X binary
package files have the extension ‘<samp>tgz</samp>’. The <small>R.APP</small> GUI provides
menus for installation of either binary or source packages, from
<acronym>CRAN</acronym> or local files.
</p>
<p>Note that many binary packages including compiled code are tied to a
particular series (e.g. R 3.0.x or 3.1.x) of R.
</p>
<p>Installing source packages which do not contain compiled code should
work with no additional tools. For others you will need the ‘Command
Line Tools’ for <code>Xcode</code> and compilers which match those used to
build R: see <a href="#OS-X">OS X</a>.
</p>
<p>Package <a href="http://CRAN.R-project.org/package=rJava"><strong>rJava</strong></a> and those which depend on it need a Java runtime
installed and several packages need X11 installed, including those using
Tk. For Mountain Lion and Mavericks see <a href="#OS-X">OS X</a> and <a href="#Java-_0028OS-X_0029">Java (OS X)</a>.
</p>
<p>Tcl/Tk extensions <code>BWidget</code> and <code>Tktable</code> are part of the
Tcl/Tk contained in the R installer. These are required by a number
of <acronym>CRAN</acronym> and Bioconductor packages.
</p>
<p>A few of the binary packages need other software to be installed on your
system. In particular packages using Gtk+ (<a href="http://CRAN.R-project.org/package=RGtk2"><strong>RGtk2</strong></a>,
<a href="http://CRAN.R-project.org/package=cairoDevice"><strong>cairoDevice</strong></a> and those that depend on them) need the GTK
framework installed from <a href="http://r.research.att.com/libs/">http://r.research.att.com/libs/</a>: the
appropriate version at the time of writing was
<a href="http://r.research.att.com/libs/GTK_2.24.17-X11.pkg">http://r.research.att.com/libs/GTK_2.24.17-X11.pkg</a>
</p>
<p>It is often possible to use other compilers with the <acronym>CRAN</acronym>
distribution of R, but the settings in the file
<samp>/Library/Frameworks/R.framework/Resources/etc/Makeconf</samp> will need
to be changed, either by editing that file or in a file such as
<samp>~/.R/Makevars</samp> (see the next section). Entries which may need to
be changed include ‘<samp>CC</samp>’, ‘<samp>CXX</samp>’, ‘<samp>FC</samp>’, ‘<samp>F77</samp>’,
‘<samp>FLIBS</samp>’ and the corresponding flags, and perhaps ‘<samp>CXXCPP</samp>’,
‘<samp>DYLIB_LD</samp>’, ‘<samp>MAIN_LD</samp>’, ‘<samp>SHLIB_CXXLD</samp>’, ‘<samp>SHLIB_FCLD</samp>’
and ‘<samp>SHLIB_LD</samp>’.
</p>
<p>So for example you could select <code>clang</code> for both C and C++ with
extensive checking by having in <samp>~/.R/Makevars</samp>
</p><div class="example">
<pre class="example">CC=clang
CXX=clang++
CFLAGS="-mtune=native -g -O2 -Wall -pedantic -Wconversion"
CXXFLAGS="-mtune=native -g -O2 -Wall -pedantic -Wconversion"
</pre></div>
<p>(this is expected to become necessary once Xcode 5 is released) and
for another version of <code>gfortran-4.2</code> we needed
</p><div class="example">
<pre class="example">FLIBS=-lgfortran
</pre></div>
<hr>
<a name="Customizing-package-compilation"></a>
<div class="header">
<p>
Next: <a href="#Multiple-sub_002darchitectures" accesskey="n" rel="next">Multiple sub-architectures</a>, Previous: <a href="#OS-X-packages" accesskey="p" rel="previous">OS X packages</a>, Up: <a href="#Installing-packages" accesskey="u" rel="up">Installing packages</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Customizing-package-compilation-1"></a>
<h4 class="subsection">6.3.3 Customizing package compilation</h4>
<p>The R system and package-specific compilation flags can be overridden or
added to by setting the appropriate Make variables in the personal file
<samp><var>HOME</var>/.R/Makevars-<var>R_PLATFORM</var></samp> (but
<samp><var>HOME</var>/.R/Makevars.win</samp> or <samp><var>HOME</var>/.R/Makevars.win64</samp>
on Windows), or if that does not exist, <samp><var>HOME</var>/.R/Makevars</samp>,
where ‘<samp>R_PLATFORM</samp>’ is the platform for which R was built, as
available in the <code>platform</code> component of the R variable
<code>R.version</code>. An alternative personal file can be specified
<em>via</em> the environment variable <code>R_MAKEVARS_USER</code>.
</p>
<p>Package developers are encouraged to use this mechanism to enable a
reasonable amount of diagnostic messaging (“warnings”) when compiling,
such as e.g. <samp>-Wall -pedantic</samp> for tools from GCC, the Gnu
Compiler Collection.
</p>
<p>Note that this mechanism can also be used when it necessary to change
the optimization level for a particular package. For example
</p>
<div class="example">
<pre class="example">## <span class="roman">for C code</span>
CFLAGS=-g -O -mtune=native
## <span class="roman">for C++ code</span>
CXXFLAGS=-g -O -mtune=native
## <span class="roman">for Fortran code</span>
FFLAGS=-g -O -mtune=native
## <span class="roman">for Fortran 95 code</span>
FCFLAGS=-g -O -mtune=native
</pre></div>
<p>There is also provision for a site-wide <samp>Makevars.site</samp> file under
<samp><var>R_HOME</var>/etc</samp> (in a sub-architecture-specific directory if
appropriate). This is read immediately after <samp>Makeconf</samp>, and an
alternative file can be specified by environment variable
<code>R_MAKEVARS_SITE</code>.
</p>
<hr>
<a name="Multiple-sub_002darchitectures"></a>
<div class="header">
<p>
Next: <a href="#Byte_002dcompilation" accesskey="n" rel="next">Byte-compilation</a>, Previous: <a href="#Customizing-package-compilation" accesskey="p" rel="previous">Customizing package compilation</a>, Up: <a href="#Installing-packages" accesskey="u" rel="up">Installing packages</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Multiple-sub_002darchitectures-1"></a>
<h4 class="subsection">6.3.4 Multiple sub-architectures</h4>
<p>When installing packages from their sources, there are some extra
considerations on installations which use sub-architectures. These are
commonly used on Windows but can in principle be used on other
platforms.
</p>
<p>When a source package is installed by a build of R which supports
multiple sub-architectures, the normal installation process installs the
packages for all sub-architectures. The exceptions are
</p>
<dl compact="compact">
<dt><em>Unix-alikes</em></dt>
<dd>
<p>where there is an <samp>configure</samp> script, or a file <samp>src/Makefile</samp>.
</p>
</dd>
<dt><em>Windows</em></dt>
<dd>
<p>where there is a non-empty <samp>configure.win</samp> script, or a file
<samp>src/Makefile.win</samp> (with some exceptions where the package is known
to have an architecture-independent <samp>configure.win</samp>, or if
<samp>--force-biarch</samp> or a field in the <samp>DESCRIPTION</samp> file is
used to assert so).
</p>
</dd>
</dl>
<p>In those cases only the current architecture is installed. Further
sub-architectures can be installed by
</p>
<div class="example">
<pre class="example">R CMD INSTALL --libs-only <var>pkg</var>
</pre></div>
<p>using the path to <code>R</code> or <code>R --arch</code> to select the
additional sub-architecture. There is also <code>R CMD INSTALL
--merge-multiarch</code> to build and merge the two architectures, starting
with a source tarball.
</p>
<hr>
<a name="Byte_002dcompilation"></a>
<div class="header">
<p>
Previous: <a href="#Multiple-sub_002darchitectures" accesskey="p" rel="previous">Multiple sub-architectures</a>, Up: <a href="#Installing-packages" accesskey="u" rel="up">Installing packages</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Byte_002dcompilation-1"></a>
<h4 class="subsection">6.3.5 Byte-compilation</h4>
<p>The base and recommended packages are byte-compiled by default. Other
packages can be byte-compiled on installation by using the option
<samp>--byte-compile</samp> with <code>R CMD INSTALL</code> or with
<code>install.packages(type = "source")</code>.
</p>
<p>Not all contributed packages work correctly when byte-compiled (for
example because they interfere with the sealing of namespaces). For
most packages (especially those which make extensive use of compiled
code) the speed-up is small. Unless a package is used frequently the
time spent in byte-compilation can outweigh the time saved in execution:
also byte-compilation can add substantially to the installed size of the
package.
</p>
<p>Byte-compilation can be controlled on a per-package basis by the
‘<samp>ByteCompile</samp>’ field in the <samp>DESCRIPTION</samp> file.
</p>
<hr>
<a name="Updating-packages"></a>
<div class="header">
<p>
Next: <a href="#Removing-packages" accesskey="n" rel="next">Removing packages</a>, Previous: <a href="#Installing-packages" accesskey="p" rel="previous">Installing packages</a>, Up: <a href="#Add_002don-packages" accesskey="u" rel="up">Add-on packages</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Updating-packages-1"></a>
<h3 class="section">6.4 Updating packages</h3>
<a name="index-update_002epackages"></a>
<a name="index-Packages_002c-updating"></a>
<p>The command <code>update.packages()</code> is the simplest way to ensure that
all the packages on your system are up to date. It downloads the list
of available packages and their current versions, compares it with those
installed and offers to fetch and install any that have later versions
on the repositories.
</p>
<p>An alternative interface to keeping packages up-to-date is provided by
the command <code>packageStatus()</code>, which returns an object with
information on all installed packages and packages available at multiple
repositories. The <code>print</code> and <code>summary</code> methods give an
overview of installed and available packages, the <code>upgrade</code> method
offers to fetch and install the latest versions of outdated packages.
</p>
<p>One sometimes-useful additional piece of information that
<code>packageStatus()</code> returns is the status of a package, as
<code>"ok"</code>, <code>"upgrade"</code> or <code>"unavailable"</code> (in the currently
selected repositories). For example
</p>
<div class="example">
<pre class="example">> inst <- packageStatus()$inst
> inst[inst$Status != "ok", c("Package", "Version", "Status")]
Package Version Status
Biobase Biobase 2.8.0 unavailable
RCurl RCurl 1.4-2 upgrade
Rgraphviz Rgraphviz 1.26.0 unavailable
rgdal rgdal 0.6-27 upgrade
</pre></div>
<hr>
<a name="Removing-packages"></a>
<div class="header">
<p>
Next: <a href="#Setting-up-a-package-repository" accesskey="n" rel="next">Setting up a package repository</a>, Previous: <a href="#Updating-packages" accesskey="p" rel="previous">Updating packages</a>, Up: <a href="#Add_002don-packages" accesskey="u" rel="up">Add-on packages</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Removing-packages-1"></a>
<h3 class="section">6.5 Removing packages</h3>
<a name="index-remove_002epackages"></a>
<a name="index-Packages_002c-removing"></a>
<p>Packages can be removed in a number of ways. From a command prompt they
can be removed by
</p>
<div class="example">
<pre class="example">R CMD REMOVE -l /path/to/library <var>pkg1</var> <var>pkg2</var> …
</pre></div>
<p>From a running R process they can be removed by
</p>
<div class="example">
<pre class="example">> remove.packages(c("pkg1", "pkg2"),
lib = file.path("path", "to", "library"))
</pre></div>
<p>Finally, in most installations one can just remove the package directory
from the library.
</p>
<hr>
<a name="Setting-up-a-package-repository"></a>
<div class="header">
<p>
Next: <a href="#Checking-installed-source-packages" accesskey="n" rel="next">Checking installed source packages</a>, Previous: <a href="#Removing-packages" accesskey="p" rel="previous">Removing packages</a>, Up: <a href="#Add_002don-packages" accesskey="u" rel="up">Add-on packages</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Setting-up-a-package-repository-1"></a>
<h3 class="section">6.6 Setting up a package repository</h3>
<a name="index-Repositories"></a>
<p>Utilities such as <code>install.packages</code> can be pointed at any
<acronym>CRAN</acronym>-style repository, and R users may want to set up their
own. The ‘base’ of a repository is a URL such as
<a href="http://www.omegahat.org/R/">http://www.omegahat.org/R/</a>: this must be an URL scheme that
<code>download.packages</code> supports (which also includes ‘<samp>ftp://</samp>’ and
‘<samp>file://</samp>’, but not on most systems ‘<samp>https://</samp>’). Under that
base URL there should be directory trees for one or more of the
following types of package distributions:
</p>
<ul>
<li> <code>"source"</code>: located at <samp>src/contrib</samp> and containing
<samp>.tar.gz</samp> files. Other forms of compression can be used, e.g.
<samp>.tar.bz2</samp> or <samp>.tar.xz</samp> files. Complete repositories contain
the sources corresponding to any binary packages, and in any case it is
wise to have a <samp>src/contrib</samp> area with a possibly empty
<samp>PACKAGES</samp> file.
</li><li> <code>"win.binary"</code>: located at <samp>bin/windows/contrib/<var>x.y</var></samp> for
R versions <var>x.y.z</var> and containing <samp>.zip</samp> files for Windows.
</li><li> <code>"mac.binary"</code>: located at
<samp>bin/macosx/contrib/<var>3.y</var></samp> for R versions
<var>3.y.z</var> and containing <samp>.tgz</samp> files.
</li><li> <code>"mac.binary.leopard"</code>: located at
<samp>bin/macosx/leopard/contrib/<var>2.y</var></samp> for R versions
<var>2.y.z</var> and containing <samp>.tgz</samp> files.
</li></ul>
<p>Each terminal directory must also contain a <samp>PACKAGES</samp> file. This
can be a concatenation of the <samp>DESCRIPTION</samp> files of the packages
separated by blank lines, but only a few of the fields are needed. The
simplest way to set up such a file is to use function
<code>write_PACKAGES</code> in the <strong>tools</strong> package, and its help explains
which fields are needed. Optionally there can also be a
<samp>PACKAGES.gz</samp> file, a <code>gzip</code>-compressed version of
<samp>PACKAGES</samp>—as this will be downloaded in preference to
<samp>PACKAGES</samp> it should be included for large repositories. (If you
have a mis-configured server that does not report correctly non-existent
files you may need <samp>PACKAGES.gz</samp>.)
</p>
<p>To add your repository to the list offered by <code>setRepositories()</code>,
see the help file for that function.
</p>
<p>Incomplete repositories are better specified <em>via</em> a
<code>contriburl</code> argument than <em>via</em> being set as a repository.
</p>
<p>A repository can contain subdirectories, when the descriptions in the
<samp>PACKAGES</samp> file of packages in subdirectories must include a line
of the form
</p>
<div class="example">
<pre class="example">Path: <var>path/to/subdirectory</var>
</pre></div>
<p>—once again <code>write_PACKAGES</code> is the simplest way to set this up.
</p>
<hr>
<a name="Checking-installed-source-packages"></a>
<div class="header">
<p>
Previous: <a href="#Setting-up-a-package-repository" accesskey="p" rel="previous">Setting up a package repository</a>, Up: <a href="#Add_002don-packages" accesskey="u" rel="up">Add-on packages</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Checking-installed-source-packages-1"></a>
<h3 class="section">6.7 Checking installed source packages</h3>
<p>It can be convenient to run <code>R CMD check</code> on an installed
package, particularly on a platform which uses sub-architectures. The
outline of how to do this is, with the source package in directory
<samp><var>pkg</var></samp> (or a tarball filename):
</p>
<div class="example">
<pre class="example">R CMD INSTALL -l <var>libdir</var> <var>pkg</var> > <var>pkg</var>.log 2>&1
R CMD check -l <var>libdir</var> --install=check:<var>pkg</var>.log <var>pkg</var>
</pre></div>
<p>Where sub-architectures are in use the <code>R CMD check</code> line can be
repeated with additional architectures by
</p>
<div class="example">
<pre class="example">R --arch <var>arch</var> CMD check -l <var>libdir</var> --extra-arch --install=check:<var>pkg</var>.log <var>pkg</var>
</pre></div>
<p>where <samp>--extra-arch</samp> selects only those checks which depend on
the installed code and not those which analyse the sources. (If
multiple sub-architectures fail only because they need different
settings, e.g. environment variables, <samp>--no-multiarch</samp> may need
to be added to the <code>INSTALL</code> lines.) On Unix-alikes the
architecture to run is selected by <samp>--arch</samp>: this can also be
used on Windows with <samp><var>R_HOME</var>/bin/R.exe</samp>, but it is more usual
to select the path to the <code>Rcmd.exe</code> of the desired
architecture.
</p>
<p>So on Windows to install, check and package for distribution a source
package from a tarball which has been tested on another platform one
might use
</p>
<div class="example">
<pre class="example">.../bin/i386/Rcmd INSTALL -l <var>libdir</var> <var>tarball</var> --build > <var>pkg</var>.log 2>&1
.../bin/i386/Rcmd check -l <var>libdir</var> --extra-arch --install=check:<var>pkg</var>.log <var>pkg</var>
.../bin/x64/Rcmd check -l <var>libdir</var> --extra-arch --install=check:<var>pkg</var>.log <var>pkg</var>
</pre></div>
<p>where one might want to run the second and third lines in a different
shell with different settings for environment variables and the path (to
find external software, notably for Gtk+).
</p>
<p><code>R CMD INSTALL</code> can do a <code>i386</code> install and then add the
<code>x64</code> DLL from a single command by
</p>
<div class="example">
<pre class="example">R CMD INSTALL --merge-multiarch -l <var>libdir</var> <var>tarball</var>
</pre></div>
<p>and <samp>--build</samp> can be added to zip up the installation.
</p>
<hr>
<a name="Internationalization"></a>
<div class="header">
<p>
Next: <a href="#Choosing-between-32_002d-and-64_002dbit-builds" accesskey="n" rel="next">Choosing between 32- and 64-bit builds</a>, Previous: <a href="#Add_002don-packages" accesskey="p" rel="previous">Add-on packages</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Internationalization-and-Localization"></a>
<h2 class="chapter">7 Internationalization and Localization</h2>
<a name="index-Internationalization"></a>
<a name="index-Localization"></a>
<p><em>Internationalization</em> refers to the process of enabling support
for many human languages, and <em>localization</em> to adapting to a
specific country and language.
</p>
<p>Current builds of R support all the character sets that the
underlying OS can handle. These are interpreted according to the
<a name="index-Locale"></a>
current <code>locale</code>, a sufficiently complicated topic to merit a
separate section. Note though that R has no built-in support for
right-to-left languages and bidirectional output, relying on the OS
services. For example, how character vectors in UTF-8 containing both
English digits and Hebrew characters are printed is OS-dependent (and
perhaps locale-dependent).
</p>
<p>The other aspect of the internationalization is support for the
translation of messages. This is enabled in almost all builds of R.
</p>
<table class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">• <a href="#Locales" accesskey="1">Locales</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Localization-of-messages" accesskey="2">Localization of messages</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
</table>
<hr>
<a name="Locales"></a>
<div class="header">
<p>
Next: <a href="#Localization-of-messages" accesskey="n" rel="next">Localization of messages</a>, Previous: <a href="#Internationalization" accesskey="p" rel="previous">Internationalization</a>, Up: <a href="#Internationalization" accesskey="u" rel="up">Internationalization</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Locales-1"></a>
<h3 class="section">7.1 Locales</h3>
<a name="index-Locale-1"></a>
<p>A <em>locale</em> is a description of the local environment of the user,
including the preferred language, the encoding of characters, the
currency used and its conventions, and so on. Aspects of the locale are
accessed by the R functions <code>Sys.getlocale</code> and
<code>Sys.localeconv</code>.
</p>
<p>The system of naming locales is OS-specific. There is quite wide
agreement on schemes, but not on the details of their implementation. A
locale needs to specify
</p><ul>
<li> A human language. These are generally specified by a lower-case
two-character abbreviation following ISO 639 (see e.g.
<a href="http://en.wikipedia.org/wiki/ISO_639-1">http://en.wikipedia.org/wiki/ISO_639-1</a>).
</li><li> A ‘territory’, used mainly to specify the currency. These are generally
specified by an upper-case two-character abbreviation following ISO 3166
(see e.g. <a href="http://en.wikipedia.org/wiki/ISO_3166">http://en.wikipedia.org/wiki/ISO_3166</a>).
</li><li> A charset encoding, which determines both how a byte stream should be
divided into characters, and which characters the subsequences of bytes
represent. Sometimes the combination of language and territory is used
to specify the encoding, for example to distinguish between traditional
and simplified Chinese.
</li><li> Optionally, a modifier, for example to indicate that Austria is to be
considered pre- or post-Euro. The modifier is also used to indicate the
script (<code>@latin</code>, <code>@cyrillic</code> for Serbian, <code>@iqtelif</code>)
or language dialect (e.g. <code>@saaho</code>, a dialect of Afar, and
<code>@bokmal</code> and <code>@nynorsk</code>, dialects of Norwegian regarded by
some OSes as separate languages, <code>no</code> and <code>nn</code>).
</li></ul>
<p>R is principally concerned with the first (for translations) and
third. Note that the charset may be deducible from the language, as
some OSes offer only one charset per language, and most OSes have only
one charset each for most languages.
</p>
<table class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">• <a href="#Locales-under-Unix_002dalikes" accesskey="1">Locales under Unix-alikes</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Locales-under-Windows" accesskey="2">Locales under Windows</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Locales-under-OS-X" accesskey="3">Locales under OS X</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
</table>
<hr>
<a name="Locales-under-Unix_002dalikes"></a>
<div class="header">
<p>
Next: <a href="#Locales-under-Windows" accesskey="n" rel="next">Locales under Windows</a>, Previous: <a href="#Locales" accesskey="p" rel="previous">Locales</a>, Up: <a href="#Locales" accesskey="u" rel="up">Locales</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Locales-under-Unix_002dalikes-1"></a>
<h4 class="subsection">7.1.1 Locales under Unix-alikes</h4>
<p>Modern Linux uses the XPG<a name="DOCF14" href="#FOOT14"><sup>14</sup></a> locale specifications which have the form
‘<samp>en_GB</samp>’, ‘<samp>en_GB.UTF-8</samp>’, ‘<samp>aa_ER.UTF-8@saaho</samp>’,
‘<samp>de_AT.iso885915@euro</samp>’, the components being in the order listed
above. (See <code>man locale</code> and <code>locale -a</code> for more
details.) Similar schemes are used by most Unix-alikes: some (including
some distributions of Linux) use ‘<samp>.utf8</samp>’ rather than ‘<samp>.UTF-8</samp>’.
</p>
<p>Note that whereas UTF-8 locales are nowadays almost universally used,
locales such as ‘<samp>en_GB</samp>’ use 8-bit encodings for backwards
compatibility.
</p>
<hr>
<a name="Locales-under-Windows"></a>
<div class="header">
<p>
Next: <a href="#Locales-under-OS-X" accesskey="n" rel="next">Locales under OS X</a>, Previous: <a href="#Locales-under-Unix_002dalikes" accesskey="p" rel="previous">Locales under Unix-alikes</a>, Up: <a href="#Locales" accesskey="u" rel="up">Locales</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Locales-under-Windows-1"></a>
<h4 class="subsection">7.1.2 Locales under Windows</h4>
<p>Windows also uses locales, but specified in a rather less concise way.
Most users will encounter locales only via drop-down menus, but more
information and lists can be found at
<a href="http://msdn.microsoft.com/en-us/library/hzz3tw78(v=vs.80)">http://msdn.microsoft.com/en-us/library/hzz3tw78(v=vs.80)</a>
(or if Microsoft moves it yet again, search for ‘<samp>Windows language
country strings</samp>’).
</p>
<p>It offers only one encoding per language.
</p>
<p>Some care is needed with Windows’ locale names. For example,
<code>chinese</code> is Traditional Chinese and not Simplified Chinese as used
in most of the Chinese-speaking world.
</p>
<hr>
<a name="Locales-under-OS-X"></a>
<div class="header">
<p>
Previous: <a href="#Locales-under-Windows" accesskey="p" rel="previous">Locales under Windows</a>, Up: <a href="#Locales" accesskey="u" rel="up">Locales</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Locales-under-OS-X-1"></a>
<h4 class="subsection">7.1.3 Locales under OS X</h4>
<p>OS X supports locales in its own particular way, but the R GUI tries to
make this easier for users. See
<a href="http://developer.apple.com/documentation/MacOSX/Conceptual/BPInternational/">http://developer.apple.com/documentation/MacOSX/Conceptual/BPInternational/</a>
for how users can set their locales. As with Windows, end users will
generally only see lists of languages/territories. Users of R in a
terminal may need to set the locale to something like ‘<samp>en_GB.UTF-8</samp>’
if it defaults to ‘<samp>C</samp>’ (as it sometimes does when logging it
remotely and in batch jobs: note whether <code>Terminal</code> sets the
<code>LANG</code> environment variable is an (advanced) option, but the
default).
</p>
<p>Internally OS X uses a form similar to Linux: the main difference from
other Unix-alikes is that where a character set is not specified it is
assumed to be <code>UTF-8</code>.
</p>
<hr>
<a name="Localization-of-messages"></a>
<div class="header">
<p>
Previous: <a href="#Locales" accesskey="p" rel="previous">Locales</a>, Up: <a href="#Internationalization" accesskey="u" rel="up">Internationalization</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Localization-of-messages-1"></a>
<h3 class="section">7.2 Localization of messages</h3>
<p>The preferred language for messages is by default taken from the locale.
This can be overridden first by the setting of the environment variable
<a name="index-LANGUAGE"></a>
<a name="index-LC_005fALL"></a>
<a name="index-LC_005fMESSAGES"></a>
<a name="index-LANG"></a>
<code>LANGUAGE</code> and then<a name="DOCF15" href="#FOOT15"><sup>15</sup></a>
by the environment variables <code>LC_ALL</code>, <code>LC_MESSAGES</code> and
<code>LANG</code>. (The last three are normally used to set the locale and so
should not be needed, but the first is only used to select the language
for messages.) The code tries hard to map locales to languages, but on
some systems (notably Windows) the locale names needed for the
environment variable <code>LC_ALL</code> do not all correspond to XPG language
names and so <code>LANGUAGE</code> may need to be set. (One example is
‘<samp>LC_ALL=es</samp>’ on Windows which sets the locale to Estonian and the
language to Spanish.)
</p>
<p>It is usually possible to change the language once R is running
<em>via</em> (not Windows) <code>Sys.setlocale("LC_MESSAGES",
"new_locale")</code>, or by setting an environment variable such as
<code>LANGUAGE</code>, <em>provided</em><a name="DOCF16" href="#FOOT16"><sup>16</sup></a> the language you are changing to can be output in
the current character set. But this is OS-specific, and has been known
to stop working on an OS upgrade.
</p>
<p>Messages are divided into <em>domains</em>, and translations may be
available for some or all messages in a domain. R makes use of the
following domains.
</p>
<ul>
<li> Domain <code>R</code> for the C-level error and warning messages from the R
interpreter.
</li><li> Domain <code>R-<var>pkg</var></code> for the R <code>stop</code>, <code>warning</code> and
<code>message</code> messages in each package, including <code>R-base</code> for the
<strong>base</strong> package.
</li><li> Domain <code><var>pkg</var></code> for the C-level messages in each package.
</li><li> Domain <code>RGui</code> for the menus etc of the R for Windows GUI front-end.
</li></ul>
<p>Dividing up the messages in this way allows R to be extensible: as
packages are loaded, their message translation catalogues can be loaded
too.
</p>
<p>R can be built without support for translations, but it is enabled by
default.
</p>
<p>R-level and C-level domains are subtly different, for example in the way
strings are canonicalized before being passed for translation.
