This file is indexed.

/usr/share/R/doc/manual/R-ints.html is in r-doc-html 3.2.3-4.

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
<!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 3.2.3 (2015-12-10).

Copyright (C) 1999-2015 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 6.0, http://www.gnu.org/software/texinfo/ -->
<head>
<title>R Internals</title>

<meta name="description" content="R Internals">
<meta name="keywords" content="R Internals">
<meta name="resource-type" content="document">
<meta name="distribution" content="global">
<meta name="Generator" content="texi2any">
<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">
<style type="text/css">
<!--
a.summary-letter {text-decoration: none}
blockquote.indentedblock {margin-right: 0em}
blockquote.smallindentedblock {margin-right: 0em; font-size: smaller}
blockquote.smallquotation {font-size: smaller}
div.display {margin-left: 3.2em}
div.example {margin-left: 3.2em}
div.lisp {margin-left: 3.2em}
div.smalldisplay {margin-left: 3.2em}
div.smallexample {margin-left: 3.2em}
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">
<h1 class="settitle" align="center">R Internals</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-R-Internal-Structures-1" href="#R-Internal-Structures">1 R Internal Structures</a>
  <ul class="no-bullet">
    <li><a name="toc-SEXPs-1" href="#SEXPs">1.1 SEXPs</a>
    <ul class="no-bullet">
      <li><a name="toc-SEXPTYPEs-1" href="#SEXPTYPEs">1.1.1 SEXPTYPEs</a></li>
      <li><a name="toc-Rest-of-header-1" href="#Rest-of-header">1.1.2 Rest of header</a></li>
      <li><a name="toc-The-_0060data_0027" href="#The-_0027data_0027">1.1.3 The &lsquo;data&rsquo;</a></li>
      <li><a name="toc-Allocation-classes-1" href="#Allocation-classes">1.1.4 Allocation classes</a></li>
    </ul></li>
    <li><a name="toc-Environments-and-variable-lookup-1" href="#Environments-and-variable-lookup">1.2 Environments and variable lookup</a>
    <ul class="no-bullet">
      <li><a name="toc-Search-paths-1" href="#Search-paths">1.2.1 Search paths</a></li>
      <li><a name="toc-Namespaces-1" href="#Namespaces">1.2.2 Namespaces</a></li>
      <li><a name="toc-Hash-table-1" href="#Hash-table">1.2.3 Hash table</a></li>
    </ul></li>
    <li><a name="toc-Attributes-1" href="#Attributes">1.3 Attributes</a></li>
    <li><a name="toc-Contexts-1" href="#Contexts">1.4 Contexts</a></li>
    <li><a name="toc-Argument-evaluation-1" href="#Argument-evaluation">1.5 Argument evaluation</a>
    <ul class="no-bullet">
      <li><a name="toc-Missingness-1" href="#Missingness">1.5.1 Missingness</a></li>
      <li><a name="toc-Dot_002ddot_002ddot-arguments-1" href="#Dot_002ddot_002ddot-arguments">1.5.2 Dot-dot-dot arguments</a></li>
    </ul></li>
    <li><a name="toc-Autoprinting-1" href="#Autoprinting">1.6 Autoprinting</a></li>
    <li><a name="toc-The-write-barrier-and-the-garbage-collector" href="#The-write-barrier">1.7 The write barrier and the garbage collector</a></li>
    <li><a name="toc-Serialization-Formats-1" href="#Serialization-Formats">1.8 Serialization Formats</a></li>
    <li><a name="toc-Encodings-for-CHARSXPs-1" href="#Encodings-for-CHARSXPs">1.9 Encodings for CHARSXPs</a></li>
    <li><a name="toc-The-CHARSXP-cache-1" href="#The-CHARSXP-cache">1.10 The CHARSXP cache</a></li>
    <li><a name="toc-Warnings-and-errors-1" href="#Warnings-and-errors">1.11 Warnings and errors</a></li>
    <li><a name="toc-S4-objects-1" href="#S4-objects">1.12 S4 objects</a>
    <ul class="no-bullet">
      <li><a name="toc-Representation-of-S4-objects-1" href="#Representation-of-S4-objects">1.12.1 Representation of S4 objects</a></li>
      <li><a name="toc-S4-classes-1" href="#S4-classes">1.12.2 S4 classes</a></li>
      <li><a name="toc-S4-methods-1" href="#S4-methods">1.12.3 S4 methods</a></li>
      <li><a name="toc-Mechanics-of-S4-dispatch-1" href="#Mechanics-of-S4-dispatch">1.12.4 Mechanics of S4 dispatch</a></li>
    </ul></li>
    <li><a name="toc-Memory-allocators-1" href="#Memory-allocators">1.13 Memory allocators</a>
    <ul class="no-bullet">
      <li><a name="toc-Internals-of-R_005falloc-1" href="#Internals-of-R_005falloc">1.13.1 Internals of R_alloc</a></li>
    </ul></li>
    <li><a name="toc-Internal-use-of-global-and-base-environments-1" href="#Internal-use-of-global-and-base-environments">1.14 Internal use of global and base environments</a>
    <ul class="no-bullet">
      <li><a name="toc-Base-environment-1" href="#Base-environment">1.14.1 Base environment</a></li>
      <li><a name="toc-Global-environment-1" href="#Global-environment">1.14.2 Global environment</a></li>
    </ul></li>