</p>
<p>Translations are looked for by domain according to the currently
specified language, as specifically as possible, so for example an
Austrian (‘<samp>de_AT</samp>’) translation catalogue will be used in preference
to a generic German one (‘<samp>de</samp>’) for an Austrian user. However, if a
specific translation catalogue exists but does not contain a
translation, the less specific catalogues are consulted. For example,
R has catalogues for ‘<samp>en_GB</samp>’ that translate the Americanisms
(e.g., ‘<samp>gray</samp>’) in the standard messages into English.<a name="DOCF17" href="#FOOT17"><sup>17</sup></a> Two other examples: there are catalogues
for ‘<samp>es</samp>’, which is Spanish as written in Spain and these will by
default also be used in Spanish-speaking Latin American countries, and
also for ‘<samp>pt_BR</samp>’, which are used for Brazilian locales but not for
locales specifying Portugal.
</p>
<p>Translations in the right language but the wrong charset are made use of
<a name="index-LANGUAGE-1"></a>
by on-the-fly re-encoding. The <code>LANGUAGE</code> variable (only) can be a
colon-separated list, for example ‘<samp>se:de</samp>’, giving a set of
languages in decreasing order of preference. One special value is
‘<samp>en@quot</samp>’, which can be used in a UTF-8 locale to have American
error messages with pairs of single quotes translated to Unicode directional
quotes.
</p>
<p>If no suitable translation catalogue is found or a particular message is
not translated in any suitable catalogue, ‘English’<a name="DOCF18" href="#FOOT18"><sup>18</sup></a> is used.
</p>
<p>See <a href="http://developer.r-project.org/Translations.html">http://developer.r-project.org/Translations.html</a> for how to
prepare and install translation catalogues.
</p>
<hr>
<a name="Choosing-between-32_002d-and-64_002dbit-builds"></a>
<div class="header">
<p>
Next: <a href="#The-standalone-Rmath-library" accesskey="n" rel="next">The standalone Rmath library</a>, Previous: <a href="#Internationalization" accesskey="p" rel="previous">Internationalization</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Choosing-between-32_002d-and-64_002dbit-builds-1"></a>
<h2 class="chapter">8 Choosing between 32- and 64-bit builds</h2>
<p>Almost all current <acronym>CPU</acronym>s have both 32- and 64-bit sets of
instructions. Most OSes running on such <acronym>CPU</acronym>s offer the choice
of building a 32-bit or a 64-bit version of R (and details are given
below under specific OSes). For most a 32-bit version is the default,
but for some (e.g., ‘<samp>x86_64</samp>’ Linux and OS X >= 10.6)
64-bit is.
</p>
<p>All current versions of R use 32-bit integers and
<acronym>ISO</acronym>/<acronym>IEC</acronym> 60559<a name="DOCF19" href="#FOOT19"><sup>19</sup></a> double-precision reals, and so compute to
the same precision<a name="DOCF20" href="#FOOT20"><sup>20</sup></a> and with the same limits on the sizes of
numerical quantities. The principal difference is in the size of the
pointers.
</p>
<p>64-bit builds have both advantages and disadvantages:
</p><ul>
<li> The total virtual memory space made available to a 32-bit process is
limited by the pointer size to 4GB, and on most OSes to 3GB (or even
2GB). The limits for 64-bit processes are much larger (e.g.
8–128TB).
<p>R allocates memory for large objects as needed, and removes any
unused ones at garbage collection. When the sizes of objects become an
appreciable fraction of the address limit, fragmentation of the address
space becomes an issue and there may be no hole available that is the
size requested. This can cause more frequent garbage collection or the
inability to allocate large objects. As a guide, this will become an
issue with objects more than 10% of the size of the address space
(around 300Mb) or when the total size of objects in use is around one
third (around 1Gb).
</p>
</li><li> Only 64-bit builds support ‘long vectors’, those with <em>2^{31}</em> or
more elements (each of which needs at least 8GB of storage, 16GB for a
numeric vector).
</li><li> Most 32-bit OSes by default limit file sizes to 2GB (and this may also
apply to 32-bit builds on 64-bit OSes). This can often be worked
around: and <code>configure</code> selects suitable defines if this is
possible. (We have also largely worked around that limit on 32-bit
Windows.) 64-bit builds have much larger limits.
</li><li> Because the pointers are larger, R’s basic structures are larger.
This means that R objects take more space and (usually) more time to
manipulate. So 64-bit builds of R will, all other things being
equal, run slower than 32-bit builds. (On Sparc Solaris the difference
was 15-20%.)
</li><li> However, ‘other things’ may not be equal. In the specific case of
‘<samp>x86_64</samp>’ <em>vs</em> ‘<samp>ix86</samp>’, the 64-bit CPU has features
(such as SSE2 instructions) which are guaranteed to be present but are
optional on the 32-bit CPU, and also has more general-purpose registers.
This means that on chips like a desktop Intel Core 2 Duo the vanilla
64-bit version of R has been around 10% faster on both Linux and OS
X. (Laptop CPUs are usually relatively slower in 64-bit mode.)
</li></ul>
<p>So, for speed you may want to use a 32-bit build (especially on a
laptop), but to handle large datasets (and perhaps large files) a 64-bit
build. You can often build both and install them in the same place:
See <a href="#Sub_002darchitectures">Sub-architectures</a>. (This is done for the Windows binary
distributions.)
</p>
<p>Even on 64-bit builds of R there are limits on the size of R
objects (see <code>help("Memory-limits")</code>, some of which stem from the
use of 32-bit integers (especially in FORTRAN code). For example, the
dimensions of an array are limited to <em>2^{31} - 1</em>.
</p>
<hr>
<a name="The-standalone-Rmath-library"></a>
<div class="header">
<p>
Next: <a href="#Essential-and-useful-other-programs-under-a-Unix_002dalike" accesskey="n" rel="next">Essential and useful other programs under a Unix-alike</a>, Previous: <a href="#Choosing-between-32_002d-and-64_002dbit-builds" accesskey="p" rel="previous">Choosing between 32- and 64-bit builds</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="The-standalone-Rmath-library-1"></a>
<h2 class="chapter">9 The standalone Rmath library</h2>
<p>The routines supporting the distribution and
special<a name="DOCF21" href="#FOOT21"><sup>21</sup></a> functions in R
and a few others are declared in C header file <samp>Rmath.h</samp>. These
can be compiled into a standalone library for linking to other
applications. (Note that they are not a separate library when R is
built, and the standalone version differs in several ways.)
</p>
<p>The makefiles and other sources needed are in directory
<samp>src/nmath/standalone</samp>, so the following instructions assume that
is the current working directory (in the build directory tree on a
Unix-alike if that is separate from the sources).
</p>
<p><samp>Rmath.h</samp> contains ‘<samp>R_VERSION_STRING</samp>’, which is a character
string containing the current R version, for example <code>"3.0.0"</code>.
</p>
<p>There is full access to R’s handling of <code>NaN</code>, <code>Inf</code> and
<code>-Inf</code> via special versions of the macros and functions
</p>
<div class="example">
<pre class="example"> ISNAN, R_FINITE, R_log, R_pow and R_pow_di
</pre></div>
<p>and (extern) constants <code>R_PosInf</code>, <code>R_NegInf</code> and <code>NA_REAL</code>.
</p>
<p>There is no support for R’s notion of missing values, in particular
not for <code>NA_INTEGER</code> nor the distinction between <code>NA</code> and
<code>NaN</code> for doubles.
</p>
<p>A little care is needed to use the random-number routines. You will
need to supply the uniform random number generator
</p>
<div class="example">
<pre class="example"> double unif_rand(void)
</pre></div>
<p>or use the one supplied (and with a shared library or DLL you will
have to use the one supplied, which is the Marsaglia-multicarry with
an entry point
</p>
<div class="example">
<pre class="example"> set_seed(unsigned int, unsigned int)
</pre></div>
<p>to set its seeds).
</p>
<p>The facilities to change the normal random number generator are
available through the constant N01_kind. This takes values
from the enumeration type
</p>
<div class="example">
<pre class="example">typedef enum {
BUGGY_KINDERMAN_RAMAGE,
AHRENS_DIETER,
BOX_MULLER,
USER_NORM,
INVERSION,
KINDERMAN_RAMAGE
} N01type;
</pre></div>
<p>(and ‘<samp>USER_NORM</samp>’ is not available).
</p>
<table class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">• <a href="#Unix_002dalike-standalone" accesskey="1">Unix-alike standalone</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Windows-standalone" accesskey="2">Windows standalone</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
</table>
<hr>
<a name="Unix_002dalike-standalone"></a>
<div class="header">
<p>
Next: <a href="#Windows-standalone" accesskey="n" rel="next">Windows standalone</a>, Previous: <a href="#The-standalone-Rmath-library" accesskey="p" rel="previous">The standalone Rmath library</a>, Up: <a href="#The-standalone-Rmath-library" accesskey="u" rel="up">The standalone Rmath library</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Unix_002dalikes"></a>
<h3 class="section">9.1 Unix-alikes</h3>
<p>If R has not already be made in the directory tree,
<code>configure</code> must be run as described in the main build
instructions.
</p>
<p>Then (in <samp>src/nmath/standalone</samp>)
</p>
<div class="example">
<pre class="example">make
</pre></div>
<p>will make standalone libraries <samp>libRmath.a</samp> and <samp>libRmath.so</samp>
(<samp>libRmath.dylib</samp> on OS X): ‘<samp>make static</samp>’ and ‘<samp>make
shared</samp>’ will create just one of them.
</p>
<p>To use the routines in your own C or C++ programs, include
</p>
<div class="example">
<pre class="example">#define MATHLIB_STANDALONE
#include <Rmath.h>
</pre></div>
<p>and link against ‘<samp>-lRmath</samp>’ (and ‘<samp>-lm</samp>’ if needed on your OS).
The example file <samp>test.c</samp> does nothing useful, but is provided to
test the process (via <code>make test</code>). Note that you will probably
not be able to run it unless you add the directory containing
<a name="index-LD_005fLIBRARY_005fPATH"></a>
<samp>libRmath.so</samp> to the <code>LD_LIBRARY_PATH</code> environment variable
(<samp>libRmath.dylib</samp>, <code>DYLD_LIBRARY_PATH</code> on OS X).
</p>
<p>The targets
</p>
<div class="example">
<pre class="example">make install
make uninstall
</pre></div>
<p>will (un)install the header <samp>Rmath.h</samp> and shared and static
<a name="index-DESTDIR-1"></a>
libraries (if built). Both <code>prefix=</code> and <code>DESTDIR</code> are
supported, together with more precise control as described for the main
build.
</p>
<p>‘<samp>make install</samp>’ installs a file for <code>pkg-config</code> to use by
e.g.
</p>
<div class="example">
<pre class="example">$(CC) `pkg-config --cflags libRmath` -c test.c
$(CC) `pkg-config --libs libRmath` test.o -o test
</pre></div>
<p>On some systems ‘<samp>make install-strip</samp>’ will install a stripped shared
library.
</p>
<hr>
<a name="Windows-standalone"></a>
<div class="header">
<p>
Previous: <a href="#Unix_002dalike-standalone" accesskey="p" rel="previous">Unix-alike standalone</a>, Up: <a href="#The-standalone-Rmath-library" accesskey="u" rel="up">The standalone Rmath library</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Windows-1"></a>
<h3 class="section">9.2 Windows</h3>
<p>You need to set up<a name="DOCF22" href="#FOOT22"><sup>22</sup></a> almost all the
tools to make R and then run (in a Unix-like shell)
</p>
<div class="example">
<pre class="example">(cd ../../gnuwin32; make MkRules)
(cd ../../include; make -f Makefile.win config.h Rconfig.h Rmath.h)
make -f Makefile.win
</pre></div>
<p>Alternatively, in a <samp>cmd.exe</samp> shell use
</p>
<div class="example">
<pre class="example">cd ../../include
make -f Makefile.win config.h Rconfig.h Rmath.h
cd ../nmath/standalone
make -f Makefile.win
</pre></div>
<p>This creates a static library <samp>libRmath.a</samp> and a DLL
<samp>Rmath.dll</samp>. If you want an import library <samp>libRmath.dll.a</samp>
(you don’t need one), use
</p>
<div class="example">
<pre class="example">make -f Makefile.win shared implib
</pre></div>
<p>To use the routines in your own C or C++ programs using MinGW, include
</p>
<div class="example">
<pre class="example">#define MATHLIB_STANDALONE
#include <Rmath.h>
</pre></div>
<p>and link against ‘<samp>-lRmath</samp>’. This will use the first found of
<samp>libRmath.dll.a</samp>, <samp>libRmath.a</samp> and <samp>Rmath.dll</samp> in that
order, so the result depends on which files are present. You should be
able to force static or dynamic linking <em>via</em>
</p>
<div class="example">
<pre class="example">-Wl,-Bstatic -lRmath -Wl,dynamic
-Wl,-Bdynamic -lRmath
</pre></div>
<p>or by linking to explicit files (as in the ‘<samp>test</samp>’ target in
<samp>Makefile.win</samp>: this makes two executables, <samp>test.exe</samp> which
is dynamically linked, and <samp>test-static.exe</samp>, which is statically
linked).
</p>
<p>It is possible to link to <samp>Rmath.dll</samp> using other compilers, either
directly or via an import library: if you make a MinGW import library as
above, you will create a file <samp>Rmath.def</samp> which can be used
(possibly after editing) to create an import library for other systems
such as Visual C++.
</p>
<p>If you make use of dynamic linking you should use
</p>
<div class="example">
<pre class="example">#define MATHLIB_STANDALONE
#define RMATH_DLL
#include <Rmath.h>
</pre></div>
<p>to ensure that the constants like <code>NA_REAL</code> are linked correctly.
(Auto-import will probably work with MinGW, but it is better to be
sure. This is likely to also work with VC++, Borland and similar
compilers.)
</p>
<hr>
<a name="Essential-and-useful-other-programs-under-a-Unix_002dalike"></a>
<div class="header">
<p>
Next: <a href="#Configuration-on-a-Unix_002dalike" accesskey="n" rel="next">Configuration on a Unix-alike</a>, Previous: <a href="#The-standalone-Rmath-library" accesskey="p" rel="previous">The standalone Rmath library</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Essential-and-useful-other-programs-under-a-Unix_002dalike-1"></a>
<h2 class="appendix">Appendix A Essential and useful other programs under a Unix-alike</h2>
<p>This appendix gives details of programs you will need to build R on
Unix-like platforms, or which will be used by R if found by
<code>configure</code>.
</p>
<p>Remember that some package management systems (such as <acronym>RPM</acronym> and
deb) make a distinction between the user version of a package and the
development version. The latter usually has the same name but with the
extension ‘<samp>-devel</samp>’ or ‘<samp>-dev</samp>’: you need both versions
installed.
</p>
<table class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">• <a href="#Essential-programs-and-libraries" accesskey="1">Essential programs and libraries</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Useful-libraries-and-programs" accesskey="2">Useful libraries and programs</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Linear-algebra" accesskey="3">Linear algebra</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
</table>
<hr>
<a name="Essential-programs-and-libraries"></a>
<div class="header">
<p>
Next: <a href="#Useful-libraries-and-programs" accesskey="n" rel="next">Useful libraries and programs</a>, Previous: <a href="#Essential-and-useful-other-programs-under-a-Unix_002dalike" accesskey="p" rel="previous">Essential and useful other programs under a Unix-alike</a>, Up: <a href="#Essential-and-useful-other-programs-under-a-Unix_002dalike" accesskey="u" rel="up">Essential and useful other programs under a Unix-alike</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Essential-programs-and-libraries-1"></a>
<h3 class="section">A.1 Essential programs and libraries</h3>
<p>You need a means of compiling C and FORTRAN 90 (see <a href="#Using-FORTRAN">Using FORTRAN</a>). Some add-on packages also need a C++ compiler. Your C
compiler should be <acronym>ISO</acronym>/<acronym>IEC</acronym> 60059<a name="DOCF23" href="#FOOT23"><sup>23</sup></a>, POSIX 1003.1 and
C99-compliant.<a name="DOCF24" href="#FOOT24"><sup>24</sup></a> R tries to choose
suitable flags for the C compilers it knows about, but you may have to
set <code>CC</code> or <code>CFLAGS</code> suitably. For recent versions of
<code>gcc</code> with <code>glibc</code> this means including
<samp>-std=gnu99</samp><a name="DOCF25" href="#FOOT25"><sup>25</sup></a>. If the compiler is
detected as <code>gcc</code>, <samp>-std=gnu99</samp> will be appended to
<code>CC</code> unless it conflicts with a setting of <code>CFLAGS</code>. (Note
that options essential to run the compiler even for linking, such as
those to set the architecture, should be specified as part of <code>CC</code>
rather than in <code>CFLAGS</code>.)
</p>
<p>Unless you do not want to view graphs on-screen (or use a Mac) you need
‘<samp>X11</samp>’ installed, including its headers and client libraries. For
recent Fedora distributions it means (at least) RPMs ‘<samp>libX11</samp>’,
‘<samp>libX11-devel</samp>’, ‘<samp>libXt</samp>’ and ‘<samp>libXt-devel</samp>’. On Debian we
recommend the meta-package ‘<samp>xorg-dev</samp>’. If you really do not want
these you will need to explicitly configure R without X11, using
<samp>--with-x=no</samp>.
</p>
<p>The command-line editing (and command completion) depends on the
<acronym>GNU</acronym> <code>readline</code> library: version 4.2 or later is needed
for all the features to be enabled. Otherwise you will need to
configure with <samp>--with-readline=no</samp> (or equivalent).
</p>
<p>A suitably comprehensive <code>iconv</code> function is essential. The R
usage requires <code>iconv</code> to be able to translate between
<code>"latin1"</code> and <code>"UTF-8"</code>, to recognize <code>""</code> (as the
current encoding) and <code>"ASCII"</code>, and to translate to and from the
Unicode wide-character formats <code>"UCS-[24][BL]E"</code> — this is true
for <code>glibc</code> but not of most commercial Unixes. However, you can
make use of <acronym>GNU</acronym> <code>libiconv</code> (possibly as a plug-in
replacement: see <a href="http://www.gnu.org/software/libiconv/">http://www.gnu.org/software/libiconv/</a>).
</p>
<p>An implementation of <acronym>XDR</acronym> is required. This is part of
<acronym>RPC</acronym> and historically has been part of <samp>libc</samp> on a
Unix-alike: however some builds<a name="DOCF26" href="#FOOT26"><sup>26</sup></a> of <code>glibc
2.14</code> hide it. The intention seems to be that the <acronym>TI-RPC</acronym>
library be used instead, in which case <code>libtirpc</code> (and its
development version) needs to be installed, and its headers need to be
on the C include path (and <code>configure</code> tries
<samp>/usr/include/tirpc</samp> if the headers are not found on the standard
include path). The R sources contain a fall-back implementation of
<acronym>XDR</acronym> which is likely to suffice on both 32- and 64-bit
platforms.
</p>
<p>The OS needs to have enough support<a name="DOCF27" href="#FOOT27"><sup>27</sup></a> for wide-character
types: this is checked at configuration.
</p>
<p>A <code>tar</code> program is needed to unpack the sources and packages
(including the recommended packages). A version<a name="DOCF28" href="#FOOT28"><sup>28</sup></a> that can
automagically detect compressed archives is preferred for use with
<code>untar()</code>: the configure script looks for <code>gtar</code> and
<code>gnutar</code> before
<a name="index-TAR"></a>
<code>tar</code>: use environment variable <code>TAR</code> to override this.
</p>
<p>There need to be suitable versions of the tools <code>grep</code> and
<code>sed</code>: the problems are usually with old AT&T and BSD variants.
<code>configure</code> will try to find suitable versions (including
looking in <samp>/usr/xpg4/bin</samp> which is used on some commercial
Unixes).
</p>
<p>You will not be able to build most of the manuals unless you have
<code>makeinfo</code> version 4.7 or later installed, and if not some of
the <acronym>HTML</acronym> manuals will be linked to <acronym>CRAN</acronym>. To make PDF
versions of the manuals you will also need file <samp>texinfo.tex</samp>
installed (which is part of the <acronym>GNU</acronym> <strong>texinfo</strong> distribution
but is often made part of the TeX package in re-distributions) as
well as <code>texi2dvi</code>.<a name="DOCF29" href="#FOOT29"><sup>29</sup></a> Further, the versions of <code>texi2dvi</code> and
<samp>texinfo.tex</samp> need to be compatible: we have seen problems with
older TeX distributions (TeXLive 2007 and MiKTeX 2.8) used with
<strong>texinfo</strong> 4.13. It should be possible to use <code>makeinfo</code>
version 5.x.
</p>
<a name="index-Vignettes"></a>
<p>The PDF documentation (including <samp>doc/NEWS.pdf</samp>) and building
vignettes needs <code>pdftex</code> and <code>pdflatex</code>. We require
LaTeX version <code>2005/12/01</code> or later (for UTF-8 support).
Building PDF package manuals (including the R reference manual) and
vignettes is sensitive to the version of the LaTeX package
<strong>hyperref</strong> and we recommend that the TeX distribution used is
kept up-to-date. A number of LaTeX packages are required (including
<strong>url.sty</strong>, and <strong>listings.sty</strong>) and others such as <strong>hyperref</strong>
and <strong>inconsolata</strong> are desirable (and without them you may need to change
R’s defaults: see <a href="#Making-the-manuals">Making the manuals</a>).
</p>
<p>If you want to build from the R Subversion repository you need both
<code>makeinfo</code> and <code>pdflatex</code>.
<a name="index-Subversion-1"></a>
</p>
<a name="index-PATH"></a>
<p>The essential programs should be in your <code>PATH</code> at the time
<code>configure</code> is run: this will capture the full paths.
</p>
<hr>
<a name="Useful-libraries-and-programs"></a>
<div class="header">
<p>
Next: <a href="#Linear-algebra" accesskey="n" rel="next">Linear algebra</a>, Previous: <a href="#Essential-programs-and-libraries" accesskey="p" rel="previous">Essential programs and libraries</a>, Up: <a href="#Essential-and-useful-other-programs-under-a-Unix_002dalike" accesskey="u" rel="up">Essential and useful other programs under a Unix-alike</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Useful-libraries-and-programs-1"></a>
<h3 class="section">A.2 Useful libraries and programs</h3>
<p>The ability to use translated messages makes use of <code>gettext</code> and
most likely needs <acronym>GNU</acronym> <code>gettext</code>: you do need this to work
with new translations, but otherwise the version contained in the R
sources will be used if no suitable external <code>gettext</code> is found.
</p>
<p>The ‘modern’ version of the <code>X11()</code>, <code>jpeg()</code>, <code>png()</code>
and <code>tiff()</code> graphics devices uses the <code>cairo</code> and
(optionally) <code>Pango</code> libraries. Cairo version 1.2.0 or later is
required. Pango needs to be at least version 1.10, and 1.12 is the
earliest version we have tested. (For Fedora users we believe the
<code>pango-devel</code> RPM and its dependencies suffice.) R checks for
<code>pkg-config</code>, and uses that to check first that the
‘<samp>pangocairo</samp>’ package is installed (and if not, ‘<samp>cairo</samp>’) and if
additional flags are needed for the ‘<samp>cairo-xlib</samp>’ package, then if
suitable code can be compiled. These tests will fail if
<code>pkg-config</code> is not installed, and are likely to fail if
<code>cairo</code> was built statically (unusual). Most systems with
<code>Gtk+</code> 2.8 or later installed will have suitable libraries. OS X
comes with none of these libraries (but XQuartz, as used for 10.8 and
later, ships <code>cairo</code>), but <code>cairo</code> support (without
<code>Pango</code>) has been added to the binary distribution (see
<a href="http://r.research.att.com/libs/">http://r.research.att.com/libs/</a> you need <code>fontconfig</code>,
<code>freetype</code> and <code>pixman</code> too): <code>pkg-config</code> is still
needed when building R from source and can be installed from its
sources.
</p>
<p>For the best font experience with these devices you need suitable fonts
installed: Linux users will want the <code>urw-fonts</code> package. On
platforms which have it available, the <code>msttcorefonts</code>
package<a name="DOCF30" href="#FOOT30"><sup>30</sup></a> provides
TrueType versions of Monotype fonts such as Arial and Times New Roman.
Another useful set of fonts is the ‘liberation’ TrueType fonts available
at
<a href="https://fedorahosted.org/liberation-fonts/">https://fedorahosted.org/liberation-fonts/</a>,<a name="DOCF31" href="#FOOT31"><sup>31</sup></a> which cover the Latin, Greek and Cyrillic alphabets
plus a fair range of signs. These share metrics with Arial, Times New
Roman and Courier New, and contain fonts rather similar to the first two
(<a href="http://en.wikipedia.org/wiki/Liberation_fonts">http://en.wikipedia.org/wiki/Liberation_fonts</a>). Then there
is the ‘Free UCS Outline Fonts’ project
(<a href="http://www.gnu.org/software/freefont/">http://www.gnu.org/software/freefont/</a>) which are
OpenType/TrueType fonts based on the URW fonts but with extended Unicode
coverage. See the R help on <code>X11</code> on selecting such fonts.
</p>
<p>The bitmapped graphics devices <code>jpeg()</code>, <code>png()</code> and
<code>tiff()</code> need the appropriate headers and libraries installed:
<code>jpeg</code> (version 6b or later, or <code>libjpeg-turbo</code>) or
<code>libpng</code> (version 1.2.7 or later) and <code>zlib</code> or <code>libtiff</code>
(any recent version – 3.9.[4567] and 4.0.[23] have been tested)
respectively. They also need support for either <code>X11</code> or
<code>cairo</code> (see above). Should support for these devices <strong>not</strong>
be required or broken system libraries need to be avoided there are
<code>configure</code> options <samp>--without-libpng</samp>,
<samp>--without-jpeglib</samp> and <samp>--without-libtiff</samp>. For most
system installations the TIFF libraries will require JPEG libraries to
be present and perhaps linked explicitly, so <samp>--without-jpeglib</samp>
may also disable the <code>tiff()</code> device. The <code>tiff()</code> devices
only require a basic build of <code>libtiff</code> (not even JPEG support is
needed). Recent versions allow several other libraries to be linked
into <code>libtiff</code> such as <code>lzma</code>, <code>jbig</code> and <code>jpeg12</code>,
and these may need also to be present.
</p>
<p>If you have them installed (including the appropriate headers and of
suitable versions), system versions of <code>zlib</code>, <code>libbz2</code> and
PCRE will be used if specified by <samp>--with-system-zlib</samp> (version
1.2.5 or later), <samp>--with-system-bzlib</samp> or
<samp>--with-system-pcre</samp> (version 8.10 or later, preferably 8.33
which is what is supplied with R): otherwise versions in the R
sources will be compiled in. As the latter suffice and are tested with
R you should not need to change this.
</p>
<p><code>liblzma</code> from <code>xz-utils</code> version 5.0.3 or later will be used
if installed: the version in the R sources can be selected instead by
configuring with <samp>--with-system-xz=no</samp>. Systems differ in what
they call the package including this: e.g. on Fedora the library is in
‘<samp>xz-libs</samp>’ and the headers in ‘<samp>xz-devel</samp>’.
</p>
<p>Use of the X11 clipboard selection requires the <code>Xmu</code> headers and
libraries. These are normally part of an X11 installation (e.g. the
Debian meta-package ‘<samp>xorg-dev</samp>’), but some distributions have split
this into smaller parts, so for example recent versions of Fedora
require the ‘<samp>libXmu</samp>’ and ‘<samp>libXmu-devel</samp>’ RPMs.
</p>
<p>Some systems (notably OS X and at least some FreeBSD systems) have
inadequate support for collation in multibyte locales. It is possible
to replace the OS’s collation support by that from ICU (International
Components for Unicode, <a href="http://site.icu-project.org/">http://site.icu-project.org/</a>), and this
provides much more precise control over collation on all systems. ICU
is available as sources and as binary distributions for (at least) most
Linux distributions, Solaris, FreeBSD and AIX, usually as <code>libicu</code>
or <code>icu4c</code>. It will be used by default where available (including
on OS X >= 10.4): should a very old or broken version of ICU be found
this can be suppressed by <samp>--without-ICU</samp>.
</p>
<p>The <code>bitmap</code> and <code>dev2bitmap</code> devices and also
<code>embedFonts()</code> use ghostscript
(<a href="http://www.ghostscript.com/">http://www.ghostscript.com/</a>). This should either be in your
path when the command is run, or its full path specified by the
environment variable <code>R_GSCMD</code> at that time.
<a name="index-R_005fGSCMD"></a>
</p>
<table class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">• <a href="#Tcl_002fTk" accesskey="1">Tcl/Tk</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Java-support" accesskey="2">Java support</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
</table>
<hr>
<a name="Tcl_002fTk"></a>
<div class="header">
<p>
Next: <a href="#Java-support" accesskey="n" rel="next">Java support</a>, Previous: <a href="#Useful-libraries-and-programs" accesskey="p" rel="previous">Useful libraries and programs</a>, Up: <a href="#Useful-libraries-and-programs" accesskey="u" rel="up">Useful libraries and programs</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Tcl_002fTk-1"></a>
<h4 class="subsection">A.2.1 Tcl/Tk</h4>
<p>The <strong>tcltk</strong> package needs Tcl/Tk >= 8.4 installed: the sources are
available at <a href="http://www.tcl.tk/">http://www.tcl.tk/</a>. To specify the locations of the
Tcl/Tk files you may need the configuration options
</p>
<dl compact="compact">
<dt><samp>--with-tcltk</samp></dt>
<dd><p>use Tcl/Tk, or specify its library directory
</p></dd>
<dt><samp>--with-tcl-config=<var>TCL_CONFIG</var></samp></dt>
<dd><p>specify location of <samp>tclConfig.sh</samp>
</p></dd>
<dt><samp>--with-tk-config=<var>TK_CONFIG</var></samp></dt>
<dd><p>specify location of <samp>tkConfig.sh</samp>
</p></dd>
</dl>
<p>or use the configure variables <code>TCLTK_LIBS</code> and
<code>TCLTK_CPPFLAGS</code> to specify the flags needed for linking against
the Tcl and Tk libraries and for finding the <samp>tcl.h</samp> and
<samp>tk.h</samp> headers, respectively. If you have both 32- and 64-bit
versions of Tcl/Tk installed, specifying the paths to the correct config
files may be necessary to avoid confusion between them.
</p>
<p>Versions of Tcl/Tk up to 8.5.12 and 8.6.0 have been tested (including
most versions of 8.4.x, but not recently).
</p>
<hr>
<a name="Java-support"></a>
<div class="header">
<p>
Previous: <a href="#Tcl_002fTk" accesskey="p" rel="previous">Tcl/Tk</a>, Up: <a href="#Useful-libraries-and-programs" accesskey="u" rel="up">Useful libraries and programs</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Java-support-1"></a>
<h4 class="subsection">A.2.2 Java support</h4>
<p>The build process looks for Java support on the host system, and if it
finds it sets some settings which are useful for Java-using packages.
<a name="index-JAVA_005fHOME"></a>
<code>JAVA_HOME</code> can be set to point to a specific JRE/JDK.
</p>
<p>Principal amongst these are setting some library paths to the Java
libraries and JVM, which are stored in environment variable
<a name="index-R_005fJAVA_005fLD_005fLIBRARY_005fPATH"></a>
<code>R_JAVA_LD_LIBRARY_PATH</code> in file <samp><var>R_HOME</var>/etc/ldpaths</samp> (or
a sub-architecture-specific version). A typical setting for
‘<samp>x86_64</samp>’ Linux is
</p>
<div class="example">
<pre class="example">JAVA_HOME=/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.25.x86_64/jre
R_JAVA_LD_LIBRARY_PATH=${JAVA_HOME}/lib/amd64/server
</pre></div>
<p>Note that this unfortunately depends on the exact version of the JRE/JDK
installed, and so may need updating if the Java installation is updated.
This can be done by running <code>R CMD javareconf</code> which updates
settings in both <samp>etc/Makeconf</samp> and
<samp><var>R_HOME</var>/etc/ldpaths</samp>. See <code>R CMD javareconf --help</code> for
details.
</p>
<p>Another way of overriding those settings is to set the environment variable
<a name="index-R_005fJAVA_005fLD_005fLIBRARY_005fPATH-1"></a>
<code>R_JAVA_LD_LIBRARY_PATH</code> (before R is started, hence not in
<samp>~/.Renviron</samp>), which suffices to run already-installed
Java-using packages. For example
</p>
<div class="example">
<pre class="example">R_JAVA_LD_LIBRARY_PATH=/usr/lib/jvm/java-1.7.0/jre/lib/amd64/server
</pre></div>
<p>It may be possible to avoid this by specifying an invariant link as the
path. For example, on that system either of
</p>
<div class="example">
<pre class="example">JAVA_HOME=/usr/lib/jvm/java-1.7.0
JAVA_HOME=/usr/lib/jvm/java-1.7.0/jre
</pre></div>
<p>worked.
</p>
<hr>
<a name="Linear-algebra"></a>
<div class="header">
<p>
Previous: <a href="#Useful-libraries-and-programs" accesskey="p" rel="previous">Useful libraries and programs</a>, Up: <a href="#Essential-and-useful-other-programs-under-a-Unix_002dalike" accesskey="u" rel="up">Essential and useful other programs under a Unix-alike</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Linear-algebra-1"></a>
<h3 class="section">A.3 Linear algebra</h3>
<a name="index-BLAS-library"></a>
<table class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">• <a href="#BLAS" accesskey="1">BLAS</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#LAPACK" accesskey="2">LAPACK</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Caveats" accesskey="3">Caveats</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
</table>
<hr>
<a name="BLAS"></a>
<div class="header">
<p>
Next: <a href="#LAPACK" accesskey="n" rel="next">LAPACK</a>, Previous: <a href="#Linear-algebra" accesskey="p" rel="previous">Linear algebra</a>, Up: <a href="#Linear-algebra" accesskey="u" rel="up">Linear algebra</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="BLAS-1"></a>
<h4 class="subsection">A.3.1 BLAS</h4>
<p>The linear algebra routines in R can make use of enhanced
<acronym>BLAS</acronym> (Basic Linear Algebra Subprograms,
<a href="http://www.netlib.org/blas/faq.html">http://www.netlib.org/blas/faq.html</a>) routines. However,
these have to be explicitly requested at configure time: R provides
an internal <acronym>BLAS</acronym> which is well-tested and will be adequate for
most uses of R.
</p>
<p>You can specify a particular <acronym>BLAS</acronym> library <em>via</em> a value
for the configuration option <samp>--with-blas</samp> and not to use an
external <acronym>BLAS</acronym> library by <samp>--without-blas</samp> (the
default). If <samp>--with-blas</samp> is given with no <code>=</code>, its value
is taken from the
<a name="index-BLAS_005fLIBS"></a>
environment variable <code>BLAS_LIBS</code>, set for example in
<samp>config.site</samp>. If neither the option nor the environment variable
supply a value, a search is made for a suitable <acronym>BLAS</acronym>. If the
value is not obviously a linker command (starting with a dash or giving
the path to a library), it is prefixed by ‘<samp>-l</samp>’, so
</p>
<div class="example">
<pre class="example">--with-blas="foo"
</pre></div>
<p>is an instruction to link against ‘<samp>-lfoo</samp>’ to find an external
<acronym>BLAS</acronym> (which needs to be found both at link time and run time).
</p>
<p>The configure code checks that the external <acronym>BLAS</acronym> is complete
(it must include all double precision and double complex routines, as
well as <code>LSAME</code>), and appears to be usable. However, an external
<acronym>BLAS</acronym> has to be usable from a shared object (so must contain
position-independent code), and that is not checked.
</p>
<p>Some enhanced <acronym>BLAS</acronym>es are compiler-system-specific
(<code>sunperf</code> on Solaris<a name="DOCF32" href="#FOOT32"><sup>32</sup></a>, <code>libessl</code> on IBM,
<code>Accelerate</code> on OS X). The correct incantation for
these is usually found <em>via</em> <samp>--with-blas</samp> with no value on
the appropriate platforms.
</p>
<p>Some of the external <acronym>BLAS</acronym>es are multi-threaded. One issue is
that R profiling (which uses the <code>SIGPROF</code> signal) may cause
problems, and you may want to disable profiling if you use a
multi-threaded <acronym>BLAS</acronym>. Note that using a multi-threaded
<acronym>BLAS</acronym> can result in taking more <acronym>CPU</acronym> time and even
more elapsed time (occasionally dramatically so) than using a similar
single-threaded <acronym>BLAS</acronym>.
</p>
<p>Note that under Unix (but not under Windows) if R is compiled against
a non-default <acronym>BLAS</acronym> and <samp>--enable-BLAS-shlib</samp> is
<strong>not</strong> used, then all <acronym>BLAS</acronym>-using packages must also be.
So if R is re-built to use an enhanced <acronym>BLAS</acronym> then packages
such as <a href="http://CRAN.R-project.org/package=quantreg"><strong>quantreg</strong></a> will need to be re-installed.
</p>
<p>R relies on <acronym>ISO</acronym>/<acronym>IEC</acronym> 60559 compliance of an
external <acronym>BLAS</acronym>. This can be broken if for example the code
assumes that terms with a zero factor are always zero and do not need to
be computed—whereas <code>x*0</code> can be <code>NaN</code>. This is checked in
the test suite.
</p>
<table class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">• <a href="#ATLAS" accesskey="1">ATLAS</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#ACML" accesskey="2">ACML</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Goto-and-OpenBLAS" accesskey="3">Goto and OpenBLAS</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#MKL" accesskey="4">MKL</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Shared-BLAS" accesskey="5">Shared BLAS</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
</table>
<hr>
<a name="ATLAS"></a>
<div class="header">
<p>
Next: <a href="#ACML" accesskey="n" rel="next">ACML</a>, Previous: <a href="#BLAS" accesskey="p" rel="previous">BLAS</a>, Up: <a href="#BLAS" accesskey="u" rel="up">BLAS</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="ATLAS-1"></a>
<h4 class="subsubsection">A.3.1.1 ATLAS</h4>
<p>ATLAS (<a href="http://math-atlas.sourceforge.net/">http://math-atlas.sourceforge.net/</a>) is a “tuned”
<acronym>BLAS</acronym> that runs on a wide range of Unix-alike platforms.
Unfortunately it is usually built as a static library that on some
platforms cannot be used with shared objects such as are used in R
packages. Be careful when using pre-built versions of ATLAS (they seem
to work on ‘<samp>ix86</samp>’ platforms, but not always on ‘<samp>x86_64</samp>’
ones).
</p>
<p>The usual way to specify ATLAS will be via
</p>
<div class="example">
<pre class="example">--with-blas="-lf77blas -latlas"
</pre></div>
<p>if the libraries are in the library path, otherwise by
</p>
<div class="example">
<pre class="example">--with-blas="-L/path/to/ATLAS/libs -lf77blas -latlas"
</pre></div>
<p>For example, ‘<samp>x86_64</samp>’ Fedora needs
</p><div class="example">
<pre class="example">--with-blas="-L/usr/lib64/atlas -lf77blas -latlas"
</pre></div>
<p>For systems with multiple CPU cores it is possible to use a
multi-threaded version of ATLAS, by specifying
</p>
<div class="example">
<pre class="example">--with-blas="-lptf77blas -lpthread -latlas"
</pre></div>
<p>Consult its file <samp>INSTALL.txt</samp> for how to build ATLAS with
position-independent code: that file also describes how to build ATLAS
as a shared library.
</p>
<hr>
<a name="ACML"></a>
<div class="header">
<p>
Next: <a href="#Goto-and-OpenBLAS" accesskey="n" rel="next">Goto and OpenBLAS</a>, Previous: <a href="#ATLAS" accesskey="p" rel="previous">ATLAS</a>, Up: <a href="#BLAS" accesskey="u" rel="up">BLAS</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="ACML-1"></a>
<h4 class="subsubsection">A.3.1.2 ACML</h4>
<p>For ‘<samp>x86_64</samp>’ and ‘<samp>i686</samp>’ processors under Linux there is
the AMD Core Math Library (ACML) <a href="http://www.amd.com/acml">http://www.amd.com/acml</a>. For
the <code>gcc</code> version we could use
</p>
<div class="example">
<pre class="example">--with-blas="-lacml"
</pre></div>
<p>if the appropriate library directory (such as
<a name="index-LD_005fLIBRARY_005fPATH-1"></a>
<samp>/opt/acml5.1.0/gfortran64/lib</samp>) is in the <code>LD_LIBRARY_PATH</code>.
For other compilers, see the ACML documentation. There is a
multithreaded Linux version of ACML available for recent versions of
<code>gfortran</code>. To make use of this you will need something like
</p>
<div class="example">
<pre class="example">--with-blas="-L/opt/acml5.1.0/gfortran64_mp/lib -lacml_mp"
</pre></div>
<p>(and you may need to arrange for the directory to be in <code>ld.so</code>
cache).
</p>
<p>See see <a href="#Shared-BLAS">Shared BLAS</a> for an alternative (and in many ways preferable)
way to use ACML.
</p>
<p>The version last tested (5.1.0) failed the <samp>reg-BLAS.R</samp> test in its
handling of <code>NA</code>s.
</p>
<hr>
<a name="Goto-and-OpenBLAS"></a>
<div class="header">
<p>
Next: <a href="#MKL" accesskey="n" rel="next">MKL</a>, Previous: <a href="#ACML" accesskey="p" rel="previous">ACML</a>, Up: <a href="#BLAS" accesskey="u" rel="up">BLAS</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Goto-and-OpenBLAS-1"></a>
<h4 class="subsubsection">A.3.1.3 Goto and OpenBLAS</h4>
<p>Dr Kazushige Goto wrote another tuned <acronym>BLAS</acronym> which is available
for several processors and OSes. The final version is known as
GotoBLAS2, and was re-released under a much less restrictive licence.
Source code can be obtained from
<a href="http://www.tacc.utexas.edu/tacc-projects/gotoblas2/">http://www.tacc.utexas.edu/tacc-projects/gotoblas2/</a>
</p>
<p>Once it is built and installed, it can be used by configuring R with
</p>
<div class="example">
<pre class="example">--with-blas="-lgoto2"
</pre></div>
<p>See see <a href="#Shared-BLAS">Shared BLAS</a> for an alternative (and in many ways preferable)
way to use it.
</p>
<p>Our understanding is that this project is now frozen and so will not be
updated for CPUs released since mid-2010. However, OpenBLAS
(<a href="http://xianyi.github.com/OpenBLAS/">http://xianyi.github.com/OpenBLAS/</a>) is a descendant project with
support for some current CPUs (e.g. Intel Sandy Bridge and AMD Bulldozer).
</p>
<hr>
<a name="MKL"></a>
<div class="header">
<p>
Next: <a href="#Shared-BLAS" accesskey="n" rel="next">Shared BLAS</a>, Previous: <a href="#Goto-and-OpenBLAS" accesskey="p" rel="previous">Goto and OpenBLAS</a>, Up: <a href="#BLAS" accesskey="u" rel="up">BLAS</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Intel-MKL"></a>
<h4 class="subsubsection">A.3.1.4 Intel MKL</h4>
<p>For Intel processors<a name="DOCF33" href="#FOOT33"><sup>33</sup></a> under Linux, there is
Intel’s Math Kernel Library
(<a href="http://www.intel.com/software/products/mkl/">http://www.intel.com/software/products/mkl/</a>). You are
strongly encouraged to read the MKL User’s Guide, which is installed
with the library, before attempting to link to MKL. There are also
versions of MKL for OS X and Windows, but they did not work with the
standard compilers used for R on those platforms.
</p>
<p>The MKL interface has changed several times, and may change again: the
following notes apply exactly only to version 10.3.
</p>
<p>Version 10 of MKL supports two linking models: the default model, which
is backward compatible with version 9 (see below), and the pure layered
model. The layered model gives the user fine-grained control over four
different library layers: interface, threading, computation, and
run-time library support. Some examples of linking to MKL using this
layered model are given below. (These examples are for GCC compilers on
‘<samp>x86_64</samp>’.) The choice of interface layer is important on
‘<samp>x86_64</samp>’ since the Intel Fortran compiler returns complex values
in different registers from the <acronym>GNU</acronym> Fortran compiler. You must
therefore use the interface layer that matches your compiler
(<code>mkl_intel*</code> or <code>mkl_gf*</code>).
</p>
<p>R can be linked to a sequential version of MKL by something like
</p>
<div class="example">
<pre class="example">MKL_LIB_PATH=/opt/intel/mkl/10.311.339/lib/intel64/
export LD_LIBRARY_PATH=$MKL_LIB_PATH
MKL="-L${MKL_LIB_PATH} -lmkl_gf_lp64 -lmkl_sequential -lmkl_core"
./configure --with-blas="$MKL" --with-lapack
</pre></div>
<p>where some versions may need <code>-lmkl_lapack</code> before
<code>-lmkl_core</code>. The order of the libraries is important. The option
<samp>--with-lapack</samp> is used since MKL contains a tuned copy of LAPACK
as well as <acronym>BLAS</acronym> (see <a href="#LAPACK">LAPACK</a>), although this can be
omitted.
</p>
<p>Threaded MKL may be used (according to Zhang Zhang of Intel) by
replacing the line defining the variable <code>MKL</code> with (Intel OMP)
</p>
<div class="example">
<pre class="example">MKL="-L${MKL_LIB_PATH} -lmkl_gf_lp64 -lmkl_intel_thread \
-lmkl_core -liomp5 -lpthread"
</pre></div>
<p>or (GNU OMP)
</p>
<div class="example">
<pre class="example">MKL="-L${MKL_LIB_PATH} -lmkl_gf_lp64 -lmkl_gnu_thread \
-lmkl_core -fopenmp -lpthread"
</pre></div>
<p>The default number of threads will be chosen by the OpenMP software,
but can be controlled by setting <code>OMP_NUM_THREADS</code> or
<code>MKL_NUM_THREADS</code>, and in recent versions seems to produce a
sensible value for sole use of the machine.
</p>
<p>Static threaded MKL may be used (GNU OpenMP) with something like
</p>
<div class="example">
<pre class="example">MKL=" -L${MKL_LIB_PATH} \
-Wl,--start-group \
${MKL_LIB_PATH}/libmkl_gf_lp64.a \
${MKL_LIB_PATH}/libmkl_gnu_thread.a \
${MKL_LIB_PATH}/libmkl_core.a \
-Wl,--end-group \
-lgomp -lpthread"
</pre></div>
<p>(Thanks to Ei-ji Nakama).
</p>
<p>The MKL documentation includes a ‘link line advisor’ which will suggest
appropriate incantations: an on-line version was available at
<a href="http://software.intel.com/en-us/articles/intel-mkl-link-line-advisor/">http://software.intel.com/en-us/articles/intel-mkl-link-line-advisor/</a>
</p>
<p>The default linking model, which was also used by version 9 of MKL, can
be used by
</p>
<div class="example">
<pre class="example">--with-blas="-lmkl -lguide -lpthread"
</pre></div>
<p>but this may not match your compiler on a 64-bit platform. This is
multi-threaded, but in version 9 the number of threads defaults to 1.
It can be increased by setting <code>OMP_NUM_THREADS</code>. (Thanks to Andy
Liaw for the information.)
</p>
<hr>
<a name="Shared-BLAS"></a>
<div class="header">
<p>
Previous: <a href="#MKL" accesskey="p" rel="previous">MKL</a>, Up: <a href="#BLAS" accesskey="u" rel="up">BLAS</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Shared-BLAS-1"></a>
<h4 class="subsubsection">A.3.1.5 Shared BLAS</h4>
<p>The <acronym>BLAS</acronym> library will be used for many of the add-on packages
as well as for R itself. This means that it is better to use a
shared/dynamic <acronym>BLAS</acronym> library, as most of a static library will
be compiled into the R executable and each <acronym>BLAS</acronym>-using
package.
</p>
<p>R offers the option of compiling the <acronym>BLAS</acronym> into a dynamic
library <code>libRblas</code> stored in <samp><var>R_HOME</var>/lib</samp> and linking
both R itself and all the add-on packages against that library.
</p>
<p>This is the default on all platforms except AIX unless an external
<acronym>BLAS</acronym> is specified and found: for the latter it can be used by
specifying the option <samp>--enable-BLAS-shlib</samp>, and it can always be
disabled via <samp>--disable-BLAS-shlib</samp>.
</p>
<p>This has both advantages and disadvantages.
</p>
<ul>
<li> It saves space by having only a single copy of the <acronym>BLAS</acronym>
routines, which is helpful if there is an external static <acronym>BLAS</acronym>
such as used to be standard for ATLAS.
</li><li> There may be performance disadvantages in using a shared <acronym>BLAS</acronym>.
Probably the most likely is when R’s internal <acronym>BLAS</acronym> is used
and R is <em>not</em> built as a shared library, when it is possible to
build the <acronym>BLAS</acronym> into <samp>R.bin</samp> (and <samp>libR.a</samp>) without
using position-independent code. However, experiments showed that in
many cases using a shared <acronym>BLAS</acronym> was as fast, provided high
levels of compiler optimization are used.
</li><li> It is easy to change the <acronym>BLAS</acronym> without needing to re-install
R and all the add-on packages, since all references to the
<acronym>BLAS</acronym> go through <code>libRblas</code>, and that can be replaced.
Note though that any dynamic libraries the replacement links to will
need to be found by the linker: this may need the library path to be
changed in <samp><var>R_HOME</var>/etc/ldpaths</samp>.
</li></ul>
<p>Another option to change the <acronym>BLAS</acronym> in use is to symlink a
dynamic <acronym>BLAS</acronym> library (such as ACML or Goto’s) to
<samp><var>R_HOME</var>/lib/libRblas.so</samp>. For example, just
</p>
<div class="example">
<pre class="example">mv <var>R_HOME</var>/lib/libRblas.so <var>R_HOME</var>/lib/libRblas.so.keep
ln -s /opt/acml5.1.0/gfortran64_mp/lib/libacml_mp.so <var>R_HOME</var>/lib/libRblas.so
</pre></div>
<p>will change the <acronym>BLAS</acronym> in use to multithreaded ACML. A similar
link works for some versions of the Goto <acronym>BLAS</acronym> and perhaps
for MKL (provided the appropriate <samp>lib</samp> directory is in the
run-time library path or <code>ld.so</code> cache).
</p>
<hr>
<a name="LAPACK"></a>
<div class="header">
<p>
Next: <a href="#Caveats" accesskey="n" rel="next">Caveats</a>, Previous: <a href="#BLAS" accesskey="p" rel="previous">BLAS</a>, Up: <a href="#Linear-algebra" accesskey="u" rel="up">Linear algebra</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="LAPACK-1"></a>
<h4 class="subsection">A.3.2 LAPACK</h4>
<a name="index-LAPACK-library"></a>
<p>Provision is made for using an external LAPACK library, principally to
cope with <acronym>BLAS</acronym> libraries which contain a copy of LAPACK (such
as <code>sunperf</code> on Solaris, <code>Accelerate</code> on OS X and ACML and MKL
on ‘<samp>ix86</samp>’/‘<samp>x86_64</samp>’ Linux). At least LAPACK version 3.2
is required. This can only be done if <samp>--with-blas</samp> has been used.
</p>
<p>However, the likely performance gains are thought to be small (and may
be negative), and the default is not to search for a suitable LAPACK
library, and this is definitely <strong>not</strong> recommended. You can
specify a specific LAPACK library or a search for a generic library by
the configuration option <samp>--with-lapack</samp>. The default for
<samp>--with-lapack</samp> is to check the <acronym>BLAS</acronym> library and then
look for an external library ‘<samp>-llapack</samp>’. Sites searching for the
fastest possible linear algebra may want to build a LAPACK library using
the ATLAS-optimized subset of LAPACK. To do so specify something like
</p>
<div class="example">
<pre class="example">--with-lapack="-L/path/to/ATLAS/libs -llapack -lcblas"
</pre></div>
<p>since the ATLAS subset of LAPACK depends on <code>libcblas</code>. A value
for <samp>--with-lapack</samp> can be set <em>via</em> the environment
variable
<a name="index-LAPACK_005fLIBS"></a>
<code>LAPACK_LIBS</code>, but this will only be used if <samp>--with-lapack</samp>
is specified (as the default value is <code>no</code>) and the <acronym>BLAS</acronym> library
does not contain LAPACK.
</p>
<p>Since ACML contains a full LAPACK, if selected as the <acronym>BLAS</acronym> it
can be used as the LAPACK <em>via</em> <samp>--with-lapack</samp>.
</p>
<p>If you do use <samp>--with-lapack</samp>, be aware of potential problems
with bugs in the LAPACK sources (or in the posted corrections to those
sources). In particular, bugs in <code>DGEEV</code> and <code>DGESDD</code> have
resulted in error messages such as
</p>
<div class="example">
<pre class="example">DGEBRD gave error code -10
</pre></div>
<p>. Other potential problems are incomplete versions of the libraries,
seen several times in Linux distributions over the years.
</p>
<p>Please <strong>do</strong> bear in mind that using <samp>--with-lapack</samp> is
‘definitely <strong>not</strong> recommended’: it is provided <strong>only</strong>
because it is necessary on some platforms and because some users want to
experiment with claimed performance improvements. Reporting problems
where it is used unnecessarily will simply irritate the R helpers.
</p>
<p>Note too the comments about <acronym>ISO</acronym>/<acronym>IEC</acronym> 60559
compliance in the section of external <acronym>BLAS</acronym>: these apply
equally to an external LAPACK, and for example the Intel MKL
documentation says
</p><blockquote>
<p>LAPACK routines assume that input matrices do not contain IEEE 754
special values such as INF or NaN values. Using these special values may
cause LAPACK to return unexpected results or become unstable.
</p></blockquote>
<p>We rely on limited support in LAPACK for matrices with <em>2^{31}</em> or
more elements: it is quite possible that an external LAPACK will not
have that support.
</p>
<p>If you have a pure FORTRAN 77 compiler which cannot compile LAPACK it
may be possible to use CLAPACK from
<a href="http://www.netlib.org/clapack/">http://www.netlib.org/clapack/</a> by something like
</p><div class="example">
<pre class="example">-with-lapack="-lclapack -lf2c"
</pre></div>
<p>provided these were built with position-independent code and the calling
conventions for double complex function return values match those in the
BLAS used, so it may be simpler to use CLAPACK built to use CBLAS and
</p><div class="example">
<pre class="example">-with-lapack="-lclapack -lcblas -lf2c"
</pre></div>
<hr>
<a name="Caveats"></a>
<div class="header">
<p>
Previous: <a href="#LAPACK" accesskey="p" rel="previous">LAPACK</a>, Up: <a href="#Linear-algebra" accesskey="u" rel="up">Linear algebra</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Caveats-1"></a>
<h4 class="subsection">A.3.3 Caveats</h4>
<p>As with all libraries, you need to ensure that they and R were
compiled with compatible compilers and flags. For example, this has
meant that on Sun Sparc using the native compilers the flag
<samp>-dalign</samp> is needed so <code>sunperf</code> can be used.