    <li><a name="toc-Modules-1" href="#Modules">1.15 Modules</a></li>
    <li><a name="toc-Visibility-1" href="#Visibility">1.16 Visibility</a>
    <ul class="no-bullet">
      <li><a name="toc-Hiding-C-entry-points-1" href="#Hiding-C-entry-points">1.16.1 Hiding C entry points</a></li>
      <li><a name="toc-Variables-in-Windows-DLLs-1" href="#Variables-in-Windows-DLLs">1.16.2 Variables in Windows DLLs</a></li>
    </ul></li>
    <li><a name="toc-Lazy-loading-1" href="#Lazy-loading">1.17 Lazy loading</a></li>
  </ul></li>
  <li><a name="toc-_002eInternal-vs-_002ePrimitive-1" href="#g_t_002eInternal-vs-_002ePrimitive">2 <code>.Internal</code> vs <code>.Primitive</code></a>
  <ul class="no-bullet">
    <li><a name="toc-Special-primitives-1" href="#Special-primitives">2.1 Special primitives</a></li>
    <li><a name="toc-Special-internals-1" href="#Special-internals">2.2 Special internals</a></li>
    <li><a name="toc-Prototypes-for-primitives-1" href="#Prototypes-for-primitives">2.3 Prototypes for primitives</a></li>
    <li><a name="toc-Adding-a-primitive-1" href="#Adding-a-primitive">2.4 Adding a primitive</a></li>
  </ul></li>
  <li><a name="toc-Internationalization-in-the-R-sources-1" href="#Internationalization-in-the-R-sources">3 Internationalization in the R sources</a>
  <ul class="no-bullet">
    <li><a name="toc-R-code-1" href="#R-code">3.1 R code</a></li>
    <li><a name="toc-Main-C-code-1" href="#Main-C-code">3.2 Main C code</a></li>
    <li><a name="toc-Windows_002dGUI_002dspecific-code-1" href="#Windows_002dGUI_002dspecific-code">3.3 Windows-GUI-specific code</a></li>
    <li><a name="toc-OS-X-GUI-1" href="#OS-X-GUI">3.4 OS X GUI</a></li>
    <li><a name="toc-Updating-1" href="#Updating">3.5 Updating</a></li>
  </ul></li>
  <li><a name="toc-Structure-of-an-Installed-Package" href="#Package-Structure">4 Structure of an Installed Package</a>
  <ul class="no-bullet">
    <li><a name="toc-Metadata-1" href="#Metadata">4.1 Metadata</a></li>
    <li><a name="toc-Help-1" href="#Help">4.2 Help</a></li>
  </ul></li>
  <li><a name="toc-Files-1" href="#Files">5 Files</a></li>
  <li><a name="toc-Graphics" href="#Graphics-Devices">6 Graphics</a>
  <ul class="no-bullet">
    <li><a name="toc-Graphics-Devices-1" href="#Graphics-devices">6.1 Graphics Devices</a>
    <ul class="no-bullet">
      <li><a name="toc-Device-structures-1" href="#Device-structures">6.1.1 Device structures</a></li>
      <li><a name="toc-Device-capabilities-1" href="#Device-capabilities">6.1.2 Device capabilities</a></li>
      <li><a name="toc-Handling-text-1" href="#Handling-text">6.1.3 Handling text</a></li>
      <li><a name="toc-Conventions-1" href="#Conventions">6.1.4 Conventions</a></li>
      <li><a name="toc-_0060Mode_0027" href="#g_t_0027Mode_0027">6.1.5 &lsquo;Mode&rsquo;</a></li>
      <li><a name="toc-Graphics-events-1" href="#Graphics-events">6.1.6 Graphics events</a></li>
      <li><a name="toc-Specific-devices-1" href="#Specific-devices">6.1.7 Specific devices</a>
      <ul class="no-bullet">
        <li><a name="toc-X11_0028_0029-1" href="#X11_0028_0029">6.1.7.1 X11()</a></li>
        <li><a name="toc-windows_0028_0029-1" href="#windows_0028_0029">6.1.7.2 windows()</a></li>
      </ul></li>
    </ul></li>
    <li><a name="toc-Colours-1" href="#Colours">6.2 Colours</a></li>
    <li><a name="toc-Base-graphics-1" href="#Base-graphics">6.3 Base graphics</a>
    <ul class="no-bullet">
      <li><a name="toc-Arguments-and-parameters-1" href="#Arguments-and-parameters">6.3.1 Arguments and parameters</a></li>
    </ul></li>
    <li><a name="toc-Grid-graphics-1" href="#Grid-graphics">6.4 Grid graphics</a></li>
  </ul></li>
  <li><a name="toc-GUI-consoles-1" href="#GUI-consoles">7 GUI consoles</a>
  <ul class="no-bullet">
    <li><a name="toc-R_002eapp-1" href="#R_002eapp">7.1 R.app</a></li>
  </ul></li>
  <li><a name="toc-Tools-1" href="#Tools">8 Tools</a></li>
  <li><a name="toc-R-coding-standards-1" href="#R-coding-standards">9 R coding standards</a></li>
  <li><a name="toc-Testing-R-code-1" href="#Testing-R-code">10 Testing R code</a></li>
  <li><a name="toc-Use-of-TeX-dialects-1" href="#Use-of-TeX-dialects">11 Use of TeX dialects</a></li>
  <li><a name="toc-Current-and-future-directions-1" href="#Current-and-future-directions">12 Current and future directions</a>
  <ul class="no-bullet">
    <li><a name="toc-Long-vectors-1" href="#Long-vectors">12.1 Long vectors</a></li>
    <li><a name="toc-64_002dbit-types-1" href="#g_t64_002dbit-types">12.2 64-bit types</a></li>
    <li><a name="toc-Large-matrices-1" href="#Large-matrices">12.3 Large matrices</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>
</ul>
</div>