</p>
<p>On some systems it is necessary that an external <acronym>BLAS</acronym>/LAPACK
was built with the same FORTRAN compiler used to build R: known
problems are with R built with <code>gfortran</code>, see <a href="#Using-gfortran">Using gfortran</a>.
</p>
<hr>
<a name="Configuration-on-a-Unix_002dalike"></a>
<div class="header">
<p>
Next: <a href="#Platform-notes" accesskey="n" rel="next">Platform notes</a>, Previous: <a href="#Essential-and-useful-other-programs-under-a-Unix_002dalike" accesskey="p" rel="previous">Essential and useful other programs under a Unix-alike</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Configuration-on-a-Unix_002dalike-1"></a>
<h2 class="appendix">Appendix B Configuration on a Unix-alike</h2>
<table class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">• <a href="#Configuration-options" accesskey="1">Configuration options</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Internationalization-support" accesskey="2">Internationalization support</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Configuration-variables" accesskey="3">Configuration variables</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Setting-the-shell" accesskey="4">Setting the shell</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Using-make" accesskey="5">Using make</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Using-FORTRAN" accesskey="6">Using FORTRAN</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Compile-and-load-flags" accesskey="7">Compile and load flags</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
</table>
<hr>
<a name="Configuration-options"></a>
<div class="header">
<p>
Next: <a href="#Internationalization-support" accesskey="n" rel="next">Internationalization support</a>, Previous: <a href="#Configuration-on-a-Unix_002dalike" accesskey="p" rel="previous">Configuration on a Unix-alike</a>, Up: <a href="#Configuration-on-a-Unix_002dalike" accesskey="u" rel="up">Configuration on a Unix-alike</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Configuration-options-1"></a>
<h3 class="section">B.1 Configuration options</h3>
<p><code>configure</code> has many options: running
</p>
<div class="example">
<pre class="example">./configure --help
</pre></div>
<p>will give a list. Probably the most important ones not covered
elsewhere are (defaults in brackets)
</p>
<dl compact="compact">
<dt><samp>--with-x</samp></dt>
<dd><p>use the X Window System [yes]
</p></dd>
<dt><samp>--x-includes=<var>DIR</var></samp></dt>
<dd><p>X include files are in <var>DIR</var>
</p></dd>
<dt><samp>--x-libraries=<var>DIR</var></samp></dt>
<dd><p>X library files are in <var>DIR</var>
</p></dd>
<dt><samp>--with-readline</samp></dt>
<dd><p>use readline library (if available) [yes]
</p></dd>
<dt><samp>--enable-R-profiling</samp></dt>
<dd><p>attempt to compile support for <code>Rprof()</code> [yes]
</p></dd>
<dt><samp>--enable-memory-profiling</samp></dt>
<dd><p>attempt to compile support for <code>Rprofmem()</code> and <code>tracemem()</code> [no]
</p></dd>
<dt><samp>--enable-R-shlib</samp></dt>
<dd><p>build R as a shared/dynamic library [no]
</p></dd>
<dt><samp>--enable-BLAS-shlib</samp></dt>
<dd><p>build the <acronym>BLAS</acronym> as a shared/dynamic library [yes, except on AIX]
</p></dd>
</dl>
<p>You can use <samp>--without-foo</samp> or <samp>--disable-foo</samp> for the
negatives.
</p>
<p>You will want to use <samp>--disable-R-profiling</samp> if you are building
a profiled executable of R (e.g. with ‘<samp>-pg)</samp>’.
</p>
<p>Flag <samp>--enable-R-shlib</samp> causes the make process to build R as
a dynamic (shared) library, typically called <samp>libR.so</samp>, and link
the main R executable <samp>R.bin</samp> against that library. This can
only be done if all the code (including system libraries) can be
compiled into a dynamic library, and there may be a
performance<a name="DOCF34" href="#FOOT34"><sup>34</sup></a> penalty. So you probably
only want this if you will be using an application which embeds R.
Note that C code in packages installed on an R system linked with
<samp>--enable-R-shlib</samp> is linked against the dynamic library and so
such packages cannot be used from an R system built in the default
way. Also, because packages are linked against R they are on some
OSes also linked against the dynamic libraries R itself is linked
against, and this can lead to symbol conflicts.
</p>
<p>If you need to re-configure R with different options you may need to run
<code>make clean</code> or even <code>make distclean</code> before doing so.
</p>
<hr>
<a name="Internationalization-support"></a>
<div class="header">
<p>
Next: <a href="#Configuration-variables" accesskey="n" rel="next">Configuration variables</a>, Previous: <a href="#Configuration-options" accesskey="p" rel="previous">Configuration options</a>, Up: <a href="#Configuration-on-a-Unix_002dalike" accesskey="u" rel="up">Configuration on a Unix-alike</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Internationalization-support-1"></a>
<h3 class="section">B.2 Internationalization support</h3>
<p>Translation of messages is supported via <acronym>GNU</acronym> <code>gettext</code>
unless disabled by the configure option <samp>--disable-nls</samp>.
The <code>configure</code> report will show <code>NLS</code> as one of the
‘Additional capabilities’ if support has been compiled in, and running
in an English locale (but not the <code>C</code> locale) will include
</p>
<div class="example">
<pre class="example"> Natural language support but running in an English locale
</pre></div>
<p>in the greeting on starting R.
</p>
<hr>
<a name="Configuration-variables"></a>
<div class="header">
<p>
Next: <a href="#Setting-the-shell" accesskey="n" rel="next">Setting the shell</a>, Previous: <a href="#Internationalization-support" accesskey="p" rel="previous">Internationalization support</a>, Up: <a href="#Configuration-on-a-Unix_002dalike" accesskey="u" rel="up">Configuration on a Unix-alike</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Configuration-variables-1"></a>
<h3 class="section">B.3 Configuration variables</h3>
<a name="index-configure-4"></a>
<p>If you need or want to set certain configure variables to something
other than their default, you can do that by either editing the file
<samp>config.site</samp> (which documents many of the variables you might want
to set: others can be seen in file <samp>etc/Renviron.in</samp>) or on the
command line as
</p>
<div class="example">
<pre class="example">./configure <var>VAR</var>=<var>value</var>
</pre></div>
<p>If you are building in a directory different from the sources, there can
be copies of <samp>config.site</samp> in the source and the build directories,
and both will be read (in that order). In addition, if there is a file
<samp>~/.R/config</samp>, it is read between the <samp>config.site</samp> files in
the source and the build directories.
</p>
<p>There is also a general <code>autoconf</code> mechanism for
<samp>config.site</samp> files, which are read before any of those mentioned
in the previous paragraph. This looks first at a file specified by the
<a name="index-CONFIG_005fSITE"></a>
environment variable <code>CONFIG_SITE</code>, and if not is set at files such
as <samp>/usr/local/share/config.site</samp> and
<samp>/usr/local/etc/config.site</samp> in the area (exemplified by
<samp>/usr/local</samp>) where R would be installed.
</p>
<p>These variables are <em>precious</em>, implying that they do not have to
be exported to the environment, are kept in the cache even if not
specified on the command line, checked for consistency between two
configure runs (provided that caching is used), and are kept during
automatic reconfiguration as if having been passed as command line
arguments, even if no cache is used.
</p>
<p>See the variable output section of <code>configure --help</code> for a list of
all these variables.
</p>
<p>If you find you need to alter configure variables, it is worth noting
that some settings may be cached in the file <samp>config.cache</samp>, and it
is a good idea to remove that file (if it exists) before re-configuring.
Note that caching is turned <em>off</em> by default: use the command line
option <samp>--config-cache</samp> (or <samp>-C</samp>) to enable caching.
</p>
<table class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">• <a href="#Setting-paper-size" accesskey="1">Setting paper size</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Setting-the-browsers" accesskey="2">Setting the browsers</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Compilation-flags" accesskey="3">Compilation flags</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Making-manuals" accesskey="4">Making manuals</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
</table>
<hr>
<a name="Setting-paper-size"></a>
<div class="header">
<p>
Next: <a href="#Setting-the-browsers" accesskey="n" rel="next">Setting the browsers</a>, Previous: <a href="#Configuration-variables" accesskey="p" rel="previous">Configuration variables</a>, Up: <a href="#Configuration-variables" accesskey="u" rel="up">Configuration variables</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Setting-paper-size-1"></a>
<h4 class="subsection">B.3.1 Setting paper size</h4>
<a name="index-R_005fPAPERSIZE-2"></a>
<p>One common variable to change is <code>R_PAPERSIZE</code>, which defaults to
‘<samp>a4</samp>’, not ‘<samp>letter</samp>’. (Valid values are ‘<samp>a4</samp>’,
‘<samp>letter</samp>’, ‘<samp>legal</samp>’ and ‘<samp>executive</samp>’.)
</p>
<p>This is used both when configuring R to set the default, and when
running R to override the default. It is also used to set the
paper size when making PDF manuals.
</p>
<p>The configure default will most often be ‘<samp>a4</samp>’ if <code>R_PAPERSIZE</code>
is unset. (If the (Debian Linux) program <code>paperconf</code> is found
<a name="index-PAPERSIZE"></a>
or the environment variable <code>PAPERSIZE</code> is set, these are used to
produce the default.)
</p>
<hr>
<a name="Setting-the-browsers"></a>
<div class="header">
<p>
Next: <a href="#Compilation-flags" accesskey="n" rel="next">Compilation flags</a>, Previous: <a href="#Setting-paper-size" accesskey="p" rel="previous">Setting paper size</a>, Up: <a href="#Configuration-variables" accesskey="u" rel="up">Configuration variables</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Setting-the-browsers-1"></a>
<h4 class="subsection">B.3.2 Setting the browsers</h4>
<a name="index-R_005fBROWSER"></a>
<p>Another precious variable is <code>R_BROWSER</code>, the default <acronym>HTML</acronym>
browser, which should take a value of an executable in the user’s path
or specify a full path.
</p>
<a name="index-R_005fPDFVIEWER"></a>
<p>Its counterpart for PDF files is <code>R_PDFVIEWER</code>.
</p>
<hr>
<a name="Compilation-flags"></a>
<div class="header">
<p>
Next: <a href="#Making-manuals" accesskey="n" rel="next">Making manuals</a>, Previous: <a href="#Setting-the-browsers" accesskey="p" rel="previous">Setting the browsers</a>, Up: <a href="#Configuration-variables" accesskey="u" rel="up">Configuration variables</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Compilation-flags-1"></a>
<h4 class="subsection">B.3.3 Compilation flags</h4>
<p>If you have libraries and header files, e.g., for <acronym>GNU</acronym>
readline, in non-system directories, use the variables <code>LDFLAGS</code>
(for libraries, using ‘<samp>-L</samp>’ flags to be passed to the linker) and
<code>CPPFLAGS</code> (for header files, using ‘<samp>-I</samp>’ flags to be passed to
the C/C++ preprocessors), respectively, to specify these locations.
These default to ‘<samp>-L/usr/local/lib</samp>’ (<code>LDFLAGS</code>,
‘<samp>-L/usr/local/lib64</samp>’ on most 64-bit Linux OSes) and
‘<samp>-I/usr/local/include</samp>’ (<code>CPPFLAGS</code>) to catch the most common
cases. If libraries are still not found, then maybe your
compiler/linker does not support re-ordering of <samp>-L</samp> and
<samp>-l</samp> flags (this has been reported to be a problem on HP-UX with
the native <code>cc</code>). In this case, use a different compiler (or a
front end shell script which does the re-ordering).
</p>
<p>These flags can also be used to build a faster-running version of R.
On most platforms using <code>gcc</code>, having ‘<samp>-O3</samp>’ in
<code>CFLAGS</code> and <code>FFLAGS</code> produces worthwhile performance gains
with <code>gcc</code> and <code>gfortran</code>, but may result in a less
reliable build (both segfaults and incorrect numeric computations have
been seen). On systems using the <acronym>GNU</acronym> linker (especially those
using R as a shared library), it is likely that including
‘<samp>-Wl,-O1</samp>’ in <code>LDFLAGS</code> is worthwhile, and
‘<samp>'-Bdirect,--hash-style=both,-Wl,-O1'</samp>’ is recommended at
<a href="http://lwn.net/Articles/192624/">http://lwn.net/Articles/192624/</a>. Tuning compilation to a
specific <acronym>CPU</acronym> family (e.g. ‘<samp>-mtune=native</samp>’ for
<code>gcc</code>) can give worthwhile performance gains, especially on
older architectures such as ‘<samp>ix86</samp>’.
</p>
<hr>
<a name="Making-manuals"></a>
<div class="header">
<p>
Previous: <a href="#Compilation-flags" accesskey="p" rel="previous">Compilation flags</a>, Up: <a href="#Configuration-variables" accesskey="u" rel="up">Configuration variables</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Making-manuals-1"></a>
<h4 class="subsection">B.3.4 Making manuals</h4>
<a name="index-R_005fRD4PDF-1"></a>
<a name="index-R_005fPAPERSIZE-3"></a>
<p>The default settings for making the manuals are controlled by
<code>R_RD4PDF</code> and <code>R_PAPERSIZE</code>.
</p>
<hr>
<a name="Setting-the-shell"></a>
<div class="header">
<p>
Next: <a href="#Using-make" accesskey="n" rel="next">Using make</a>, Previous: <a href="#Configuration-variables" accesskey="p" rel="previous">Configuration variables</a>, Up: <a href="#Configuration-on-a-Unix_002dalike" accesskey="u" rel="up">Configuration on a Unix-alike</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Setting-the-shell-1"></a>
<h3 class="section">B.4 Setting the shell</h3>
<p>By default the shell scripts such as <samp>R</samp> will be ‘<samp>#!/bin/sh</samp>’
scripts (or using the <code>SHELL</code> chosen by <samp>configure</samp>). This is
almost always satisfactory, but on a few systems <samp>/bin/sh</samp> is not a
Bourne shell or clone, and the shell to be used can be changed by
setting the configure variable <code>R_SHELL</code> to a suitable value (a full
path to a shell, e.g. <samp>/usr/local/bin/bash</samp>).
</p>
<hr>
<a name="Using-make"></a>
<div class="header">
<p>
Next: <a href="#Using-FORTRAN" accesskey="n" rel="next">Using FORTRAN</a>, Previous: <a href="#Setting-the-shell" accesskey="p" rel="previous">Setting the shell</a>, Up: <a href="#Configuration-on-a-Unix_002dalike" accesskey="u" rel="up">Configuration on a Unix-alike</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Using-make-1"></a>
<h3 class="section">B.5 Using make</h3>
<a name="index-make"></a>
<p>To compile R, you will most likely find it easiest to use
<acronym>GNU</acronym> <code>make</code>, although the Sun <code>make</code> works on
Solaris, as does the native FreeBSD <code>make</code>. The native
<code>make</code> has been reported to fail on SGI Irix 6.5 and Alpha/OSF1
(aka Tru64).
</p>
<p>To build in a separate directory you need a <code>make</code> that uses the
<code>VPATH</code> variable, for example <acronym>GNU</acronym> <code>make</code>, or Sun
<code>make</code> on Solaris 7 or later.
</p>
<p><code>dmake</code> has also been used. e.g, on Solaris 10.
</p>
<p>If you want to use a <code>make</code> by another name, for example if your
<acronym>GNU</acronym> <code>make</code> is called ‘<samp>gmake</samp>’, you need to set the
variable <code>MAKE</code> at configure time, for example
</p>
<a name="index-configure-5"></a>
<div class="example">
<pre class="example">./configure MAKE=gmake
</pre></div>
<hr>
<a name="Using-FORTRAN"></a>
<div class="header">
<p>
Next: <a href="#Compile-and-load-flags" accesskey="n" rel="next">Compile and load flags</a>, Previous: <a href="#Using-make" accesskey="p" rel="previous">Using make</a>, Up: <a href="#Configuration-on-a-Unix_002dalike" accesskey="u" rel="up">Configuration on a Unix-alike</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Using-FORTRAN-1"></a>
<h3 class="section">B.6 Using FORTRAN</h3>
<a name="index-FORTRAN"></a>
<table class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">• <a href="#Using-gfortran" accesskey="1">Using gfortran</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
</table>
<p>To compile R, you need a FORTRAN compiler. The default
is to search for
<code>f95</code>, <code>fort</code>, <code>xlf95</code>,
<code>ifort</code>, <code>ifc</code>, <code>efc</code>, <code>pgf95</code>
<code>lf95</code>, <code>gfortran</code>, <code>ftn</code>, <code>g95</code>,
<code>f90</code>, <code>xlf90</code>, <code>pghpf</code>, <code>pgf90</code>,
<code>epcf90</code>,
<code>g77</code>, <code>f77</code>, <code>xlf</code>, <code>frt</code>,
<code>pgf77</code>, <code>cf77</code>, <code>fort77</code>, <code>fl32</code>,
<code>af77</code> (in that order)<a name="DOCF35" href="#FOOT35"><sup>35</sup></a>, and use whichever is found first; if none is found,
R cannot be compiled.
However, if <code>CC</code> is <code>gcc</code>, the matching FORTRAN compiler
(<code>g77</code> for <code>gcc</code> 3 and <code>gfortran</code> for
<code>gcc</code> 4) is used if available.
</p>
<p>The search mechanism can be changed using the configure variable
<code>F77</code> which specifies the command that runs the FORTRAN 77
compiler. If your FORTRAN compiler is in a non-standard location, you
<a name="index-PATH-1"></a>
should set the environment variable <code>PATH</code> accordingly before
running <code>configure</code>, or use the configure variable <code>F77</code> to
specify its full path.
</p>
<p>If your FORTRAN libraries are in slightly peculiar places, you should
<a name="index-LD_005fLIBRARY_005fPATH-2"></a>
also look at <code>LD_LIBRARY_PATH</code> or your system’s equivalent to make
sure that all libraries are on this path.
</p>
<p>Note that only FORTRAN compilers which convert identifiers to lower case
are supported.
</p>
<p>You must set whatever compilation flags (if any) are needed to ensure
that FORTRAN <code>integer</code> is equivalent to a C <code>int</code> pointer and
FORTRAN <code>double precision</code> is equivalent to a C <code>double</code>
pointer. This is checked during the configuration process.
</p>
<p>Some of the FORTRAN code makes use of <code>COMPLEX*16</code> variables, which
is a Fortran 90 extension. This is checked for at configure
time<a name="DOCF36" href="#FOOT36"><sup>36</sup></a>, but you may need to avoid
compiler flags asserting FORTRAN 77 compliance.
</p>
<p>Compiling the version of LAPACK in the R sources also requires some
Fortran 90 extensions, but these are not needed if an external LAPACK is
used.
</p>
<p>It might be possible to use <code>f2c</code>, the FORTRAN-to-C converter
(<a href="http://www.netlib.org/f2c">http://www.netlib.org/f2c</a>), via a script. (An example script
is given in <samp>scripts/f77_f2c</samp>: this can be customized by setting
<a name="index-F2C"></a>
<a name="index-F2CLIBS"></a>
<a name="index-CC"></a>
the environment variables <code>F2C</code>, <code>F2CLIBS</code>, <code>CC</code> and
<a name="index-CPP"></a>
<code>CPP</code>.) You will need to ensure that the FORTRAN type
<code>integer</code> is translated to the C type <code>int</code>. Normally
<samp>f2c.h</samp> contains ‘<samp>typedef long int integer;</samp>’, which will work
on a 32-bit platform but needs to be changed to ‘<samp>typedef int
integer;</samp>’ on a 64-bit platform. If your compiler is not <code>gcc</code>
you will need to set
<a name="index-FPICFLAGS"></a>
<code>FPICFLAGS</code> appropriately. Also, the included LAPACK sources
contain constructs that <code>f2c</code> is unlikely to be able to process,
so you would need to use an external LAPACK library (such as CLAPACK
from <a href="http://www.netlib.org/clapack/">http://www.netlib.org/clapack/</a>).
</p>
<hr>
<a name="Using-gfortran"></a>
<div class="header">
<p>
Previous: <a href="#Using-FORTRAN" accesskey="p" rel="previous">Using FORTRAN</a>, Up: <a href="#Using-FORTRAN" accesskey="u" rel="up">Using FORTRAN</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Using-gfortran-1"></a>
<h4 class="subsection">B.6.1 Using gfortran</h4>
<p><code>gfortran</code> is the F95 compiler that is part of
<code>gcc</code> 4.<var>x</var>.<var>y</var>.
</p>
<p>On Linux ‘<samp>x86_64</samp>’ systems there is an incompatibility in the
return conventions for double-complex functions between
<code>gfortran</code> and <code>g77</code> which results in the final example
in <code>example(eigen)</code> hanging or segfaulting under external
<acronym>BLAS</acronym>s built under <code>g77</code> (and also some external
LAPACKs). The commonest cases will be detected by a <code>configure</code>
test. Although <code>g77</code> is long obsolete this is still sometimes
seen with C versions of external software using <code>g77</code>
conventions.
</p>
<p>The default <code>FFLAGS</code> and <code>FCFLAGS</code> chosen (by
<code>autoconf</code>) for a <acronym>GNU</acronym> FORTRAN compiler is ‘<samp>-g
-O2</samp>’. This has caused problems (segfaults and infinite loops) on
‘<samp>x86_64</samp>’ Linux in the past, but seems fine with
<code>gfortran 4.4.4</code> and later: for <code>gfortran 4.3.x</code> set
<code>FFLAGS</code> and <code>FCFLAGS</code> to use at most ‘<samp>-O</samp>’.
</p>
<hr>
<a name="Compile-and-load-flags"></a>
<div class="header">
<p>
Previous: <a href="#Using-FORTRAN" accesskey="p" rel="previous">Using FORTRAN</a>, Up: <a href="#Configuration-on-a-Unix_002dalike" accesskey="u" rel="up">Configuration on a Unix-alike</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Compile-and-load-flags-1"></a>
<h3 class="section">B.7 Compile and load flags</h3>
<p>A wide range of flags can be set in the file <samp>config.site</samp> or as
configure variables on the command line. We have already mentioned
</p>
<dl compact="compact">
<dt><code>CPPFLAGS</code></dt>
<dd><p>header file search directory (<samp>-I</samp>) and any other miscellaneous
options for the C and C++ preprocessors and compilers
</p></dd>
<dt><code>LDFLAGS</code></dt>
<dd><p>path (<samp>-L</samp>), stripping (<samp>-s</samp>) and any other miscellaneous
options for the linker
</p></dd>
</dl>
<p>and others include
</p>
<dl compact="compact">
<dt><code>CFLAGS</code></dt>
<dd><p>debugging and optimization flags, C
</p></dd>
<dt><code>MAIN_CFLAGS</code></dt>
<dd><p>ditto, for compiling the main program
</p></dd>
<dt><code>SHLIB_CFLAGS</code></dt>
<dd><p>for shared objects
</p></dd>
<dt><code>FFLAGS</code></dt>
<dd><p>debugging and optimization flags, FORTRAN
</p></dd>
<dt><code>SAFE_FFLAGS</code></dt>
<dd><p>ditto for source files which need exact floating point behaviour
</p></dd>
<dt><code>MAIN_FFLAGS</code></dt>
<dd><p>ditto, for compiling the main program
</p></dd>
<dt><code>SHLIB_FFLAGS</code></dt>
<dd><p>for shared objects
</p></dd>
<dt><code>MAIN_LDFLAGS</code></dt>
<dd><p>additional flags for the main link
</p></dd>
<dt><code>SHLIB_LDFLAGS</code></dt>
<dd><p>additional flags for linking the shared objects
</p></dd>
<dt><code>LIBnn</code></dt>
<dd><p>the primary library directory, <samp>lib</samp> or <samp>lib64</samp>
</p></dd>
<dt><code>CPICFLAGS</code></dt>
<dd><p>special flags for compiling C code to be turned into a shared object
</p></dd>
<dt><code>FPICFLAGS</code></dt>
<dd><p>special flags for compiling Fortran code to be turned into a shared object
</p></dd>
<dt><code>CXXPICFLAGS</code></dt>
<dd><p>special flags for compiling C++ code to be turned into a shared object
</p></dd>
<dt><code>FCPICFLAGS</code></dt>
<dd><p>special flags for compiling Fortran 95 code to be turned into a shared object
</p></dd>
<dt><code>DEFS</code></dt>
<dd><p>defines to be used when compiling C code in R itself
</p></dd>
</dl>
<p>Library paths specified as <samp>-L/lib/path</samp> in <code>LDFLAGS</code> are
<a name="index-LD_005fLIBRARY_005fPATH-3"></a>
collected together and prepended to <code>LD_LIBRARY_PATH</code> (or your
system’s equivalent), so there should be no need for <samp>-R</samp> or
<samp>-rpath</samp> flags.
</p>
<p>Variables such as <code>CPICFLAGS</code> are determined where possible by
<code>configure</code>. Some systems allows two types of PIC flags, for
example ‘<samp>-fpic</samp>’ and ‘<samp>-fPIC</samp>’, and if they differ the first
allows only a limited number of symbols in a shared object. Since R
as a shared library has about 6200 symbols, if in doubt use the larger
version.
</p>
<p>To compile a profiling version of R, one might for example want to
use ‘<samp>MAIN_CFLAGS=-pg</samp>’, ‘<samp>MAIN_FFLAGS=-pg</samp>’,
‘<samp>MAIN_LDFLAGS=-pg</samp>’ on platforms where ‘<samp>-pg</samp>’ cannot be used
with position-independent code.
</p>
<p><strong>Beware</strong>: it may be necessary to set <code>CFLAGS</code> and
<code>FFLAGS</code> in ways compatible with the libraries to be used: one
possible issue is the alignment of doubles, another is the way
structures are passed.
</p>
<p>On some platforms <code>configure</code> will select additional flags for
<code>CFLAGS</code>, <code>CPPFLAGS</code>, <code>FFLAGS</code>, <code>CXXFLAGS</code> and
<code>LIBS</code> in <code>R_XTRA_CFLAGS</code> (and so on). These are for options
which are always required, for example to force <acronym>IEC</acronym> 60559
compliance.
</p>
<hr>
<a name="Platform-notes"></a>
<div class="header">
<p>
Next: <a href="#The-Windows-toolset" accesskey="n" rel="next">The Windows toolset</a>, Previous: <a href="#Configuration-on-a-Unix_002dalike" accesskey="p" rel="previous">Configuration on a Unix-alike</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Platform-notes-1"></a>
<h2 class="appendix">Appendix C Platform notes</h2>
<p>This section provides some notes on building R on different Unix-alike
platforms. These notes are based on tests run on one or two systems in
each case with particular sets of compilers and support libraries.
Success in building R depends on the proper installation and functioning
of support software; your results may differ if you have other versions
of compilers and support libraries.
</p>
<p>Older versions of this manual (for R < 2.10.0) contain notes on
platforms such as HP-UX, IRIX and Alpha/OSF1 for which we have had no
recent reports.
</p>
<p>C macros to select particular platforms can be tricky to track down
(there is a fair amount of misinformation on the Web). The Wiki
(currently) at <a href="http://sourceforge.net/p/predef/wiki/Home/">http://sourceforge.net/p/predef/wiki/Home/</a> can be
helpful. The R sources currently use
</p><div class="example">
<pre class="example">AIX: _AIX
Cygwin: __CYGWIN__
FreeBSD: __FreeBSD__
HP-UX: __hpux__, __hpux
IRIX: sgi, __sgi
Linux: __linux__
OS X: __APPLE__
NetBSD: __NetBSD__
OpenBSD: __OpenBSD__
Solaris: __sun, sun
Windows: _WIN32, _WIN64
</pre></div>
<table class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">• <a href="#X11-issues" accesskey="1">X11 issues</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Linux" accesskey="2">Linux</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#OS-X" accesskey="3">OS X</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Solaris" accesskey="4">Solaris</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#AIX" accesskey="5">AIX</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#FreeBSD" accesskey="6">FreeBSD</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Cygwin" accesskey="7">Cygwin</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#New-platforms" accesskey="8">New platforms</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
</table>
<hr>
<a name="X11-issues"></a>
<div class="header">
<p>
Next: <a href="#Linux" accesskey="n" rel="next">Linux</a>, Previous: <a href="#Platform-notes" accesskey="p" rel="previous">Platform notes</a>, Up: <a href="#Platform-notes" accesskey="u" rel="up">Platform notes</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="X11-issues-1"></a>
<h3 class="section">C.1 X11 issues</h3>
<p>The ‘<samp>X11()</samp>’ graphics device is the one started automatically on
Unix-alikes when plotting. As its name implies, it displays on a (local
or remote) X server, and relies on the services provided by the X
server.
</p>
<p>The ‘modern’ version of the ‘<samp>X11()</samp>’ device is based on ‘<samp>cairo</samp>’
graphics and (in most implementations) uses ‘<samp>fontconfig</samp>’ to pick and
render fonts. This is done on the server, and although there can be
selection issues, they are more amenable than the issues with
‘<samp>X11()</samp>’ discussed in the rest of this section.
</p>
<p>When X11 was designed, most displays were around 75dpi, whereas today
they are of the order of 100dpi or more. If you find that X11()
is reporting<a name="DOCF37" href="#FOOT37"><sup>37</sup></a> missing font sizes, especially larger ones, it is likely
that you are not using scalable fonts and have not installed the 100dpi
versions of the X11 fonts. The names and details differ by system, but
will likely have something like Fedora’s
</p><div class="example">
<pre class="example">xorg-x11-fonts-75dpi
xorg-x11-fonts-100dpi
xorg-x11-fonts-ISO8859-2-75dpi
xorg-x11-fonts-Type1
xorg-x11-fonts-cyrillic
</pre></div>
<p>and you need to ensure that the ‘<samp>-100dpi</samp>’ versions are installed
and on the X11 font path (check via <code>xset -q</code>). The
‘<samp>X11()</samp>’ device does try to set a pointsize and not a pixel size:
laptop users may find the default setting of 12 too large (although very
frequently laptop screens are set to a fictitious dpi to appear like a
scaled-down desktop screen).
</p>
<p>More complicated problems can occur in non-Western-European locales, so
if you are using one, the first thing to check is that things work in
the <code>C</code> locale. The likely issues are a failure to find any fonts
or glyphs being rendered incorrectly (often as a pair of <acronym>ASCII</acronym>
characters). X11 works by being asked for a font specification and
coming up with its idea of a close match. For text (as distinct from
the symbols used by plotmath), the specification is the first element of
the option <code>"X11fonts"</code> which defaults to
</p>
<div class="example">
<pre class="example">"-adobe-helvetica-%s-%s-*-*-%d-*-*-*-*-*-*-*"
</pre></div>
<p>If you are using a single-byte encoding, for example ISO 8859-2 in
Eastern Europe or KOI8-R in Russian, use <code>xlsfonts</code> to find an
appropriate family of fonts in your encoding (the last field in the
listing). If you find none, it is likely that you need to install
further font packages, such as ‘<samp>xorg-x11-fonts-ISO8859-2-75dpi</samp>’ and
‘<samp>xorg-x11-fonts-cyrillic</samp>’ shown in the listing above.
</p>
<p>Multi-byte encodings (most commonly UTF-8) are even more complicated.
There are few fonts in ‘<samp>iso10646-1</samp>’, the Unicode encoding, and they
only contain a subset of the available glyphs (and are often fixed-width
designed for use in terminals). In such locales <em>fontsets</em> are
used, made up of fonts encoded in other encodings. If the locale you
are using has an entry in the ‘<samp>XLC_LOCALE</samp>’ directory (typically
<samp>/usr/share/X11/locale</samp>, it is likely that all you need to do is to
pick a suitable font specification that has fonts in the encodings
specified there. If not, you may have to get hold of a suitable locale
entry for X11. This may mean that, for example, Japanese text can be
displayed when running in ‘<samp>ja_JP.UTF-8</samp>’ but not when running in
‘<samp>en_GB.UTF-8</samp>’ on the same machine (although on some systems many
UTF-8 X11 locales are aliased to ‘<samp>en_US.UTF-8</samp>’ which covers several
character sets, e.g. ISO 8859-1 (Western European), JISX0208 (Kanji),
KSC5601 (Korean), GB2312 (Chinese Han) and JISX0201 (Kana)).
</p>
<p>On some systems scalable fonts are available covering a wide range of
glyphs. One source is TrueType/OpenType fonts, and these can provide
high coverage. Another is Type 1 fonts: the URW set of Type 1 fonts
provides standard typefaces such as Helvetica with a larger coverage of
Unicode glyphs than the standard X11 bitmaps, including Cyrillic. These
are generally not part of the default install, and the X server may need
to be configured to use them. They might be under the X11 <samp>fonts</samp>
directory or elsewhere, for example,
</p>
<div class="example">
<pre class="example">/usr/share/fonts/default/Type1
/usr/share/fonts/ja/TrueType
</pre></div>
<hr>
<a name="Linux"></a>
<div class="header">
<p>
Next: <a href="#OS-X" accesskey="n" rel="next">OS X</a>, Previous: <a href="#X11-issues" accesskey="p" rel="previous">X11 issues</a>, Up: <a href="#Platform-notes" accesskey="u" rel="up">Platform notes</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Linux-1"></a>
<h3 class="section">C.2 Linux</h3>
<a name="index-Linux-1"></a>
<p>Linux is the main development platform for R, so compilation from the
sources is normally straightforward with the standard compilers.
</p>
<p>Remember that some package management systems (such as <acronym>RPM</acronym> and
deb) make a distinction between the user version of a package and the
developer version. The latter usually has the same name but with the
extension ‘<samp>-devel</samp>’ or ‘<samp>-dev</samp>’: you need both versions
installed. So please check the <code>configure</code> output to see if the
expected features are detected: if for example ‘<samp>readline</samp>’ is
missing add the developer package. (On most systems you will also need
‘<samp>ncurses</samp>’ and its developer package, although these should be
dependencies of the ‘<samp>readline</samp>’ package(s).)
</p>
<p>When R has been installed from a binary distribution there are
sometimes problems with missing components such as the FORTRAN
compiler. Searching the ‘<samp>R-help</samp>’ archives will normally reveal
what is needed.
</p>
<p>It seems that ‘<samp>ix86</samp>’ Linux accepts non-PIC code in shared
libraries, but this is not necessarily so on other platforms, in
particular on 64-bit <acronym>CPU</acronym>s such as ‘<samp>x86_64</samp>’. So care
can be needed with <acronym>BLAS</acronym> libraries and when building R as a
shared library to ensure that position-independent code is used in any
static libraries (such as the Tcl/Tk libraries, <code>libpng</code>,
<code>libjpeg</code> and <code>zlib</code>) which might be linked against.
Fortunately these are normally built as shared libraries with the
exception of the ATLAS <acronym>BLAS</acronym> libraries.
</p>
<p>The default optimization settings chosen for <code>CFLAGS</code> etc are
conservative. It is likely that using <samp>-mtune</samp> will result in
significant performance improvements on recent CPUs (especially for
‘<samp>ix86</samp>’): one possibility is to add <samp>-mtune=native</samp> for
the best possible performance on the machine on which R is being
installed: if the compilation is for a site-wide installation, it may
still be desirable to use something like
<samp>-mtume=core2</samp>.<a name="DOCF38" href="#FOOT38"><sup>38</sup></a> It is also possible to increase the
optimization levels to <samp>-O3</samp>: however for many versions of the
compilers this has caused problems in at least one <acronym>CRAN</acronym>
package.
</p>
<p>For platforms with both 64- and 32-bit support, it is likely that
</p>
<div class="example">
<pre class="example">LDFLAGS="-L/usr/local/lib64 -L/usr/local/lib"
</pre></div>
<p>is appropriate since most (but not all) software installs its 64-bit
libraries in <samp>/usr/local/lib64</samp>. To build a 32-bit version of R
on ‘<samp>x86_64</samp>’ with Fedora 18 we used
</p>
<div class="example">
<pre class="example">CC="gcc -m32"
CXX="g++ -m32"
F77="gfortran -m32"
FC=${F77}
OBJC=${CC}
LDFLAGS="-L/usr/local/lib"
LIBnn=lib
</pre></div>
<p>Note the use of ‘<samp>LIBnn</samp>’: ‘<samp>x86_64</samp>’ Fedora installs its
64-bit software in <samp>/usr/lib64</samp> and 32-bit software in
<samp>/usr/lib</samp>. Linking will skip over inappropriate binaries, but for
example the 32-bit Tcl/Tk configure scripts are in <samp>/usr/lib</samp>. It
may also be necessary to set the <code>pkg-config</code> path, e.g. by
</p>
<div class="example">
<pre class="example">export PKG_CONFIG_PATH=/usr/local/lib/pkgconfig:/usr/lib/pkgconfig
</pre></div>
<p>64-bit versions of Linux are built with support for files > 2Gb, and
32-bit versions will be if possible unless <samp>--disable-largefile</samp>
is specified.
</p>
<p>To build a 64-bit version of R on ‘<samp>ppc64</samp>’ (also known as
‘<samp>powerpc64</samp>’) with <code>gcc</code> 4.1.1, Ei-ji Nakama used
</p>
<div class="example">
<pre class="example">CC="gcc -m64"
CXX="gxx -m64"
F77="gfortran -m64"
FC="gfortran -m64"
CFLAGS="-mminimal-toc -fno-optimize-sibling-calls -g -O2"
FFLAGS="-mminimal-toc -fno-optimize-sibling-calls -g -O2"
</pre></div>
<p>the additional flags being needed to resolve problems linking against
<samp>libnmath.a</samp> and when linking R as a shared library.
</p>
<table class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">• <a href="#Clang" accesskey="1">Clang</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Intel-compilers" accesskey="2">Intel compilers</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Oracle-Solaris-Studio-compilers" accesskey="3">Oracle Solaris Studio compilers</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
</table>
<hr>
<a name="Clang"></a>
<div class="header">
<p>
Next: <a href="#Intel-compilers" accesskey="n" rel="next">Intel compilers</a>, Previous: <a href="#Linux" accesskey="p" rel="previous">Linux</a>, Up: <a href="#Linux" accesskey="u" rel="up">Linux</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Clang-1"></a>
<h4 class="subsection">C.2.1 Clang</h4>
<p>R has been built with Linux ‘<samp>ix86</samp>’ and ‘<samp>x86_64</samp>’ C and
C++ compilers (<a href="http://clang.llvm.org">http://clang.llvm.org</a>, versions 3.0, 3.2 and 3.3)
based on the Clang front-ends, invoked by <code>CC=clang CXX=clang++</code>,
together with <code>gfortran</code>. These take very similar options to
the corresponding GCC compilers.
</p>
<p>This has to be used in conjunction with a Fortran compiler: the
<code>configure</code> code will remove <samp>-lgcc</samp> from <code>FLIBS</code>,
which is needed for some versions of <code>gfortran</code>.
</p>
<hr>
<a name="Intel-compilers"></a>
<div class="header">
<p>
Next: <a href="#Oracle-Solaris-Studio-compilers" accesskey="n" rel="next">Oracle Solaris Studio compilers</a>, Previous: <a href="#Clang" accesskey="p" rel="previous">Clang</a>, Up: <a href="#Linux" accesskey="u" rel="up">Linux</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Intel-compilers-1"></a>
<h4 class="subsection">C.2.2 Intel compilers</h4>
<p>Intel compilers have been used under ‘<samp>ix86</samp>’ and ‘<samp>x86_64</samp>’
Linux. Brian Ripley used version 9.0 of the compilers for
‘<samp>x86_64</samp>’ on Fedora Core 5 with
</p>
<div class="example">
<pre class="example">CC=icc
CFLAGS="-g -O3 -wd188 -ip -mp"
F77=ifort
FLAGS="-g -O3 -mp"
CXX=icpc
CXXFLAGS="-g -O3 -mp"
FC=ifort
FCFLAGS="-g -O3 -mp"
ICC_LIBS=/opt/compilers/intel/cce/9.1.039/lib
IFC_LIBS=/opt/compilers/intel/fce/9.1.033/lib
LDFLAGS="-L$ICC_LIBS -L$IFC_LIBS -L/usr/local/lib64"
SHLIB_CXXLD=icpc
</pre></div>
<p><code>configure</code> will add ‘<samp>-c99</samp>’ to <code>CC</code> for
C99-compliance. This causes warnings with <code>icc</code> 10 and later, so
use <code>CC="icc -std=c99"</code> there. The flag <samp>-wd188</samp> suppresses
a large number of warnings about the enumeration type ‘<samp>Rboolean</samp>’.
Because the Intel C compiler sets ‘<samp>__GNUC__</samp>’ without complete
emulation of <code>gcc</code>, we suggest adding <code>CPPFLAGS=-no-gcc</code>.
</p>
<p>To maintain correct <acronym>IEC</acronym> 60559 arithmetic you most likely
need add flags to <code>CFLAGS</code>, <code>FFLAGS</code> and <code>CXXFLAGS</code> such
as <samp>-mp</samp> (shown above) or <samp>-fp-model precise -fp-model
source</samp>, depending on the compiler version.
</p>
<p>Others have reported success with versions 10.x and 11.x.
</p>
<hr>
<a name="Oracle-Solaris-Studio-compilers"></a>
<div class="header">
<p>
Previous: <a href="#Intel-compilers" accesskey="p" rel="previous">Intel compilers</a>, Up: <a href="#Linux" accesskey="u" rel="up">Linux</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Oracle-Solaris-Studio-compilers-1"></a>
<h4 class="subsection">C.2.3 Oracle Solaris Studio compilers</h4>
<p>Brian Ripley tested the Sun Studio 12 compilers, since renamed to Oracle
Solaris Studio,
(<a href="http://developers.sun.com/sunstudio/index.jsp">http://developers.sun.com/sunstudio/index.jsp</a>)
On
‘<samp>x86_64</samp>’ Linux with
</p>
<div class="example">
<pre class="example">CC=suncc
CFLAGS="-xO5 -xc99 -xlibmil -nofstore"
CPICFLAGS=-Kpic
F77=sunf95
FFLAGS="-O5 -libmil -nofstore"
FPICFLAGS=-Kpic
CXX="sunCC -library=stlport4"
CXXFLAGS="-xO5 -xlibmil -nofstore -features=tmplrefstatic"
CXXPICFLAGS=-Kpic
FC=sunf95
FCFLAGS=$FFLAGS
FCPICFLAGS=-Kpic
LDFLAGS=-L/opt/sunstudio12.1/rtlibs/amd64
SHLIB_LDFLAGS=-shared
SHLIB_CXXLDFLAGS=-G
SHLIB_FCLDFLAGS=-G
SAFE_FFLAGS="-O5 -libmil"
</pre></div>
<p><samp>-m64</samp> could be added, but was the default. Do not use
<samp>-fast</samp>: see the warnings under Solaris. (The C++ options are
also explained under Solaris.)
</p>
<p>Others have found on at least some versions of ‘<samp>ix86</samp>’ Linux that
the configure flag <samp>--disable-largefile</samp> was needed (since
<samp>glob.h</samp> on that platform presumed <code>gcc</code> was being used).
</p>
<hr>
<a name="OS-X"></a>
<div class="header">
<p>
Next: <a href="#Solaris" accesskey="n" rel="next">Solaris</a>, Previous: <a href="#Linux" accesskey="p" rel="previous">Linux</a>, Up: <a href="#Platform-notes" accesskey="u" rel="up">Platform notes</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="OS-X-2"></a>
<h3 class="section">C.3 OS X</h3>
<a name="index-OS-X-2"></a>
<p>You can build R using Apple’s ‘Command Line Tools for Xcode’ and and
suitable compilers. You will also need <code>readline</code> (or to configure
with <samp>--without-readline</samp>).
</p>
<p>You may also need to install an X sub-system (or you will need to
configure with <samp>--without-x</samp>): X is part of the standard OS X
distribution in versions prior to Mountain Lion, but not always
installed. For Mountain Lion and later, see
<a href="http://xquartz.macosforge.org/">http://xquartz.macosforge.org/</a>: some people prefer to use XQuartz
on earlier versions of OS X instead of the Apple version.
</p>
<p>In principle R can be built for 10.4.x, 10.5.x and for PowerPC Macs
but this has not been tested recently: 10.6 (Snow Leopard) is the
earliest version currently tested. 32-bit Intel builds of R 3.0.0
were tested: they would be needed for Snow Leopard running on very old
machines with Core Solo or Core Duo CPUs. The instructions here
concentrate on ‘<samp>x86_64</samp>’ builds.
</p>
<p>To use the <code>quartz()</code> graphics device you need to configure with
<samp>--with-aqua</samp> (which is the default): <code>quartz()</code> then
becomes the default device when running R at the console and X11
would only be used for the data editor/viewer. (This needs an
Objective-C compiler<a name="DOCF39" href="#FOOT39"><sup>39</sup></a> which can compile the code for <code>quartz()</code>.)
</p>
<p>Use <samp>--without-aqua</samp> if you want a standard Unix-alike build:
apart from disabling <code>quartz()</code> and the ability to use the build
with <small>R.APP</small>, it also changes the default location of the personal
library (see <code>?.libPaths()</code>). Also use
<samp>--disable-R-framework</samp> to install in the standard layout.
</p>
<p>‘Command Line Tools for Xcode’ used to be part of the Apple
Developer Tools (‘Xcode’) but nowadays need to be installed
separately. They can be downloaded from
<a href="http://developer.apple.com/devcenter/mac/">http://developer.apple.com/devcenter/mac/</a> (you will need to register
there) or if you have a recent Xcode installed (from the App Store or
from <a href="https://developer.apple.com/devcenter/mac/">https://developer.apple.com/devcenter/mac/</a>) you can install
the command-line tools from within Xcode, from the ‘<samp>Downloads</samp>’ pane
in the ‘<samp>Preferences</samp>’.
</p>
<p>Various compilers can be used. The <acronym>CRAN</acronym> distribution of R
is built using
</p>
<ul>
<li> <code>gcc</code>
from the Xcode distribution. This is a version of gcc 4.2.1 with an
LLVM backend. Note that Apple have announced that Xcode 4.6 will be the
last ‘release’ with this compiler (4.6.2 does contain it but 5 is
expected not to), and it is likely that <code>clang</code> will be used
before R 3.1.0 is released.
</li><li> <code>gfortran</code>
from
<a href="http://cran.r-project.org/bin/macosx/tools/gfortran-4.2.3.pkg">http://cran.r-project.org/bin/macosx/tools/gfortran-4.2.3.pkg</a>.
Note that this installs into <samp>/usr/local/bin</samp>, so make sure that is
on your path. Other compilers from
<a href="http://r.research.att.com/tools/">http://r.research.att.com/tools/</a> can also be used.
</li><li> <code>clang</code>
from the Xcode distribution, to compile the Objective-C parts of the
<code>quartz()</code> device.
</li></ul>
<p>To use these, have in <samp>config.site</samp> something like
</p>
<div class="example">
<pre class="example">CC="llvm-gcc-4.2"
CXX="llvm-g++-4.2"
F77="gfortran-4.2 -arch x86_64"
FC=$F77
OBJC="clang"
</pre></div>
<p>Full names are not needed, but help to ensure that the intended
compilers are used. The recommended Fortran compiler defaults to
32-bit, so <code>-arch x86_64</code> is needed. (For a 32-bit build, use
<code>-arch i386</code> for all compiler commands.)
</p>
<p>The OpenMP support in this version of <code>gcc</code> is problematic, so
the <acronym>CRAN</acronym> build is configured with <samp>--disable-openmp</samp>.
The alternative, <code>clang</code>, has no OpenMP support.
</p>
<p>Pre-compiled versions of many of the <a href="#Useful-libraries-and-programs">Useful libraries and programs</a>
are available from <a href="http://r.research.att.com/libs/">http://r.research.att.com/libs/</a>. You will
most likely want at least <code>jpeg</code>, <code>libpng</code> and <code>readline</code>
(and perhaps <code>tiff</code>). <code>pkg-config</code> is not provided by Apple
and useful for many packages.
</p>
<a name="index-BLAS-library-1"></a>
<a name="index-LAPACK-library-1"></a>
<p>The <code>Accelerate</code> library can be used <em>via</em> the configuration options
</p>
<div class="example">
<pre class="example">--with-blas="-framework Accelerate" --with-lapack
</pre></div>
<p>to provide higher-performance versions of the <acronym>BLAS</acronym> and LAPACK
routines. (Use of <code>Accelerate</code> with <samp>--with-lapack</samp> does
not work on Snow Leopard: it may work there without.)
</p>
<p>Looking at the top of
<samp>/Library/Frameworks/R.framework/Resources/etc/Makeconf</samp>
will show the compilers and configuration options used for the
<acronym>CRAN</acronym> binary package for R: at the time of writing
</p><div class="example">
<pre class="example">--with-system-zlib --enable-memory-profiling --disable-openmp
</pre></div>
<p>was used.
</p>
<p>The TeX implementation used by the developers is MacTeX
(<a href="http://www.tug.org/mactex/">http://www.tug.org/mactex/</a>): the full installation is several
gigabytes, but a smaller version (ca 300MB) is available at
<a href="http://www.tug.org/mactex/morepackages.html">http://www.tug.org/mactex/morepackages.html</a>: you will want to add
some packages, including <strong>inconsolata</strong>.
</p>
<table class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">• <a href="#Snow-Leopard" accesskey="1">Snow Leopard</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Lion" accesskey="2">Lion</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Mountain-Lion" accesskey="3">Mountain Lion</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Mavericks" accesskey="4">Mavericks</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Tcl_002fTk-headers-and-libraries" accesskey="5">Tcl/Tk headers and libraries</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Java-_0028OS-X_0029" accesskey="6">Java (OS X)</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Frameworks" accesskey="7">Frameworks</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Building-R_002eapp" accesskey="8">Building R.app</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
</table>
<hr>
<a name="Snow-Leopard"></a>
<div class="header">
<p>
Next: <a href="#Lion" accesskey="n" rel="next">Lion</a>, Previous: <a href="#OS-X" accesskey="p" rel="previous">OS X</a>, Up: <a href="#OS-X" accesskey="u" rel="up">OS X</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Snow-Leopard-1"></a>
<h4 class="subsection">C.3.1 Snow Leopard</h4>
<p>A quirk on Snow Leopard is that the X11 libraries are not in the default
linking path, so something like ‘<samp>LIBS=-L/usr/X11/lib</samp>’ may be
required in <samp>config.site</samp>, or you can use the <code>configure</code>
options <samp>--x-includes=/usr/X11/include
--x-libraries=/usr/X11/lib.</samp>.
</p>
<p>The <acronym>CRAN</acronym> binaries are built using Xcode 4.2, a version
available only to subscribing developers. It is expected that 3.2.6 (the
last public free version for Snow Leopard) will work.
</p>
<hr>
<a name="Lion"></a>
<div class="header">
<p>
Next: <a href="#Mountain-Lion" accesskey="n" rel="next">Mountain Lion</a>, Previous: <a href="#Snow-Leopard" accesskey="p" rel="previous">Snow Leopard</a>, Up: <a href="#OS-X" accesskey="u" rel="up">OS X</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Lion-1"></a>
<h4 class="subsection">C.3.2 Lion</h4>
<p>No tweaks are known to be needed on Lion. See the notes on Mountain
Lion if XQuartz is in use.
</p>
<hr>
<a name="Mountain-Lion"></a>
<div class="header">
<p>
Next: <a href="#Mavericks" accesskey="n" rel="next">Mavericks</a>, Previous: <a href="#Lion" accesskey="p" rel="previous">Lion</a>, Up: <a href="#OS-X" accesskey="u" rel="up">OS X</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Mountain-Lion-1"></a>
<h4 class="subsection">C.3.3 Mountain Lion</h4>
<p>The X11 system used with Mountain Lion is XQuartz (see above).
</p>
<p>To build the graphics devices depending on cairographics the XQuartz
path for <code>pkg-config</code> files needs to be known to
<code>pkg-config</code> when <code>configure</code> is run: this usually means
adding it to the <code>PKG_CONFIG_PATH</code> environment variable, e.g.
</p>
<div class="example">
<pre class="example">export PKG_CONFIG_PATH= \
/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr/lib/pkgconfig
</pre></div>
<p>For some pre-compiled software, for example the GTK framework,
<samp>/opt/X11/include</samp> may need to be added to the include paths.
</p>
<hr>
<a name="Mavericks"></a>
<div class="header">
<p>
Next: <a href="#Tcl_002fTk-headers-and-libraries" accesskey="n" rel="next">Tcl/Tk headers and libraries</a>, Previous: <a href="#Mountain-Lion" accesskey="p" rel="previous">Mountain Lion</a>, Up: <a href="#OS-X" accesskey="u" rel="up">OS X</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Mavericks-1"></a>
<h4 class="subsection">C.3.4 Mavericks</h4>
<p>Mavericks is associated with Xcode 5, and is said to download software
components as needed without installing all of Xcode.
</p>
<p>It is likely that <code>clang</code> will be the preferred C compiler,
using something like
</p>
<div class="example">
<pre class="example">CC="clang"
CXX="clang++"
F77="gfortran-4.2 -arch x86_64"
FC=$F77
OBJC="clang"
</pre></div>
<p>See the comments under Mountain Lion about X11 and GTK.
</p>
<hr>
<a name="Tcl_002fTk-headers-and-libraries"></a>
<div class="header">
<p>
Next: <a href="#Java-_0028OS-X_0029" accesskey="n" rel="next">Java (OS X)</a>, Previous: <a href="#Mavericks" accesskey="p" rel="previous">Mavericks</a>, Up: <a href="#OS-X" accesskey="u" rel="up">OS X</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Tcl_002fTk-headers-and-libraries-1"></a>
<h4 class="subsection">C.3.5 Tcl/Tk headers and libraries</h4>
<p>If you plan to use the <code>tcltk</code> package for R, you need to
install a distribution of Tcl/Tk. There are two alternatives. If you
use <small>R.APP</small> you will want to use X11-based Tcl/Tk (as used on other
Unix-alikes), which is installed as part of the CRAN binary for R.
This may need
</p><div class="example">
<pre class="example">--with-tcl-config=/usr/local/lib/tclConfig.sh
--with-tk-config=/usr/local/lib/tkConfig.sh
</pre></div>
<p>Note that this expects a fully-updated X11 installation: it was built
against the Apple X11 from Snow Leopard, but XQuartz will work if recent
enough (e.g. version 2.7.4).
</p>
<p>There is also a native (‘Aqua’) version of Tcl/Tk which produces widgets
in the native OS X style: this will not work with <small>R.APP</small> because of
conflicting event loops, but for those only using command-line R this
provides a much more intuitive interface to Tk for experienced Mac
users. Most versions of OS X come with Aqua Tcl/Tk libraries, but these
are not current versions of Tcl/Tk (8.5.9 in Mountain Lion). It is
better to install Tcl/Tk 8.6.x or 8.5.x from the sources or the binary
distribution at <a href="http://www.activestate.com/activetcl/downloads">http://www.activestate.com/activetcl/downloads</a>.
Configure R with
</p><div class="example">
<pre class="example">--with-tcl-config=/Library/Frameworks/Tcl.framework/tclConfig.sh
--with-tk-config=/Library/Frameworks/Tk.framework/tkConfig.sh
</pre></div>
<p>(for the versions bundled with OS X, use paths starting with
<samp>/System/Library</samp>).