<a name="Top"></a>
<div class="header">
<p>
Next: <a href="#R-Internal-Structures" accesskey="n" rel="next">R Internal Structures</a> &nbsp; [<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-Internals"></a>
<h1 class="top">R Internals</h1>

<p>This is a guide to the internal structures of R and coding standards for
the core team working on R itself.
</p>
<p>This manual is for R, version 3.2.3 (2015-12-10).
</p>
<p>Copyright &copy; 1999&ndash;2015 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 summary="" class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">&bull; <a href="#R-Internal-Structures" accesskey="1">R Internal Structures</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">&bull; <a href="#g_t_002eInternal-vs-_002ePrimitive" accesskey="2">.Internal vs .Primitive</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">&bull; <a href="#Internationalization-in-the-R-sources" accesskey="3">Internationalization in the R sources</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">&bull; <a href="#Package-Structure" accesskey="4">Package Structure</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">&bull; <a href="#Files" accesskey="5">Files</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">&bull; <a href="#Graphics-Devices" accesskey="6">Graphics Devices</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">&bull; <a href="#GUI-consoles" accesskey="7">GUI consoles</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">&bull; <a href="#Tools" accesskey="8">Tools</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">&bull; <a href="#R-coding-standards" accesskey="9">R coding standards</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">&bull; <a href="#Testing-R-code">Testing R code</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">&bull; <a href="#Use-of-TeX-dialects">Use of TeX dialects</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">&bull; <a href="#Current-and-future-directions">Current and future directions</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">&bull; <a href="#Function-and-variable-index">Function and variable index</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">&bull; <a href="#Concept-index">Concept index</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
</table>

<hr>
<a name="R-Internal-Structures"></a>
<div class="header">
<p>
Next: <a href="#g_t_002eInternal-vs-_002ePrimitive" accesskey="n" rel="next">.Internal vs .Primitive</a>, Previous: <a href="#Top" accesskey="p" rel="prev">Top</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> &nbsp; [<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-Internal-Structures-1"></a>
<h2 class="chapter">1 R Internal Structures</h2>

<p>This chapter is the beginnings of documentation about R internal
structures.  It is written for the core team and others studying the
code in the <samp>src/main</samp> directory.
</p>
<p>It is a work-in-progress and should be checked against the current
version of the source code.  Versions for R 2.x.y contain historical
comments about when features were introduced: this version is for the
3.x.y series.
</p>
<table summary="" class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">&bull; <a href="#SEXPs" accesskey="1">SEXPs</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">&bull; <a href="#Environments-and-variable-lookup" accesskey="2">Environments and variable lookup</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">&bull; <a href="#Attributes" accesskey="3">Attributes</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">&bull; <a href="#Contexts" accesskey="4">Contexts</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">&bull; <a href="#Argument-evaluation" accesskey="5">Argument evaluation</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">&bull; <a href="#Autoprinting" accesskey="6">Autoprinting</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">&bull; <a href="#The-write-barrier" accesskey="7">The write barrier</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">&bull; <a href="#Serialization-Formats" accesskey="8">Serialization Formats</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">&bull; <a href="#Encodings-for-CHARSXPs" accesskey="9">Encodings for CHARSXPs</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">&bull; <a href="#The-CHARSXP-cache">The CHARSXP cache</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">&bull; <a href="#Warnings-and-errors">Warnings and errors</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">&bull; <a href="#S4-objects">S4 objects</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">&bull; <a href="#Memory-allocators">Memory allocators</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">&bull; <a href="#Internal-use-of-global-and-base-environments">Internal use of global and base environments</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">&bull; <a href="#Modules">Modules</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">&bull; <a href="#Visibility">Visibility</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">&bull; <a href="#Lazy-loading">Lazy loading</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
</table>