</p>
<hr>
<a name="Java-_0028OS-X_0029"></a>
<div class="header">
<p>
Next: <a href="#Frameworks" accesskey="n" rel="next">Frameworks</a>, Previous: <a href="#Tcl_002fTk-headers-and-libraries" accesskey="p" rel="previous">Tcl/Tk headers and libraries</a>, Up: <a href="#OS-X" accesskey="u" rel="up">OS X</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Java"></a>
<h4 class="subsection">C.3.6 Java</h4>
<p>The situation with Java support on OS X is messy, with Apple essentially
no longer supporting Java (and what it does support is Java 6, which has
reached end-of-life). Snow Leopard and Lion shipped with a Java 6
runtime (JRE).
</p>
<p>Mountain Lion did not come with an installed JRE, and an upgrade to
Mountain Lion removed one if already installed. It is intended to be
installed at first use. Check if a JRE is installed by running
<code>java -version</code> in a <code>Terminal</code> window: if Java is not
installed this should prompt you to install it.
</p>
<p>However, for security reasons you may want/need to install the latest
Java from Oracle (currently Java 7 from
<a href="http://www.oracle.com/technetwork/java/javase/downloads/index.html">http://www.oracle.com/technetwork/java/javase/downloads/index.html</a>);
this is for Lion and later.
</p>
<p>To see what compatible versions of Java are currently installed, run
<code>/usr/libexec/java_home -V -a x86_64</code>. If needed, set the
environment variable <code>JAVA_HOME</code> to choose between these, both when
R is built from the sources and when <code>R CMD javareconf</code> is
run.
</p>
<p>Configuring and building R both looks for a JRE and for support for
compiling JNI programs (used by packages <a href="http://CRAN.R-project.org/package=rJava"><strong>rJava</strong></a> and
<a href="http://CRAN.R-project.org/package=JavaGD"><strong>JavaGD</strong></a>); the latter requires a JDK (Java SDK) and not just a
JRE.
</p>
<p>The build process tries to fathom out what JRE/JDK to use, but it may
need some help, e.g. by setting <code>JAVA_HOME</code>. The Apple JRE can be
specified explicitly by something like
</p><div class="example">
<pre class="example">JAVA_HOME=/System/Library/Frameworks/JavaVM.framework/Home
JAVA_CPPFLAGS="-I/System/Library/Frameworks/JavaVM.framework/Headers"
JAVA_LD_LIBRARY_PATH=
JAVA_LIBS="-framework JavaVM"
</pre></div>
<p>The Apple developer versions of the JDK install somewhere like
</p><div class="example">
<pre class="example">JAVA_HOME=/Library/Java/JavaVirtualMachines/1.6.0_43-b01-447.jdk/Contents/Home
</pre></div>
<p>The Oracle JDK can be specified explicitly by something like
</p><div class="example">
<pre class="example">JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.7.0_17.jdk/Contents/Home
JAVA_CPPFLAGS="-I/${JAVA_HOME}/include -I/${JAVA_HOME}/include/darwin"
JAVA_LD_LIBRARY_PATH="${JAVA_HOME}/jre/lib/server"
JAVA_LIBS="-L/${JAVA_HOME}/jre/lib/server -ljvm"
</pre></div>
<p>in <samp>config.site</samp>. <code>JAVA_LD_LIBRARY_PATH</code> is used as part of
<code>DYLD_FALLBACK_LIBRARY_PATH</code> and so is less likely to cause
conflicts, but <samp>${JAVA_HOME}/jre/lib</samp> is still best avoided as in
some JDKs it contains libraries which conflict with system libraries.
</p>
<p>Note that it is necessary to set the environment variable <code>NOAWT</code>
to <code>1</code> to install many of the Java-using packages.
</p>
<hr>
<a name="Frameworks"></a>
<div class="header">
<p>
Next: <a href="#Building-R_002eapp" accesskey="n" rel="next">Building R.app</a>, Previous: <a href="#Java-_0028OS-X_0029" accesskey="p" rel="previous">Java (OS X)</a>, Up: <a href="#OS-X" accesskey="u" rel="up">OS X</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Frameworks-1"></a>
<h4 class="subsection">C.3.7 Frameworks</h4>
<p>The <acronym>CRAN</acronym> build of R is installed as a framework, which is
selected by the default option
</p>
<div class="example">
<pre class="example">./configure --enable-R-framework
</pre></div>
<p>This is only needed if you want to build R for use with the
<small>R.APP</small> console, and implies <samp>--enable-R-shlib</samp> to build
R as a dynamic library. This option configures R to be built and
installed as a framework called <samp>R.framework</samp>. The default
installation path for <samp>R.framework</samp> is <samp>/Library/Frameworks</samp>
but this can be changed at configure time by specifying the flag
<samp>--enable-R-framework[=<var>DIR</var>]</samp> or at install time as
</p>
<div class="example">
<pre class="example">make prefix=/where/you/want/R.framework/to/go install
</pre></div>
<hr>
<a name="Building-R_002eapp"></a>
<div class="header">
<p>
Previous: <a href="#Frameworks" accesskey="p" rel="previous">Frameworks</a>, Up: <a href="#OS-X" accesskey="u" rel="up">OS X</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Building-R_002eapp-1"></a>
<h4 class="subsection">C.3.8 Building R.app</h4>
<p>Note that building the <small>R.APP</small> GUI console is a separate project, using
Xcode. Before compiling <small>R.APP</small> make sure the current version of R
is installed in <samp>/Library/Frameworks/R.framework</samp> and working at
the command-line (this can be a binary install).
</p>
<p>The current sources can be checked out by
</p><div class="example">
<pre class="example">svn co https://svn.r-project.org/R-packages/trunk/Mac-GUI
</pre></div>
<p>This can be built by loading the <code>R.xcodeproj</code> project (select the
<code>R</code> target and the <code>SnowLeopard64</code> or <code>Lion64</code>
configuration), or from the command-line by e.g.
</p><div class="example">
<pre class="example">xcodebuild -target R -configuration SnowLeopard64
</pre></div>
<p>See also the <samp>INSTALL</samp> file in the checkout or directly at <a href="https://svn.r-project.org/R-packages/trunk/Mac-GUI/INSTALL">https://svn.r-project.org/R-packages/trunk/Mac-GUI/INSTALL</a>.
</p>
<p><small>R.APP</small> does not need to be installed in any specific way. Building
<small>R.APP</small> results in the <small>R.APP</small> bundle which appears as one R icon. This
application bundle can be run anywhere and it is customary to place it
in the <em>Applications</em> folder.
</p>
<hr>
<a name="Solaris"></a>
<div class="header">
<p>
Next: <a href="#AIX" accesskey="n" rel="next">AIX</a>, Previous: <a href="#OS-X" accesskey="p" rel="previous">OS X</a>, Up: <a href="#Platform-notes" accesskey="u" rel="up">Platform notes</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Solaris-1"></a>
<h3 class="section">C.4 Solaris</h3>
<a name="index-Solaris"></a>
<p>R has been built successfully on Solaris 10 (both Sparc and
‘<samp>x86</samp>’) using the (zero cost) Oracle Solaris Studio compilers:
there has been some success with
<code>gcc</code> 4/<code>gfortran</code>. (Recent Sun machines are AMD
Opterons or Intel Xeons (‘<samp>amd64</samp>’) rather than ‘<samp>x86</samp>’, but
32-bit ‘<samp>x86</samp>’ executables are the default.)
</p>
<p>There have been few reports on Solaris 11, with no known extra issues.
Solaris 9 and earlier are now so old that it is unlikely that R is
still used with them, and they will not be considered here.
</p>
<p>The Solaris versions of several of the tools needed to build R
(e.g. <code>make</code>, <code>ar</code> and <code>ld</code>) are in
<samp>/usr/ccs/bin</samp>, so if using those tools ensure this is in your
path. A version of the preferred <acronym>GNU</acronym> <code>tar</code> is (if
installed) in <samp>/usr/sfw/bin</samp>, as sometimes are tools like
<code>makeinfo</code>. It may be necessary to avoid the tools in
<samp>/usr/ucb</samp>: POSIX-compliant versions of some tools can be found in
<samp>/usr/xpg4/bin</samp> and <samp>/usr/xpg6/bin</samp>.
</p>
<p>A large selection of Open Source software can be installed from
<a href="http://www.opencsw.org">http://www.opencsw.org</a>, by default installed under
<samp>/opt/csw</samp>.
</p>
<p>You will need <acronym>GNU</acronym> <code>libiconv</code> and <code>readline</code>: the
Solaris version of <code>iconv</code> is not sufficiently powerful.
</p>
<p>The native <code>make</code> suffices to build R but a small number of
packages require <acronym>GNU</acronym> <code>make</code> (some without good reason
and without declaring it as ‘<samp>SystemRequirements</samp>’ in the
<samp>DESCRIPTION</samp> file).
</p>
<p>Some people have reported that the Solaris <code>libintl</code> needs to be
avoided, for example by using <samp>--disable-nls</samp> or
<samp>--with-included-gettext</samp> or using <code>libintl</code> from OpenCSW.
</p>
<p>The support for the C99 <code>long double</code> type on Sparc hardware uses
quad-precision arithmetic, and this is usually slow because it is done
by software emulation. On such systems <code>configure</code> option
<samp>--disable-long-double</samp> can be used for faster but less accurate
computations.
</p>
<p>When using the Oracle compilers<a name="DOCF40" href="#FOOT40"><sup>40</sup></a> do <em>not</em> specify <samp>-fast</samp>, as this
disables <acronym>IEEE</acronym> arithmetic and <code>make check</code> will fail.
</p>
<p>A little juggling of paths was needed to ensure <acronym>GNU</acronym>
<code>libiconv</code> (in <samp>/usr/local</samp>) was used rather than the Solaris
<code>iconv</code>:
</p>
<div class="example">
<pre class="example">CC="cc -xc99"
CFLAGS="-O -xlibmieee"
F77=f95
FFLAGS=-O
CXX="CC -library=stlport4"
CXXFLAGS=-O
FC=f95
FCFLAGS=$FFLAGS
FCLIBS="-lfai -lfsu"
R_LD_LIBRARY_PATH="/usr/local/lib:/opt/csw/gcc4/lib:/opt/csw/lib"
</pre></div>
<p>For a 64-bit target add <samp>-m64</samp> to the compiler macros
and use something like <code>LDFLAGS=-L/usr/local/lib/sparcv9</code> or
<code>LDFLAGS=-L/usr/local/lib/amd64</code> as appropriate.
It will also be necessary to point <code>pkg-config</code> at the 64-bit
directories, e.g. one of
</p>
<div class="example">
<pre class="example">PKG_CONFIG_PATH=/opt/csw/lib/amd64/pkgconfig:/usr/lib/amd64/pkgconfig
PKG_CONFIG_PATH=/opt/csw/lib/sparcv9/pkgconfig:/usr/lib/sparcv9/pkgconfig
</pre></div>
<p>and to specify a 64-bit Java VM by e.g.
</p>
<div class="example">
<pre class="example">JAVA_CPPFLAGS="-I${JAVA_HOME}/../include -I${JAVA_HOME}/../include/solaris"
JAVA_LD_LIBRARY_PATH=${JAVA_HOME}/lib/amd64/server
JAVA_LIBS="-L${JAVA_HOME}/lib/amd64/server \
-R${JAVA_HOME}/lib/amd64/server -ljvm"
</pre></div>
<p>With Solaris Studio 12.[23] on Sparc, <code>FCLIBS</code> needs to be
</p>
<div class="example">
<pre class="example">FCLIBS="-lfai -lfai2 -lfsu"
</pre></div>
<p>(and possibly other Fortran libraries, but this suffices for the
packages currently on CRAN).
</p>
<p>Currently ‘<samp>amd64</samp>’ and ‘<samp>sparcv9</samp>’ builds work
out-of-the-box with Sun Studio 12u1 but not Solaris Studio 12.2 and
later: <samp>libRblas.so</samp> and <samp>lapack.so</samp> are generated with code
that causes relocation errors (which is being linked in from the Fortran
libraries). This means that building R as a shared library may be
impossible with Solaris Studio >= 12.2. For a standard build the trick
seems to be to manually set <code>FLIBS</code> to avoid the troublesome
libraries. For example, on ‘<samp>amd64</samp>’ set in <samp>config.site</samp>
something like
</p>
<div class="example">
<pre class="example">FLIBS_IN_SO="-R/opt/solarisstudio12.3/lib/amd64
/opt/solarisstudio12.3/lib/amd64/libfui.so
/opt/solarisstudio12.3/lib/amd64/libfsu.so"
</pre></div>
<p>For 64-bit Sparc, set in <samp>config.site</samp> something like
</p><div class="example">
<pre class="example">FLIBS="-R/opt/solarisstudio12.3/prod/lib/sparc/64
-lifai -lsunimath -lfai -lfai2 -lfsumai -lfprodai -lfminlai -lfmaxlai
-lfminvai -lfmaxvai -lfui -lsunmath -lmtsk
/opt/solarisstudio12.3/prod/lib/sparc/64/libfsu.so.1"
</pre></div>
<p>By default the Solaris Studio compilers do not by default conform to the C99
standard (appendix F 8.9) on the return values of functions such as
<code>log</code>: use <samp>-xlibmieee</samp> to ensure this.
</p>
<p>You can target specific Sparc architectures for (slightly) higher
performance: <samp>-xtarget=native</samp> (in <code>CFLAGS</code> etc) tunes the
compilation to the current machine.
</p>
<p>Using <code>-xlibmil</code> in <code>CFLAGS</code> and <code>-xlibmil</code> in
<code>FFLAGS</code> allows more system mathematical functions to be inlined.
</p>
<p>On ‘<samp>x86</samp>’ you will get marginally higher performance <em>via</em>
</p>
<div class="example">
<pre class="example">CFLAGS="-xO5 -xc99 -xlibmieee -xlibmil -nofstore -xtarget=native"
FFLAGS="-O5 -libmil -nofstore -xtarget=native"
CXXFLAGS="-xO5 -xlibmil -nofstore -xtarget=native"
SAFE_FFLAGS="-libmil -fstore -xtarget=native"
</pre></div>
<p>but the use of <code>-nofstore</code> can be less numerically stable, and some
packages (notably <a href="http://CRAN.R-project.org/package=mgcv"><strong>mgcv</strong></a> on ‘<samp>x86</samp>’) failed to compile at
higher optimization levels with version 12.3.
</p>
<p>The Solaris Studio compilers provide several implementations of the C++
standard which select both the set of headers and a C++ runtime library.
These are selected by the <samp>-library</samp> flag, which as it is needed
for both compiling and linking is best specified as part of the
compiler. The examples above use ‘<samp>stlport4</samp>’, currently the most
modern of the options: the default (but still needed to be specified as
it is needed for linking) is ‘<samp>Cstd</samp>’: see
<a href="http://developers.sun.com/solaris/articles/cmp_stlport_libCstd.html">http://developers.sun.com/solaris/articles/cmp_stlport_libCstd.html</a>.
Note though that most external Solaris C++ libraries will have been
built with ‘<samp>Cstd</samp>’ and so an R package using such libraries also
needs to be. Occasionally the flag <samp>-library=stlport4,Crun</samp> has
been needed.
</p>
<p>Several <acronym>CRAN</acronym> packages using C++ need the more liberal interpretation
given by adding
</p>
<div class="example">
<pre class="example">CXXFLAGS="-features=tmplrefstatic"
</pre></div>
<a name="index-BLAS-library-2"></a>
<a name="index-LAPACK-library-2"></a>
<p>The performance library <code>sunperf</code> is available for use with the
Solaris Studio compilers. If selected as a <acronym>BLAS</acronym>, it must also
be selected as LAPACK <em>via</em> (for Solaris Studio 12.2)
</p>
<div class="example">
<pre class="example">./configure --with-blas='-library=sunperf' --with-lapack
</pre></div>
<p>This has often given test failures in the past, in several different
places. At the time of writing it fails in <samp>tests/reg-BLAS.R</samp>, and on
some builds, including for ‘<samp>amd64</samp>’, it fails in
<code>example(eigen)</code>.
</p>
<p>Parsing very complex expressions needs a lot of stack space when the
Oracle compilers are used: several packages require the stack increased
to say 20MB.
</p>
<table class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">• <a href="#Using-gcc" accesskey="1">Using gcc</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
</table>
<hr>
<a name="Using-gcc"></a>
<div class="header">
<p>
Previous: <a href="#Solaris" accesskey="p" rel="previous">Solaris</a>, Up: <a href="#Solaris" accesskey="u" rel="up">Solaris</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Using-gcc-1"></a>
<h4 class="subsection">C.4.1 Using gcc</h4>
<p>If using <code>gcc</code>, ensure that the compiler was compiled for the
version of Solaris in use. (This can be ascertained from <code>gcc
-v</code>.) <code>gcc</code> makes modified versions of some header files, and
several reports of problems were due to using <code>gcc</code> compiled on
one version of Solaris on a later version.
</p>
<p>The notes here are for <code>gcc</code> set up to use the Solaris linker:
it can also be set up to use GNU <code>ld</code>, but that has not been
tested.
</p>
<p>Compilation for a 32-bit Sparc target with <code>gcc</code> 4.8.1
needed
</p>
<div class="example">
<pre class="example">CPPFLAGS=-I/opt/csw/include
LDFLAGS="-L/opt/csw/gcc4/lib -L/opt/csw/lib"
</pre></div>
<p>and for a 64-bit Sparc target
</p><div class="example">
<pre class="example">CC="gcc -m64"
F77="gfortran -m64"
CXX="g++ -m64"
FC=$F77
CPPFLAGS=-I/opt/csw/include
LDFLAGS="-L/opt/csw/gcc4/lib/sparcv9 -L/opt/csw/lib/sparcv9"
</pre></div>
<p>Note that paths such as <samp>/opt/csw/gcc4/lib/sparcv9</samp> may need to
be in the
<a name="index-LD_005fLIBRARY_005fPATH-4"></a>
<code>LD_LIBRARY_PATH</code> during configuration.
</p>
<p>The compilation can be tuned to a particular cpu: the <acronym>CRAN</acronym>
check system uses <code>-mtune=niagara2</code>.
</p>
<p>Compilation for an ‘<samp>x86</samp>’ target with <code>gcc</code> 4.8.1
needed
</p>
<div class="example">
<pre class="example">CC="/opt/csw/gcc4/bin/gcc -m32"
CPPFLAGS="-I/opt/csw/include -I/usr/local/include"
F77="/opt/csw/gcc4/bin/gfortran -m32"
CXX="/opt/csw/gcc4/bin/g++ -m32"
FC="/opt/csw/gcc4/bin/gfortran -m32"
LDFLAGS="-L/opt/csw/gcc4/lib -L/opt/csw/lib -L/usr/local/lib"
</pre></div>
<p>(<code>-L/opt/csw/lib</code> is needed since TeXLive was built using
32-bit <code>gcc</code>, and we need <samp>/opt/csw/lib</samp> in
<code>R_LD_LIBRARY_PATH</code>.)
</p>
<p>For an ‘<samp>amd64</samp>’ target with <code>gcc</code> 4.8.1
we used
</p>
<div class="example">
<pre class="example">CC="/opt/csw/gcc4/bin/gcc -m64"
CPPFLAGS="-I/opt/csw/include -I/usr/local/include"
F77="/opt/csw/gcc4/bin/gfortran -m64"
FPICFLAGS=-fPIC
CXX="/opt/csw/gcc4/bin/g++ -m64"
FC=$F77
FCPICFLAGS=$FPICFLAGS
LDFLAGS="-L/opt/csw/gcc4/lib/amd64 -L/opt/csw/lib/amd64"
</pre></div>
<hr>
<a name="AIX"></a>
<div class="header">
<p>
Next: <a href="#FreeBSD" accesskey="n" rel="next">FreeBSD</a>, Previous: <a href="#Solaris" accesskey="p" rel="previous">Solaris</a>, Up: <a href="#Platform-notes" accesskey="u" rel="up">Platform notes</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="AIX-1"></a>
<h3 class="section">C.5 AIX</h3>
<a name="index-AIX"></a>
<p>We no longer support AIX prior to 4.2, and <code>configure</code> will
throw an error on such systems.
</p>
<p>Ei-ji Nakama was able to build under AIX 5.2 on ‘<samp>powerpc</samp>’ with
GCC 4.0.3 in several configurations. 32-bit versions could be
configured with <samp>--without-iconv</samp> as well as
<samp>--enable-R-shlib</samp>. For 64-bit versions he used
</p>
<div class="example">
<pre class="example">OBJECT_MODE=64
CC="gcc -maix64"
CXX="g++ -maix64"
F77="gfortran -maix64"
FC="gfortran -maix64"
</pre></div>
<p>and was also able to build with the IBM <code>xlc</code> and Hitachi
<code>f90</code> compilers by
</p>
<div class="example">
<pre class="example">OBJECT_MODE=64
CC="xlc -q64"
CXX="g++ -maix64"
F77="f90 -cpu=pwr4 -hf77 -parallel=0 -i,L -O3 -64"
FC="f90 -cpu=pwr4 -hf77 -parallel=0 -i,L -O3 -64"
FLIBS="-L/opt/ofort90/lib -lhf90vecmath -lhf90math -lf90"
</pre></div>
<p>Some systems have <code>f95</code> as an IBM compiler that does not by
default accept FORTRAN 77. It needs the flag <samp>-qfixed=72</samp>, or to
be invoked as <code>xlf_r</code>.
</p>
<p>The AIX native <code>iconv</code> does not support encodings ‘<samp>latin1</samp>’ nor
‘<samp>""</samp>’ and so cannot be used. (As far as we know <acronym>GNU</acronym>
<code>libiconv</code> could be installed.)
</p>
<p>Fan Long reports success on AIX 5.3 using
</p>
<div class="example">
<pre class="example">OBJECT_MODE=64
LIBICONV=<var>/where/libiconv/installed</var>
CC="xlc_r -q64"
CFLAGS="-O -qstrict"
CXX="xlC_r -q64"
CXXFLAGS="-O -qstrict"
F77="xlf_r -q64"
AR="ar -X64"
CPPFLAGS="-I$LIBICONV/include -I/usr/lpp/X11/include/X11"
LDFLAGS="-L$LIBICONV/lib -L/usr/lib -L/usr/X11R6/lib"
</pre></div>
<a name="index-R_005fSHELL"></a>
<p>On one AIX 6.x system it was necessary to use <code>R_SHELL</code> to set the
default shell to be Bash rather than Zsh.
</p>
<p>Kurt Hornik and Stefan Theussl at WU (Wirtschaftsuniversität Wien)
successfully built R on a ‘<samp>powerpc</samp>’ (8-<acronym>CPU</acronym> Power6
system) running AIX 6.1, configuring with or without
<samp>--enable-R-shlib</samp> (Ei-ji Nakama’s support is gratefully
acknowledged).
</p>
<p>It helps to describe the WU build environment first. A small part of
the software needed to build R and/or install packages is available
directly from the AIX Installation DVDs, e.g., Java 6, X11, and Perl.
Additional open source software (OSS) is packaged for AIX in <samp>.rpm</samp>
files and available from both IBM’s “AIX Toolbox for Linux
Applications”
(<a href="http://www-03.ibm.com/systems/power/software/aix/linux/">http://www-03.ibm.com/systems/power/software/aix/linux/</a>) and
<a href="http://www.oss4aix.org/download/">http://www.oss4aix.org/download/</a>. The latter website typically
offers more recent versions of the available OSS. All tools needed and
libraries downloaded from these repositories (e.g., GCC, Make,
<code>libreadline</code>, etc.) are typically installed to
<samp>/opt/freeware</samp>, hence corresponding executables are found in
<a name="index-PATH-2"></a>
<samp>/opt/freeware/bin</samp> which thus needs to be in <code>PATH</code> for using
these tools. As on other Unix systems one needs <acronym>GNU</acronym>
<code>libiconv</code> as the AIX version of iconv is not sufficiently
powerful. Additionally, for proper Unicode compatibility one should
install the corresponding package from the ICU project
(<a href="http://www.icu-project.org/download/">http://www.icu-project.org/download/</a>), which offers pre-compiled
binaries for various platforms which in case of AIX can be installed via
unpacking the tarball to the root file system. For full LaTeX
support one can install the TeX Live DVD distribution
(<a href="http://www.tug.org/texlive/">http://www.tug.org/texlive/</a>): it is recommended to update the
distribution using the <code>tlmgr</code> update manager. For 64-bit R builds
supporting Tcl/Tk this needs to installed from the sources as available
pre-compiled binaries supply only 32-bit shared objects.
</p>
<p>The recent WU testing was done using compilers from both the
<acronym>GNU</acronym> Compiler Collection (version 4.2.4) which is available
from one of the above OSS repositories, and the IBM C/C++ (XL C/C++
10.01) as well as FORTRAN (XL Fortran 12.01) compilers
(<a href="http://www14.software.ibm.com/webapp/download/byproduct.jsp#X">http://www14.software.ibm.com/webapp/download/byproduct.jsp#X</a>).
</p>
<p>To compile for a 64-bit ‘<samp>powerpc</samp>’ (Power6 <acronym>CPU</acronym>) target
one can use
</p>
<div class="example">
<pre class="example">CC ="gcc -maix64 -pthread"
CXX="g++ -maix64 -pthread"
FC="gfortran -maix64 -pthread"
F77="gfortran -maix64 -pthread"
CFLAGS="-O2 -g -mcpu=power6"
FFLAGS="-O2 -g -mcpu=power6"
FCFLAGS="-O2 -g -mcpu=power6"
</pre></div>
<p>for the GCC and
</p>
<div class="example">
<pre class="example">CC=xlc
CXX=xlc++
FC=xlf
F77=xlf
CFLAGS="-qarch=auto -qcache=auto -qtune=auto -O3 -qstrict -ma"
FFLAGS="-qarch=auto -qcache=auto -qtune=auto -O3 -qstrict"
FCFLAGS="-qarch=auto -qcache=auto -qtune=auto -O3 -qstrict"
CXXFLAGS="-qarch=auto -qcache=auto -qtune=auto -O3 -qstrict"
</pre></div>
<p>for the IBM XL compilers. For the latter, it is important to note that
the decision for generating 32-bit or 64-bit code is done by setting the
<a name="index-OBJECT_005fMODE"></a>
<code>OBJECT_MODE</code> environment variable appropriately (recommended) or
using an additional compiler flag (<samp>-q32</samp> or <samp>-q64</samp>). By
default the IBM XL compilers produce 32 bit code. Thus, to build R with
64-bit support one needs to either export <code>OBJECT_MODE=64</code> in the
environment or, alternatively, use the <samp>-q64</samp> compiler options.
</p>
<p>It is strongly recommended to install Bash and use it as the configure
shell, e.g., via setting <code>CONFIG_SHELL=/usr/bin/bash</code> in the
environment, and to use <acronym>GNU</acronym> Make (e.g., via
(<code>MAKE=/opt/freeware/bin/make</code>).
</p>
<p>Further installation instructions to set up a proper R development
environment can be found in the “R on AIX” project on R-Forge
(<a href="http://R-Forge.R-project.org/projects/aix/">http://R-Forge.R-project.org/projects/aix/</a>).
</p>
<hr>
<a name="FreeBSD"></a>
<div class="header">
<p>
Next: <a href="#Cygwin" accesskey="n" rel="next">Cygwin</a>, Previous: <a href="#AIX" accesskey="p" rel="previous">AIX</a>, Up: <a href="#Platform-notes" accesskey="u" rel="up">Platform notes</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="FreeBSD-1"></a>
<h3 class="section">C.6 FreeBSD</h3>
<a name="index-FreeBSD"></a>
<p>The reports here were for R 2.15.x.
</p>
<p>Rainer Hurling has reported success on ‘<samp>amd64</samp>’ FreeBSD 9.0 (and
on earlier versions in the past), and Brian Ripley tested
‘<samp>amd64</samp>’ FreeBSD 8.2. Since Darwin (the base OS of OS X) is
based on FreeBSD we find testing on Darwin tends to pick up most
potential problems on FreeBSD. However, FreeBSD lacks adequate
character type (e.g. which are alphabetic) and collation support for
multi-byte locales (but a port of ICU is available), and does not yet
implement C99 complex math functions (for which R’s substitutes are
used).
</p>
<p>The native BSD <code>make</code> suffices to build R but a number of
packages require <acronym>GNU</acronym> <code>make</code>, despite the
recommendations of the “Writing R Extensions” manual.
</p>
<p>The simplest way to get the additional software needed to build R is
to install a pre-compiled version first, e.g. by
</p>
<div class="example">
<pre class="example">pkg_add -r R
</pre></div>
<p>(on the system this was tested on, this installed Tcl, Tk, blas, lapack
and <code>gcc-4.6.2</code> which includes <code>gfortran46</code>). A listing of
dependencies (not necessarily for current R) can be found at
<a href="http://www.freebsd.org/ports/lang.html">http://www.freebsd.org/ports/lang.html</a>: you will however also
need a TeX system<a name="DOCF41" href="#FOOT41"><sup>41</sup></a> to build the
manuals.
</p>
<p>Then R itself can be built by something like
</p>
<div class="example">
<pre class="example">./configure CC=gcc46 F77=gfortran46 CXX=g++46 FC=gfortran46
</pre></div>
<p>There are also FreeBSD packages for a small eclectic collection of
<acronym>CRAN</acronym> packages.
</p>
<p>Beware that the lack of adequate support for non-<acronym>ASCII</acronym>
characters in UTF-8 locales has many consequences in R: for example
names will not be recognized as alphabetic by <code>make.names</code>.
</p>
<hr>
<a name="Cygwin"></a>
<div class="header">
<p>
Next: <a href="#New-platforms" accesskey="n" rel="next">New platforms</a>, Previous: <a href="#FreeBSD" accesskey="p" rel="previous">FreeBSD</a>, Up: <a href="#Platform-notes" accesskey="u" rel="up">Platform notes</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Cygwin-1"></a>
<h3 class="section">C.7 Cygwin</h3>
<p>The Cygwin emulation layer on Windows can be treated as a Unix-alike OS.
This is unsupported, but experiments have been conducted and a few
workarounds added. R requires C99 complex type support, which is
available as from Cygwin 1.7.8 (March 2011). However, the (new)
implementation of <code>cacos</code> gives incorrect results, so we undefine
<code>HAVE_CACOS</code> in <samp>src/main/complex.c</samp> on that platform.
</p>
<p>Many versions of Cygwin during 2011 were unable to build R: 1.7.9-1
with <acronym>GCC</acronym> 4.5.3-3 in November 2011 was able to do so. Cygwin
has not been tested for R 3.0.0 or later.
</p>
<p>Only building as a shared library can possibly work,<a name="DOCF42" href="#FOOT42"><sup>42</sup></a> so use e.g
</p>
<div class="example">
<pre class="example">./configure --disable-nls --enable-R-shlib FLIBS=-lgfortran
make
</pre></div>
<p>Enabling NLS does work if required, although adding
<samp>--with-included-gettext</samp> is preferable. You will see many
warnings about the use of auto-import. Setting ‘<samp>FLIBS</samp>’ explicitly
seems needed currently as the auto-detection gives an incorrect value.
</p>
<p>You will need the <strong>tetex-extra</strong> Cygwin package to build
<samp>NEWS.pdf</samp> and the vignettes.
</p>
<p>Note that this gives you a command-line application using <code>readline</code>
for command editing. The ‘<samp>X11</samp>’ graphics device will work if a
suitable X server is running, and the standard Unix-alike ways of
installing source packages work. There was a bug in the
<samp>/usr/lib/tkConfig.sh</samp> script in the version we looked at, which
needs to have
</p>
<div class="example">
<pre class="example">TK_LIB_SPEC='-ltk84'
</pre></div>
<p>The overhead of using shell scripts makes this noticeably slower than a
native build of R on Windows.
</p>
<p>Even when R can be built, not all the tests passed: there were
incorrect results from wide-character regular expressions code and from
sourcing CR-delimited files.
</p>
<p>Do not use Cygwin’s BLAS library: it is known to give incorrect results.
</p>
<hr>
<a name="New-platforms"></a>
<div class="header">
<p>
Previous: <a href="#Cygwin" accesskey="p" rel="previous">Cygwin</a>, Up: <a href="#Platform-notes" accesskey="u" rel="up">Platform notes</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="New-platforms-1"></a>
<h3 class="section">C.8 New platforms</h3>
<p>There are a number of sources of problems when installing R on a new
hardware/OS platform. These include
</p>
<p><strong>Floating Point Arithmetic</strong>: R requires arithmetic compliant
with <acronym>IEC</acronym> 60559, also known as <acronym>IEEE</acronym> 754.
This mandates the use of plus and minus infinity and <code>NaN</code> (not a
number) as well as specific details of rounding. Although almost all
current FPUs can support this, selecting such support can be a pain.
The problem is that there is no agreement on how to set the signalling
behaviour; Sun/Sparc, SGI/IRIX and ‘<samp>ix86</samp>’ Linux require no
special action, FreeBSD requires a call to (the macro)
<code>fpsetmask(0)</code> and OSF1 required that computation be done with a
<samp>-ieee_with_inexact</samp> flag etc. On a new platform you must find
out the magic recipe and add some code to make it work. This can often
be done via the file <samp>config.site</samp> which resides in the top level
directory.
</p>
<p>Beware of using high levels of optimization, at least initially. On
many compilers these reduce the degree of compliance to the
<acronym>IEEE</acronym> model. For example, using <samp>-fast</samp> on the Solaris
Studio compilers has caused R’s <code>NaN</code> to be set incorrectly, and
<code>gcc</code>’s <samp>-ffast-math</samp> has given incorrect results.
</p>
<p><strong>Shared Objects</strong>: There seems to be very little agreement
across platforms on what needs to be done to build shared objects.
there are many different combinations of flags for the compilers and
loaders. <acronym>GNU</acronym> libtool cannot be used (yet), as it currently
does not fully support FORTRAN: one would need a shell wrapper for
this). The technique we use is to first interrogate the X window system
about what it does (using <code>xmkmf</code>), and then override this in
situations where we know better (for tools from the <acronym>GNU</acronym>
Compiler Collection and/or platforms we know about). This typically
works, but you may have to manually override the results. Scanning the
manual entries for <code>cc</code> and <code>ld</code> usually reveals the
correct incantation. Once you know the recipe you can modify the file
<samp>config.site</samp> (following the instructions therein) so that the
build will use these options.
</p>
<p>It seems that <code>gcc</code> 3.4.x and later on ‘<samp>ix86</samp>’ Linux
defeat attempts by the LAPACK code to avoid computations entirely in
extended-precision registers, so file <samp>src/modules/lapack/dlamc.f</samp>
may need to be compiled without optimization. Set the configure
variable <code>SAFE_FFLAGS</code> to the flags to be used for this file. If
configure detects <acronym>GNU</acronym> FORTRAN it adds flag
<samp>-ffloat-store</samp> to <code>FFLAGS</code>. (Other settings are needed when
using <code>icc</code> on ‘<samp>ix86</samp>’ Linux, for example. Using
<samp>-mpc64</samp> is preferable on more recent GCC compilers.)
</p>
<p>If you do manage to get R running on a new platform please let us
know about it so we can modify the configuration procedures to include
that platform.
</p>
<p>If you are having trouble getting R to work on your platform please
feel free to use the ‘<samp>R-devel</samp>’ mailing list to ask questions. We
have had a fair amount of practice at porting R to new platforms
<small class="enddots">...</small>
</p>
<hr>
<a name="The-Windows-toolset"></a>
<div class="header">
<p>
Next: <a href="#Function-and-variable-index" accesskey="n" rel="next">Function and variable index</a>, Previous: <a href="#Platform-notes" accesskey="p" rel="previous">Platform notes</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="The-Windows-toolset-1"></a>
<h2 class="appendix">Appendix D The Windows toolset</h2>
<p>If you want to build R or add-on packages from source in Windows, you
will need to collect, install and test an extensive set of tools. See
<a href="http://CRAN.R-project.org/bin/windows/Rtools/">http://CRAN.R-project.org/bin/windows/Rtools/</a> for the current
locations and other updates to these instructions. (Most Windows users
will not need to build add-on packages from source; see <a href="#Add_002don-packages">Add-on packages</a> for details.)
</p>
<p>We have found that the build process for R is quite sensitive to
the choice of tools: please follow our instructions <strong>exactly</strong>,
even to the choice of particular versions of the tools.<a name="DOCF43" href="#FOOT43"><sup>43</sup></a> The build process for add-on packages is somewhat more
forgiving, but we recommend using the exact toolset at first, and only
substituting other tools once you are familiar with the process.
</p>
<p><em>This appendix contains a lot of prescriptive comments. They are
here as a result of bitter experience. Please do not report problems to
the R mailing lists unless you have followed all the prescriptions.</em>
</p>
<p>We have collected most of the necessary tools (unfortunately not all,
due to license or size limitations) into an executable installer
named<a name="DOCF44" href="#FOOT44"><sup>44</sup></a> <samp>Rtools30.exe</samp>,
available from <a href="http://CRAN.R-project.org/bin/windows/Rtools/">http://CRAN.R-project.org/bin/windows/Rtools/</a>. You
should download and run it, choosing the default “Package authoring
installation” to build add-on packages, or the “full installation” if
you intend to build R.
</p>
<p>You will need the following items to build R and packages.
See the subsections below for detailed descriptions.
</p><ul>
<li> The command line tools (in <samp>Rtools*.exe</samp>)
</li><li> The MinGW-w64 32/64-bit toolchain to compile C, Fortran and C++.
</li></ul>
<p>For installing simple source packages containing data or R source but
no compiled code, none of these are needed. Perl is no longer needed to
build R nor to install nor develop source packages.
</p>
<p>A complete build of R including PDF manuals, and producing the
installer will also need the following:
</p><ul>
<li> LaTeX
</li><li> The Inno Setup installer
</li><li> (optional) <code>qpdf</code>
</li></ul>
<a name="index-PATH-3"></a>
<p>It is important to set your <code>PATH</code> properly. The installer
<samp>Rtools*.exe</samp> optionally sets the path to components that it
installs.
</p>
<p>Your <code>PATH</code> may include <samp>.</samp> first, then the <samp>bin</samp>
directories of the tools, the compiler toolchain and LaTeX. Do not
use filepaths containing spaces: you can always use the short forms
(found by <code>dir /x</code> at the Windows command line). Network shares
(with paths starting <code>\\</code>) are not supported.
</p>
<p>For example for a 32-bit build, all on one line,
</p>
<div class="example">
<pre class="example">PATH=c:\Rtools\bin;c:\Rtools\gcc-4.6.3\bin;c:\MiKTeX\miktex\bin;
c:\R\R-3.0\bin\i386;c:\windows;c:\windows\system32
</pre></div>
<p>It is essential that the directory containing the command line tools
comes first or second in the path: there are typically like-named
tools<a name="DOCF45" href="#FOOT45"><sup>45</sup></a> in other directories, and they will <strong>not</strong>
work. The ordering of the other directories is less important, but if in
doubt, use the order above.
</p>
<p>Our toolset contains copies of Cygwin DLLs that may conflict with other
ones on your system if both are in the path at once. The normal
recommendation is to delete the older ones; however, at one time we
found our tools did not work with a newer version of the Cygwin DLLs, so
it may be safest not to have any other version of the Cygwin DLLs in your
path.
</p>
<table class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">• <a href="#LaTeX" accesskey="1">LaTeX</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#The-Inno-Setup-installer" accesskey="2">The Inno Setup installer</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#The-command-line-tools" accesskey="3">The command line tools</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#The-MinGW_002dw64-toolchain" accesskey="4">The MinGW-w64 toolchain</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">• <a href="#Useful-additional-programs" accesskey="5">Useful additional programs</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
</table>
<hr>
<a name="LaTeX"></a>
<div class="header">
<p>
Next: <a href="#The-Inno-Setup-installer" accesskey="n" rel="next">The Inno Setup installer</a>, Previous: <a href="#The-Windows-toolset" accesskey="p" rel="previous">The Windows toolset</a>, Up: <a href="#The-Windows-toolset" accesskey="u" rel="up">The Windows toolset</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="LaTeX-1"></a>
<h3 class="section">D.1 LaTeX</h3>
<p>The ‘<samp>MiKTeX</samp>’ (<a href="http://www.miktex.org/">http://www.miktex.org/</a>) distribution of
LaTeX includes a suitable port of <code>pdftex</code>. The ‘basic’ version
of ‘<samp>MiKTeX</samp>’ almost suffices (the <strong>grid</strong> vignettes need
<samp>fancyvrb.sty</samp>), but it will install the 15Mb ‘<samp>lm</samp>’ package if
allowed to (although that is not actually used). The <samp>Rtools*.exe</samp>
installer does <em>not</em> include any version of LaTeX.
</p>
<p>It is also possible to use the TeXLive distribution from
<a href="http://www.tug.org/texlive/">http://www.tug.org/texlive/</a>.
</p>
<a name="index-R_005fRD4PDF-2"></a>
<p>Please read <a href="#Making-the-manuals">Making the manuals</a> about how to make <samp>fullrefman.pdf</samp>
and set the environment variable <code>R_RD4PDF</code> suitably; ensure you
have the required fonts installed or that ‘<samp>MiKTeX</samp>’ is set up to
install LaTeX packages on first use. (In any case ensure that the
<strong>inconsolata</strong> package is installed—you can check with the MiKTeX
Package Manager.)
</p>
<hr>
<a name="The-Inno-Setup-installer"></a>
<div class="header">
<p>
Next: <a href="#The-command-line-tools" accesskey="n" rel="next">The command line tools</a>, Previous: <a href="#LaTeX" accesskey="p" rel="previous">LaTeX</a>, Up: <a href="#The-Windows-toolset" accesskey="u" rel="up">The Windows toolset</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="The-Inno-Setup-installer-1"></a>
<h3 class="section">D.2 The Inno Setup installer</h3>
<p>To make the installer package (<samp>R-3.0.2-win.exe</samp>) we
currently require the Unicode version of Inno Setup 5.3.7 or later from
<a href="http://jrsoftware.org/">http://jrsoftware.org/</a>. This is <em>not</em> included in
<samp>Rtools*.exe</samp>.
</p>
<p>Copy file <samp>src/gnuwin32/MkRules.dist</samp> to
<samp>src/gnuwin32/MkRules.local</samp> and edit it to set <code>ISDIR</code> to the
location where Inno Setup was installed.
</p>
<hr>
<a name="The-command-line-tools"></a>
<div class="header">
<p>
Next: <a href="#The-MinGW_002dw64-toolchain" accesskey="n" rel="next">The MinGW-w64 toolchain</a>, Previous: <a href="#The-Inno-Setup-installer" accesskey="p" rel="previous">The Inno Setup installer</a>, Up: <a href="#The-Windows-toolset" accesskey="u" rel="up">The Windows toolset</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="The-command-line-tools-1"></a>
<h3 class="section">D.3 The command line tools</h3>
<p>This item is installed by the <samp>Rtools*.exe</samp> installer.
</p>
<p>If you choose to install these yourself, you will need suitable versions
of at least <code>basename</code>, <code>cat</code>, <code>cmp</code>, <code>comm</code>,
<code>cp</code>, <code>cut</code>, <code>date</code>, <code>diff</code>, <code>du</code>, <code>echo</code>,
<code>expr</code>, <code>gzip</code>, <code>ls</code>, <code>make</code>, <code>makeinfo</code>,
<code>mkdir</code>, <code>mv</code>, <code>rm</code>, <code>rsync</code>, <code>sed</code>, <code>sh</code>,
<code>sort</code>, <code>tar</code>, <code>texindex</code>, <code>touch</code> and <code>uniq</code>;
we use those from the Cygwin distribution
(<a href="http://www.cygwin.com/">http://www.cygwin.com/</a>) or compiled from the sources. You will
also need <code>zip</code> and <code>unzip</code> from the Info-ZIP project
(<a href="http://www.info-zip.org/">http://www.info-zip.org/</a>). All of these tools are in
<samp>Rtools*.exe</samp>.
</p>
<p><strong>Beware</strong>: ‘Native’ ports of make are <strong>not</strong> suitable
(including those called ‘MinGW make’ at the MinGW SourceForge site and
<code>mingw32-make</code> in some MinGW-w64 distributions). There were
also problems with other versions of the Cygwin tools and DLLs. To
avoid frustration, please use our tool set, and make sure it is at the
front of your path (including before the Windows system directories).
If you are using a Windows shell, type <code>PATH</code> at the prompt to find
out.
</p>
<a name="index-CYGWIN"></a>
<p>You may need to set the environment variable <code>CYGWIN</code> to a value
including ‘<samp>nodosfilewarning</samp>’ to suppress messages about
Windows-style paths.
</p>
<hr>
<a name="The-MinGW_002dw64-toolchain"></a>
<div class="header">
<p>
Next: <a href="#Useful-additional-programs" accesskey="n" rel="next">Useful additional programs</a>, Previous: <a href="#The-command-line-tools" accesskey="p" rel="previous">The command line tools</a>, Up: <a href="#The-Windows-toolset" accesskey="u" rel="up">The Windows toolset</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="The-MinGW_002dw64-toolchain-1"></a>
<h3 class="section">D.4 The MinGW-w64 toolchain</h3>
<p>Technically you need more than just a compiler so the set of tools is
referred to as a ‘toolchain’.
</p>
<p>The preferred toolchain since R 2.14.2 is part of
<code>Rtools30.exe</code>: this uses a beta version of <code>gcc 4.6.3</code>
and version 2.0.1 of the MinGW-w64 project’s runtime.
</p>
<p>This toolchain uses <em>multilib</em>: that is there is a single front-end
such as <code>gcc.exe</code> for each of the compilers and 32-bit (the
default) and 64-bit compilation are selected by the flags<a name="DOCF46" href="#FOOT46"><sup>46</sup></a> <samp>-m32</samp> and <samp>-m64</samp>
respectively. The tools are all 32-bit Windows executables and should
be able to run on any current version of Windows—however you do need a
64-bit version of Windows to build 64-bit R as the build process runs
R.
</p>
<p>To select a 32-bit or 64-bit build of R, set the options in
<samp>MkRules.local</samp> appropriately (following the comments in the file).
</p>
<p>Some external software libraries will need to be re-compiled under the
new toolchain: especially those providing a C++ interface. Many of
those used by <acronym>CRAN</acronym> packages are available from
<a href="http://www.stats.ox.ac.uk/pub/Rtools/multilib/">http://www.stats.ox.ac.uk/pub/Rtools/multilib/</a>. Users
developing packages with <a href="http://CRAN.R-project.org/package=Rcpp"><strong>Rcpp</strong></a> need to ensure that they use a
version built with exactly the same toolchain as their package: the
recommendation is to build <a href="http://CRAN.R-project.org/package=Rcpp"><strong>Rcpp</strong></a> from its sources yourself.
</p>
<p>There is support for OpenMP and pthreads in this toolchain. As the
performance of OpenMP on Windows is poor for small tasks, it is not used
for R itself.
</p>
<hr>
<a name="Useful-additional-programs"></a>
<div class="header">
<p>
Previous: <a href="#The-MinGW_002dw64-toolchain" accesskey="p" rel="previous">The MinGW-w64 toolchain</a>, Up: <a href="#The-Windows-toolset" accesskey="u" rel="up">The Windows toolset</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Useful-additional-programs-1"></a>
<h3 class="section">D.5 Useful additional programs</h3>
<p>The process of making the installer will make use of <code>qpdf</code> to
compact some of the package vignettes, if it is available. Windows
binaries of <code>qpdf</code> are available from
<a href="http://sourceforge.net/projects/qpdf/files/">http://sourceforge.net/projects/qpdf/files/</a>. Set the path
to the <code>qpdf</code> installation in file <samp>MkRules.local</samp>.
</p>
<p>Developers of packages will find some of the ‘goodies’ at
<a href="http://www.stats.ox.ac.uk/pub/Rtools/goodies">http://www.stats.ox.ac.uk/pub/Rtools/goodies</a> useful.
</p>
<p>There is a version of the <code>file</code> command that identifies the
type of files, and is used by <code>Rcmd check</code> if available. The
binary distribution is included in <samp>Rtools30.exe</samp>.
</p>
<p>The file <samp>xzutils.zip</samp> contains the program <code>xz</code> which can
be used to (de)compress files with that form of compression.
</p>
<hr>
<a name="Function-and-variable-index"></a>
<div class="header">
<p>
Next: <a href="#Concept-index" accesskey="n" rel="next">Concept index</a>, Previous: <a href="#The-Windows-toolset" accesskey="p" rel="previous">The Windows toolset</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Function-and-variable-index-1"></a>
<h2 class="unnumbered">Function and variable index</h2>
<table><tr><th valign="top">Jump to: </th><td><a class="summary-letter" href="#Function-and-variable-index_vr_letter-C"><b>C</b></a>
<a class="summary-letter" href="#Function-and-variable-index_vr_letter-I"><b>I</b></a>
<a class="summary-letter" href="#Function-and-variable-index_vr_letter-M"><b>M</b></a>
<a class="summary-letter" href="#Function-and-variable-index_vr_letter-R"><b>R</b></a>
<a class="summary-letter" href="#Function-and-variable-index_vr_letter-U"><b>U</b></a>
</td></tr></table>
<table class="index-vr" border="0">
<tr><td></td><th align="left">Index Entry</th><td> </td><th align="left"> Section</th></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Function-and-variable-index_vr_letter-C">C</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-configure"><code>configure</code></a>:</td><td> </td><td valign="top"><a href="#Simple-compilation">Simple compilation</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-configure-1"><code>configure</code></a>:</td><td> </td><td valign="top"><a href="#Simple-compilation">Simple compilation</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-configure-2"><code>configure</code></a>:</td><td> </td><td valign="top"><a href="#Installation">Installation</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-configure-3"><code>configure</code></a>:</td><td> </td><td valign="top"><a href="#Installation">Installation</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-configure-4"><code>configure</code></a>:</td><td> </td><td valign="top"><a href="#Configuration-variables">Configuration variables</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-configure-5"><code>configure</code></a>:</td><td> </td><td valign="top"><a href="#Using-make">Using make</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Function-and-variable-index_vr_letter-I">I</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-install_002epackages"><code>install.packages</code></a>:</td><td> </td><td valign="top"><a href="#Installing-packages">Installing packages</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Function-and-variable-index_vr_letter-M">M</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-make"><code>make</code></a>:</td><td> </td><td valign="top"><a href="#Using-make">Using make</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Function-and-variable-index_vr_letter-R">R</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-remove_002epackages"><code>remove.packages</code></a>:</td><td> </td><td valign="top"><a href="#Removing-packages">Removing packages</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-R_005fHOME"><code>R_HOME</code></a>:</td><td> </td><td valign="top"><a href="#Simple-compilation">Simple compilation</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Function-and-variable-index_vr_letter-U">U</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-update_002epackages"><code>update.packages</code></a>:</td><td> </td><td valign="top"><a href="#Updating-packages">Updating packages</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
</table>
<table><tr><th valign="top">Jump to: </th><td><a class="summary-letter" href="#Function-and-variable-index_vr_letter-C"><b>C</b></a>
<a class="summary-letter" href="#Function-and-variable-index_vr_letter-I"><b>I</b></a>
<a class="summary-letter" href="#Function-and-variable-index_vr_letter-M"><b>M</b></a>
<a class="summary-letter" href="#Function-and-variable-index_vr_letter-R"><b>R</b></a>
<a class="summary-letter" href="#Function-and-variable-index_vr_letter-U"><b>U</b></a>
</td></tr></table>
<hr>
<a name="Concept-index"></a>
<div class="header">
<p>
Next: <a href="#Environment-variable-index" accesskey="n" rel="next">Environment variable index</a>, Previous: <a href="#Function-and-variable-index" accesskey="p" rel="previous">Function and variable index</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Concept-index-1"></a>
<h2 class="unnumbered">Concept index</h2>
<table><tr><th valign="top">Jump to: </th><td><a class="summary-letter" href="#Concept-index_cp_letter-A"><b>A</b></a>
<a class="summary-letter" href="#Concept-index_cp_letter-B"><b>B</b></a>
<a class="summary-letter" href="#Concept-index_cp_letter-F"><b>F</b></a>
<a class="summary-letter" href="#Concept-index_cp_letter-I"><b>I</b></a>
<a class="summary-letter" href="#Concept-index_cp_letter-L"><b>L</b></a>
<a class="summary-letter" href="#Concept-index_cp_letter-M"><b>M</b></a>
<a class="summary-letter" href="#Concept-index_cp_letter-O"><b>O</b></a>
<a class="summary-letter" href="#Concept-index_cp_letter-P"><b>P</b></a>
<a class="summary-letter" href="#Concept-index_cp_letter-R"><b>R</b></a>
<a class="summary-letter" href="#Concept-index_cp_letter-S"><b>S</b></a>
<a class="summary-letter" href="#Concept-index_cp_letter-U"><b>U</b></a>
<a class="summary-letter" href="#Concept-index_cp_letter-V"><b>V</b></a>
<a class="summary-letter" href="#Concept-index_cp_letter-W"><b>W</b></a>
</td></tr></table>
<table class="index-cp" border="0">
<tr><td></td><th align="left">Index Entry</th><td> </td><th align="left"> Section</th></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Concept-index_cp_letter-A">A</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-AIX">AIX</a>:</td><td> </td><td valign="top"><a href="#AIX">AIX</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Concept-index_cp_letter-B">B</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-BLAS-library">BLAS library</a>:</td><td> </td><td valign="top"><a href="#Linear-algebra">Linear algebra</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-BLAS-library-1">BLAS library</a>:</td><td> </td><td valign="top"><a href="#OS-X">OS X</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-BLAS-library-2">BLAS library</a>:</td><td> </td><td valign="top"><a href="#Solaris">Solaris</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Concept-index_cp_letter-F">F</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-FORTRAN">FORTRAN</a>:</td><td> </td><td valign="top"><a href="#Using-FORTRAN">Using FORTRAN</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-FreeBSD">FreeBSD</a>:</td><td> </td><td valign="top"><a href="#FreeBSD">FreeBSD</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Concept-index_cp_letter-I">I</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-Installation">Installation</a>:</td><td> </td><td valign="top"><a href="#Installation">Installation</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-Installing-under-Unix_002dalikes">Installing under Unix-alikes</a>:</td><td> </td><td valign="top"><a href="#Installing-R-under-Unix_002dalikes">Installing R under Unix-alikes</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-Installing-under-Windows">Installing under Windows</a>:</td><td> </td><td valign="top"><a href="#Installing-R-under-Windows">Installing R under Windows</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-Internationalization">Internationalization</a>:</td><td> </td><td valign="top"><a href="#Internationalization">Internationalization</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Concept-index_cp_letter-L">L</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-LAPACK-library">LAPACK library</a>:</td><td> </td><td valign="top"><a href="#LAPACK">LAPACK</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-LAPACK-library-1">LAPACK library</a>:</td><td> </td><td valign="top"><a href="#OS-X">OS X</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-LAPACK-library-2">LAPACK library</a>:</td><td> </td><td valign="top"><a href="#Solaris">Solaris</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-Libraries">Libraries</a>:</td><td> </td><td valign="top"><a href="#Add_002don-packages">Add-on packages</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-Libraries_002c-managing">Libraries, managing</a>:</td><td> </td><td valign="top"><a href="#Managing-libraries">Managing libraries</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-Libraries_002c-site">Libraries, site</a>:</td><td> </td><td valign="top"><a href="#Managing-libraries">Managing libraries</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-Libraries_002c-user">Libraries, user</a>:</td><td> </td><td valign="top"><a href="#Managing-libraries">Managing libraries</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-Linux">Linux</a>:</td><td> </td><td valign="top"><a href="#Installing-R-under-Unix_002dalikes">Installing R under Unix-alikes</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-Linux-1">Linux</a>:</td><td> </td><td valign="top"><a href="#Linux">Linux</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-Locale">Locale</a>:</td><td> </td><td valign="top"><a href="#Internationalization">Internationalization</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-Locale-1">Locale</a>:</td><td> </td><td valign="top"><a href="#Locales">Locales</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-Localization">Localization</a>:</td><td> </td><td valign="top"><a href="#Internationalization">Internationalization</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Concept-index_cp_letter-M">M</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-Manuals">Manuals</a>:</td><td> </td><td valign="top"><a href="#Making-the-manuals">Making the manuals</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-Manuals_002c-installing">Manuals, installing</a>:</td><td> </td><td valign="top"><a href="#Installation">Installation</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Concept-index_cp_letter-O">O</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-Obtaining-R">Obtaining R</a>:</td><td> </td><td valign="top"><a href="#Obtaining-R">Obtaining R</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-OS-X">OS X</a>:</td><td> </td><td valign="top"><a href="#Installing-R-under-Unix_002dalikes">Installing R under Unix-alikes</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-OS-X-1">OS X</a>:</td><td> </td><td valign="top"><a href="#Installing-R-under-OS-X">Installing R under OS X</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-OS-X-2">OS X</a>:</td><td> </td><td valign="top"><a href="#OS-X">OS X</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Concept-index_cp_letter-P">P</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-Packages">Packages</a>:</td><td> </td><td valign="top"><a href="#Add_002don-packages">Add-on packages</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-Packages_002c-default">Packages, default</a>:</td><td> </td><td valign="top"><a href="#Default-packages">Default packages</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-Packages_002c-installing">Packages, installing</a>:</td><td> </td><td valign="top"><a href="#Installing-packages">Installing packages</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-Packages_002c-removing">Packages, removing</a>:</td><td> </td><td valign="top"><a href="#Removing-packages">Removing packages</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-Packages_002c-updating">Packages, updating</a>:</td><td> </td><td valign="top"><a href="#Updating-packages">Updating packages</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Concept-index_cp_letter-R">R</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-Rbitmap_002edll">Rbitmap.dll</a>:</td><td> </td><td valign="top"><a href="#Building-the-bitmap-files">Building the bitmap files</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-Repositories">Repositories</a>:</td><td> </td><td valign="top"><a href="#Setting-up-a-package-repository">Setting up a package repository</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Concept-index_cp_letter-S">S</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-Site-libraries">Site libraries</a>:</td><td> </td><td valign="top"><a href="#Managing-libraries">Managing libraries</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-Solaris">Solaris</a>:</td><td> </td><td valign="top"><a href="#Solaris">Solaris</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-Sources-for-R">Sources for R</a>:</td><td> </td><td valign="top"><a href="#Getting-and-unpacking-the-sources">Getting and unpacking the sources</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-Subversion">Subversion</a>:</td><td> </td><td valign="top"><a href="#Using-Subversion-and-rsync">Using Subversion and rsync</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-Subversion-1">Subversion</a>:</td><td> </td><td valign="top"><a href="#Essential-programs-and-libraries">Essential programs and libraries</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Concept-index_cp_letter-U">U</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-User-libraries">User libraries</a>:</td><td> </td><td valign="top"><a href="#Managing-libraries">Managing libraries</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Concept-index_cp_letter-V">V</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-Vignettes">Vignettes</a>:</td><td> </td><td valign="top"><a href="#Essential-programs-and-libraries">Essential programs and libraries</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Concept-index_cp_letter-W">W</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-winCairo_002edll">winCairo.dll</a>:</td><td> </td><td valign="top"><a href="#Building-the-cairo-devices-files">Building the cairo devices files</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
</table>
<table><tr><th valign="top">Jump to: </th><td><a class="summary-letter" href="#Concept-index_cp_letter-A"><b>A</b></a>
<a class="summary-letter" href="#Concept-index_cp_letter-B"><b>B</b></a>
<a class="summary-letter" href="#Concept-index_cp_letter-F"><b>F</b></a>
<a class="summary-letter" href="#Concept-index_cp_letter-I"><b>I</b></a>
<a class="summary-letter" href="#Concept-index_cp_letter-L"><b>L</b></a>
<a class="summary-letter" href="#Concept-index_cp_letter-M"><b>M</b></a>
<a class="summary-letter" href="#Concept-index_cp_letter-O"><b>O</b></a>
<a class="summary-letter" href="#Concept-index_cp_letter-P"><b>P</b></a>
<a class="summary-letter" href="#Concept-index_cp_letter-R"><b>R</b></a>
<a class="summary-letter" href="#Concept-index_cp_letter-S"><b>S</b></a>
<a class="summary-letter" href="#Concept-index_cp_letter-U"><b>U</b></a>
<a class="summary-letter" href="#Concept-index_cp_letter-V"><b>V</b></a>
<a class="summary-letter" href="#Concept-index_cp_letter-W"><b>W</b></a>
</td></tr></table>
<hr>
<a name="Environment-variable-index"></a>
<div class="header">
<p>
Previous: <a href="#Concept-index" accesskey="p" rel="previous">Concept index</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Environment-variable-index-1"></a>
<h2 class="unnumbered">Environment variable index</h2>
<table><tr><th valign="top">Jump to: </th><td><a class="summary-letter" href="#Environment-variable-index_en_letter-B"><b>B</b></a>
<a class="summary-letter" href="#Environment-variable-index_en_letter-C"><b>C</b></a>
<a class="summary-letter" href="#Environment-variable-index_en_letter-D"><b>D</b></a>
<a class="summary-letter" href="#Environment-variable-index_en_letter-F"><b>F</b></a>
<a class="summary-letter" href="#Environment-variable-index_en_letter-J"><b>J</b></a>
<a class="summary-letter" href="#Environment-variable-index_en_letter-L"><b>L</b></a>
<a class="summary-letter" href="#Environment-variable-index_en_letter-O"><b>O</b></a>
<a class="summary-letter" href="#Environment-variable-index_en_letter-P"><b>P</b></a>
<a class="summary-letter" href="#Environment-variable-index_en_letter-R"><b>R</b></a>
<a class="summary-letter" href="#Environment-variable-index_en_letter-T"><b>T</b></a>
</td></tr></table>
<table class="index-en" border="0">
<tr><td></td><th align="left">Index Entry</th><td> </td><th align="left"> Section</th></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Environment-variable-index_en_letter-B">B</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-BLAS_005fLIBS"><code>BLAS_LIBS</code></a>:</td><td> </td><td valign="top"><a href="#BLAS">BLAS</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Environment-variable-index_en_letter-C">C</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-CC"><code>CC</code></a>:</td><td> </td><td valign="top"><a href="#Using-FORTRAN">Using FORTRAN</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-CONFIG_005fSITE"><code>CONFIG_SITE</code></a>:</td><td> </td><td valign="top"><a href="#Configuration-variables">Configuration variables</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-CPP"><code>CPP</code></a>:</td><td> </td><td valign="top"><a href="#Using-FORTRAN">Using FORTRAN</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-CYGWIN"><code>CYGWIN</code></a>:</td><td> </td><td valign="top"><a href="#The-command-line-tools">The command line tools</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Environment-variable-index_en_letter-D">D</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-DESTDIR"><code>DESTDIR</code></a>:</td><td> </td><td valign="top"><a href="#Installation">Installation</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-DESTDIR-1"><code>DESTDIR</code></a>:</td><td> </td><td valign="top"><a href="#Unix_002dalike-standalone">Unix-alike standalone</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Environment-variable-index_en_letter-F">F</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-F2C"><code>F2C</code></a>:</td><td> </td><td valign="top"><a href="#Using-FORTRAN">Using FORTRAN</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-F2CLIBS"><code>F2CLIBS</code></a>:</td><td> </td><td valign="top"><a href="#Using-FORTRAN">Using FORTRAN</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-FPICFLAGS"><code>FPICFLAGS</code></a>:</td><td> </td><td valign="top"><a href="#Using-FORTRAN">Using FORTRAN</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Environment-variable-index_en_letter-J">J</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-JAVA_005fHOME"><code>JAVA_HOME</code></a>:</td><td> </td><td valign="top"><a href="#Java-support">Java support</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Environment-variable-index_en_letter-L">L</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-LANG"><code>LANG</code></a>:</td><td> </td><td valign="top"><a href="#Localization-of-messages">Localization of messages</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-LANGUAGE"><code>LANGUAGE</code></a>:</td><td> </td><td valign="top"><a href="#Localization-of-messages">Localization of messages</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-LANGUAGE-1"><code>LANGUAGE</code></a>:</td><td> </td><td valign="top"><a href="#Localization-of-messages">Localization of messages</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-LAPACK_005fLIBS"><code>LAPACK_LIBS</code></a>:</td><td> </td><td valign="top"><a href="#LAPACK">LAPACK</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-LC_005fALL"><code>LC_ALL</code></a>:</td><td> </td><td valign="top"><a href="#Localization-of-messages">Localization of messages</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-LC_005fCOLLATE"><code>LC_COLLATE</code></a>:</td><td> </td><td valign="top"><a href="#Testing-a-Unix_002dalike-Installation">Testing a Unix-alike Installation</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-LC_005fMESSAGES"><code>LC_MESSAGES</code></a>:</td><td> </td><td valign="top"><a href="#Localization-of-messages">Localization of messages</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-LD_005fLIBRARY_005fPATH"><code>LD_LIBRARY_PATH</code></a>:</td><td> </td><td valign="top"><a href="#Unix_002dalike-standalone">Unix-alike standalone</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-LD_005fLIBRARY_005fPATH-1"><code>LD_LIBRARY_PATH</code></a>:</td><td> </td><td valign="top"><a href="#ACML">ACML</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-LD_005fLIBRARY_005fPATH-2"><code>LD_LIBRARY_PATH</code></a>:</td><td> </td><td valign="top"><a href="#Using-FORTRAN">Using FORTRAN</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-LD_005fLIBRARY_005fPATH-3"><code>LD_LIBRARY_PATH</code></a>:</td><td> </td><td valign="top"><a href="#Compile-and-load-flags">Compile and load flags</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-LD_005fLIBRARY_005fPATH-4"><code>LD_LIBRARY_PATH</code></a>:</td><td> </td><td valign="top"><a href="#Using-gcc">Using gcc</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-LOCAL_005fSOFT"><code>LOCAL_SOFT</code></a>:</td><td> </td><td valign="top"><a href="#Windows-packages">Windows packages</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Environment-variable-index_en_letter-O">O</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-OBJECT_005fMODE"><code>OBJECT_MODE</code></a>:</td><td> </td><td valign="top"><a href="#AIX">AIX</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Environment-variable-index_en_letter-P">P</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-PAPERSIZE"><code>PAPERSIZE</code></a>:</td><td> </td><td valign="top"><a href="#Setting-paper-size">Setting paper size</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-PATH"><code>PATH</code></a>:</td><td> </td><td valign="top"><a href="#Essential-programs-and-libraries">Essential programs and libraries</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-PATH-1"><code>PATH</code></a>:</td><td> </td><td valign="top"><a href="#Using-FORTRAN">Using FORTRAN</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-PATH-2"><code>PATH</code></a>:</td><td> </td><td valign="top"><a href="#AIX">AIX</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-PATH-3"><code>PATH</code></a>:</td><td> </td><td valign="top"><a href="#The-Windows-toolset">The Windows toolset</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Environment-variable-index_en_letter-R">R</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-R_005fARCH"><code>R_ARCH</code></a>:</td><td> </td><td valign="top"><a href="#Sub_002darchitectures">Sub-architectures</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-R_005fARCH-1"><code>R_ARCH</code></a>:</td><td> </td><td valign="top"><a href="#Sub_002darchitectures">Sub-architectures</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-R_005fBROWSER"><code>R_BROWSER</code></a>:</td><td> </td><td valign="top"><a href="#Setting-the-browsers">Setting the browsers</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-R_005fDEFAULT_005fPACKAGES"><code>R_DEFAULT_PACKAGES</code></a>:</td><td> </td><td valign="top"><a href="#Default-packages">Default packages</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-R_005fDISABLE_005fHTTPD"><code>R_DISABLE_HTTPD</code></a>:</td><td> </td><td valign="top"><a href="#Help-options">Help options</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-R_005fGSCMD"><code>R_GSCMD</code></a>:</td><td> </td><td valign="top"><a href="#Useful-libraries-and-programs">Useful libraries and programs</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-R_005fINSTALL_005fTAR"><code>R_INSTALL_TAR</code></a>:</td><td> </td><td valign="top"><a href="#Windows-packages">Windows packages</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-R_005fJAVA_005fLD_005fLIBRARY_005fPATH"><code>R_JAVA_LD_LIBRARY_PATH</code></a>:</td><td> </td><td valign="top"><a href="#Java-support">Java support</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-R_005fJAVA_005fLD_005fLIBRARY_005fPATH-1"><code>R_JAVA_LD_LIBRARY_PATH</code></a>:</td><td> </td><td valign="top"><a href="#Java-support">Java support</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-R_005fLIBS"><code>R_LIBS</code></a>:</td><td> </td><td valign="top"><a href="#Add_002don-packages">Add-on packages</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-R_005fLIBS_005fSITE"><code>R_LIBS_SITE</code></a>:</td><td> </td><td valign="top"><a href="#Managing-libraries">Managing libraries</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-R_005fLIBS_005fUSER"><code>R_LIBS_USER</code></a>:</td><td> </td><td valign="top"><a href="#Managing-libraries">Managing libraries</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-R_005fPAPERSIZE"><code>R_PAPERSIZE</code></a>:</td><td> </td><td valign="top"><a href="#Making-the-manuals">Making the manuals</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-R_005fPAPERSIZE-1"><code>R_PAPERSIZE</code></a>:</td><td> </td><td valign="top"><a href="#Running-R">Running R</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-R_005fPAPERSIZE-2"><code>R_PAPERSIZE</code></a>:</td><td> </td><td valign="top"><a href="#Setting-paper-size">Setting paper size</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-R_005fPAPERSIZE-3"><code>R_PAPERSIZE</code></a>:</td><td> </td><td valign="top"><a href="#Making-manuals">Making manuals</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-R_005fPDFVIEWER"><code>R_PDFVIEWER</code></a>:</td><td> </td><td valign="top"><a href="#Setting-the-browsers">Setting the browsers</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-R_005fRD4PDF"><code>R_RD4PDF</code></a>:</td><td> </td><td valign="top"><a href="#Making-the-manuals">Making the manuals</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-R_005fRD4PDF-1"><code>R_RD4PDF</code></a>:</td><td> </td><td valign="top"><a href="#Making-manuals">Making manuals</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-R_005fRD4PDF-2"><code>R_RD4PDF</code></a>:</td><td> </td><td valign="top"><a href="#LaTeX">LaTeX</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-R_005fSHELL"><code>R_SHELL</code></a>:</td><td> </td><td valign="top"><a href="#AIX">AIX</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-R_005fUSER"><code>R_USER</code></a>:</td><td> </td><td valign="top"><a href="#Running-R">Running R</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Environment-variable-index_en_letter-T">T</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-TAR"><code>TAR</code></a>:</td><td> </td><td valign="top"><a href="#Essential-programs-and-libraries">Essential programs and libraries</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-TAR_005fOPTIONS"><code>TAR_OPTIONS</code></a>:</td><td> </td><td valign="top"><a href="#Getting-and-unpacking-the-sources">Getting and unpacking the sources</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-TAR_005fOPTIONS-1"><code>TAR_OPTIONS</code></a>:</td><td> </td><td valign="top"><a href="#Getting-the-source-files">Getting the source files</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-TEMP"><code>TEMP</code></a>:</td><td> </td><td valign="top"><a href="#Running-R">Running R</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-TMP"><code>TMP</code></a>:</td><td> </td><td valign="top"><a href="#Running-R">Running R</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-TMPDIR"><code>TMPDIR</code></a>:</td><td> </td><td valign="top"><a href="#Simple-compilation">Simple compilation</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-TMPDIR-1"><code>TMPDIR</code></a>:</td><td> </td><td valign="top"><a href="#Building-the-core-files">Building the core files</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-TMPDIR-2"><code>TMPDIR</code></a>:</td><td> </td><td valign="top"><a href="#Running-R">Running R</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-TMPDIR-3"><code>TMPDIR</code></a>:</td><td> </td><td valign="top"><a href="#Running-R">Running R</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-TMPDIR-4"><code>TMPDIR</code></a>:</td><td> </td><td valign="top"><a href="#Installing-packages">Installing packages</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
</table>
<table><tr><th valign="top">Jump to: </th><td><a class="summary-letter" href="#Environment-variable-index_en_letter-B"><b>B</b></a>
<a class="summary-letter" href="#Environment-variable-index_en_letter-C"><b>C</b></a>
<a class="summary-letter" href="#Environment-variable-index_en_letter-D"><b>D</b></a>
<a class="summary-letter" href="#Environment-variable-index_en_letter-F"><b>F</b></a>
<a class="summary-letter" href="#Environment-variable-index_en_letter-J"><b>J</b></a>
<a class="summary-letter" href="#Environment-variable-index_en_letter-L"><b>L</b></a>
<a class="summary-letter" href="#Environment-variable-index_en_letter-O"><b>O</b></a>
<a class="summary-letter" href="#Environment-variable-index_en_letter-P"><b>P</b></a>
<a class="summary-letter" href="#Environment-variable-index_en_letter-R"><b>R</b></a>
<a class="summary-letter" href="#Environment-variable-index_en_letter-T"><b>T</b></a>
</td></tr></table>
<div class="footnote">
<hr>
<h4 class="footnotes-heading">Footnotes</h4>
<h3><a name="FOOT1" href="#DOCF1">(1)</a></h3>
<p>e.g. <acronym>GNU</acronym>
<code>tar</code> version 1.15 or later, or that from the ‘<samp>libarchive</samp>’
(as used on OS 10.6 and later) or ‘Heirloom Toolchest’ distributions.</p>
<h3><a name="FOOT2" href="#DOCF2">(2)</a></h3>
<p>for some Subversion clients
‘<samp>http:</samp>’ may appear to work, but requires continual redirection.</p>
<h3><a name="FOOT3" href="#DOCF3">(3)</a></h3>
<p>Most aspects will work with paths containing spaces,
but external software used by R, e.g. <code>texi2dvi</code> version
<code>4.8</code>, may not.</p>
<h3><a name="FOOT4" href="#DOCF4">(4)</a></h3>
<p>which use <samp>lib</samp> rather than
<samp>lib64</samp> for their primary 64-bit library directories.</p>
<h3><a name="FOOT5" href="#DOCF5">(5)</a></h3>
<p>for example, if you configured R with
<samp>--without-recommended</samp>.</p>
<h3><a name="FOOT6" href="#DOCF6">(6)</a></h3>
<p>on a
Unix-alike, ‘<samp>incosolata</samp>’ is omitted if not found by
<code>configure</code>.</p>
<h3><a name="FOOT7" href="#DOCF7">(7)</a></h3>
<p>with possible values
‘<samp>i386</samp>’, ‘<samp>x64</samp>’, ‘<samp>32</samp>’ and ‘<samp>64</samp>’.</p>
<h3><a name="FOOT8" href="#DOCF8">(8)</a></h3>
<p>mainly on RedHat and Fedora, whose layout is described
here.</p>
<h3><a name="FOOT9" href="#DOCF9">(9)</a></h3>
<p>unless they were excluded in the build.</p>
<h3><a name="FOOT10" href="#DOCF10">(10)</a></h3>
<p>its binding is locked once the startup files have been
read, so users cannot easily change it.</p>
<h3><a name="FOOT11" href="#DOCF11">(11)</a></h3>
<p>If a proxy needs to be set, see
<code>?download.file</code>.</p>
<h3><a name="FOOT12" href="#DOCF12">(12)</a></h3>
<p>for a small number of
<acronym>CRAN</acronym> packages where this is known to be safe and is needed by
the autobuilder this is the default. Look at the source of
<samp>tools:::.install_packages</samp> for the list. It can also be specified
in the package’s <samp>DESCRIPTION</samp> file.</p>
<h3><a name="FOOT13" href="#DOCF13">(13)</a></h3>
<p>or by adding it in
a file such as <samp>etc/i386/Makevars.site</samp>, which does not exist by
default.</p>
<h3><a name="FOOT14" href="#DOCF14">(14)</a></h3>
<p>‘X/Open Portability Guide’, which has
had several versions.</p>
<h3><a name="FOOT15" href="#DOCF15">(15)</a></h3>
<p>On some systems setting
<code>LC_ALL</code> or <code>LC_MESSAGES</code> to ‘<samp>C</samp>’ disables <code>LANGUAGE</code>.</p>
<h3><a name="FOOT16" href="#DOCF16">(16)</a></h3>
<p>If you try changing from French
to Russian except in a UTF-8 locale, you will most likely find messages
change to English.</p>
<h3><a name="FOOT17" href="#DOCF17">(17)</a></h3>
<p>the
language written in England: some people living in the USA appropriate
this name for their language.</p>
<h3><a name="FOOT18" href="#DOCF18">(18)</a></h3>
<p>with
Americanisms.</p>
<h3><a name="FOOT19" href="#DOCF19">(19)</a></h3>
<p>also known as
<acronym>IEEE</acronym> 754</p>
<h3><a name="FOOT20" href="#DOCF20">(20)</a></h3>
<p>at least when storing quantities: the on-FPU
precision is allowed to vary</p>
<h3><a name="FOOT21" href="#DOCF21">(21)</a></h3>
<p>e.g. Bessel, beta and gamma functions</p>
<h3><a name="FOOT22" href="#DOCF22">(22)</a></h3>
<p>including copying <samp>MkRules.dist</samp> to
<samp>MkRule.local</samp> and selecting the architecture.</p>
<h3><a name="FOOT23" href="#DOCF23">(23)</a></h3>
<p>also
known as <acronym>IEEE</acronym> 754</p>
<h3><a name="FOOT24" href="#DOCF24">(24)</a></h3>
<p>Note that C11 compilers (when they appear) need
not be C99-compliant: R requires support for <code>double complex</code>
which is optional in C11 but is mandatory in C99.</p>
<h3><a name="FOOT25" href="#DOCF25">(25)</a></h3>
<p><samp>-std=c99</samp> excludes POSIX
functionality, but <samp>config.h</samp> will turn on all <acronym>GNU</acronym>
extensions to include the POSIX functionality.</p>
<h3><a name="FOOT26" href="#DOCF26">(26)</a></h3>
<p>apparently when built by
default, but not for example as built for Fedora 15.</p>
<h3><a name="FOOT27" href="#DOCF27">(27)</a></h3>
<p>specifically, the C99
functionality of headers <samp>wchar.h</samp> and <samp>wctype.h</samp>, types
<code>wctans_t</code> and <code>mbstate_t</code> and functions <code>mbrtowc</code>,
<code>mbstowcs</code>, <code>wcrtomb</code>, <code>wcscoll</code>, <code>wcstombs</code>,
<code>wctrans</code>, <code>wctype</code>, and <code>iswctype</code>.</p>
<h3><a name="FOOT28" href="#DOCF28">(28)</a></h3>
<p>Such as
<acronym>GNU</acronym> <code>tar</code> 1.15 or later, <code>bsdtar</code> (from
<a href="http://code.google.com/p/libarchive/">http://code.google.com/p/libarchive/</a>, as used by FreeBSD and OS
10.6 and later) or <code>tar</code> from the Heirloom Toolchest
(<a href="http://heirloom.sourceforge.net/tools.html">http://heirloom.sourceforge.net/tools.html</a>).</p>
<h3><a name="FOOT29" href="#DOCF29">(29)</a></h3>
<p><code>texi2dvi</code> is normally a
shell script. Some versions, e.g. that from <strong>texinfo</strong> 4.13a, need
to be run under <code>bash</code> rather than a Bourne shell as on, say,
Solaris.</p>
<h3><a name="FOOT30" href="#DOCF30">(30)</a></h3>
<p>also known as <code>ttf-mscorefonts-installer</code> in the
Debian/Ubuntu world: see also
<a href="http://en.wikipedia.org/wiki/Core_fonts_for_the_Web">http://en.wikipedia.org/wiki/Core_fonts_for_the_Web</a>.</p>
<h3><a name="FOOT31" href="#DOCF31">(31)</a></h3>
<p><code>ttf-liberation</code>
in Debian/Ubuntu.</p>
<h3><a name="FOOT32" href="#DOCF32">(32)</a></h3>
<p>Using the Oracle Solaris Studio
<code>cc</code> and <code>f95</code> compilers</p>
<h3><a name="FOOT33" href="#DOCF33">(33)</a></h3>
<p>and perhaps others</p>
<h3><a name="FOOT34" href="#DOCF34">(34)</a></h3>
<p>We have measured 15–20% on ‘<samp>i686</samp>’ Linux
and around 10% on ‘<samp>x86_64</samp>’ Linux.</p>
<h3><a name="FOOT35" href="#DOCF35">(35)</a></h3>
<p>On HP-UX <code>fort77</code> is the
<acronym>POSIX</acronym> compliant FORTRAN compiler, and comes after
<code>g77</code>.</p>
<h3><a name="FOOT36" href="#DOCF36">(36)</a></h3>
<p>as well as its equivalence to the <code>Rcomplex</code>
structure defined in <samp>R_ext/Complex.h</samp>.</p>
<h3><a name="FOOT37" href="#DOCF37">(37)</a></h3>
<p>for example, <code>X11 font at size 14 could not
be loaded</code>.</p>
<h3><a name="FOOT38" href="#DOCF38">(38)</a></h3>
<p>or <code>-mtune=corei7</code> for Intel Core
i3/15/17 with <code>gcc >= 4.6.0</code>.</p>
<h3><a name="FOOT39" href="#DOCF39">(39)</a></h3>
<p>Apple’s <code>clang</code> should be able to:
some builds of <code>gcc</code> can, but not all built with Objective C
support work.</p>
<h3><a name="FOOT40" href="#DOCF40">(40)</a></h3>
<p>including <code>gcc</code> for
Sparc from Oracle.</p>
<h3><a name="FOOT41" href="#DOCF41">(41)</a></h3>
<p>TeXLive is recommended.</p>
<h3><a name="FOOT42" href="#DOCF42">(42)</a></h3>
<p>Windows
DLLs need to have all links resolved at build time and so cannot resolve
against <samp>R.bin</samp>.</p>
<h3><a name="FOOT43" href="#DOCF43">(43)</a></h3>
<p>For
example, the Cygwin version of <code>make 3.81</code> fails to work
correctly.</p>
<h3><a name="FOOT44" href="#DOCF44">(44)</a></h3>
<p>for R 2.15.3 and later.</p>
<h3><a name="FOOT45" href="#DOCF45">(45)</a></h3>
<p>such as <code>sort</code>, <code>find</code> and perhaps
<code>make</code>.</p>
<h3><a name="FOOT46" href="#DOCF46">(46)</a></h3>
<p>these
flags apply to the compilers: some of the tools use different flags.
32-bit builds are the default.</p>
</div>
<hr>
</body>
</html>
|