<hr>
<a name="SEXPs"></a>
<div class="header">
<p>
Next: <a href="#Environments-and-variable-lookup" accesskey="n" rel="next">Environments and variable lookup</a>, Previous: <a href="#R-Internal-Structures" accesskey="p" rel="prev">R Internal Structures</a>, Up: <a href="#R-Internal-Structures" accesskey="u" rel="up">R Internal Structures</a> &nbsp; [<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="SEXPs-1"></a>
<h3 class="section">1.1 SEXPs</h3>

<a name="index-SEXP"></a>
<a name="index-SEXPRREC"></a>
<p>What R users think of as <em>variables</em> or <em>objects</em> are
symbols which are bound to a value.  The value can be thought of as
either a <code>SEXP</code> (a pointer), or the structure it points to, a
<code>SEXPREC</code> (and there are alternative forms used for vectors, namely
<code>VECSXP</code> pointing to <code>VECTOR_SEXPREC</code> structures).
So the basic building blocks of R objects are often called
<em>nodes</em>, meaning <code>SEXPREC</code>s or <code>VECTOR_SEXPREC</code>s.
</p>
<p>Note that the internal structure of the <code>SEXPREC</code> is not made
available to R Extensions: rather <code>SEXP</code> is an opaque pointer,
and the internals can only be accessed by the functions provided.
</p>
<a name="index-node"></a>
<p>Both types of node structure have as their first three fields a 32-bit
<code>sxpinfo</code> header and then three pointers (to the attributes and the
previous and next node in a doubly-linked list), and then some further
fields.  On a 32-bit platform a node<a name="DOCF1" href="#FOOT1"><sup>1</sup></a> occupies 28 bytes: on a 64-bit platform typically 56
bytes (depending on alignment constraints).
</p>
<p>The first five bits of the <code>sxpinfo</code> header specify one of up to 32
<code>SEXPTYPE</code>s.
</p>
<table summary="" class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">&bull; <a href="#SEXPTYPEs" accesskey="1">SEXPTYPEs</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">&bull; <a href="#Rest-of-header" accesskey="2">Rest of header</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">&bull; <a href="#The-_0027data_0027" accesskey="3">The 'data'</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">&bull; <a href="#Allocation-classes" accesskey="4">Allocation classes</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
</table>

<hr>
<a name="SEXPTYPEs"></a>
<div class="header">
<p>
Next: <a href="#Rest-of-header" accesskey="n" rel="next">Rest of header</a>, Previous: <a href="#SEXPs" accesskey="p" rel="prev">SEXPs</a>, Up: <a href="#SEXPs" accesskey="u" rel="up">SEXPs</a> &nbsp; [<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="SEXPTYPEs-1"></a>
<h4 class="subsection">1.1.1 SEXPTYPEs</h4>

<a name="index-SEXPTYPE"></a>
<p>Currently <code>SEXPTYPE</code>s 0:10 and 13:25 are in use.  Values 11 and 12
were used for internal factors and ordered factors and have since been
withdrawn.  Note that the <code>SEXPTYPE</code> numbers are stored in
<code>save</code>d objects and that the ordering of the types is used, so the
gap cannot easily be reused.
</p>
<a name="index-SEXPTYPE-table"></a>
<blockquote>
<table summary="">
<thead><tr><th>no</th><th>SEXPTYPE</th><th>Description</th></tr></thead>
<tr><td><code>0</code></td><td><code>NILSXP</code></td><td><code>NULL</code></td></tr>
<tr><td><code>1</code></td><td><code>SYMSXP</code></td><td>symbols</td></tr>
<tr><td><code>2</code></td><td><code>LISTSXP</code></td><td>pairlists</td></tr>
<tr><td><code>3</code></td><td><code>CLOSXP</code></td><td>closures</td></tr>
<tr><td><code>4</code></td><td><code>ENVSXP</code></td><td>environments</td></tr>
<tr><td><code>5</code></td><td><code>PROMSXP</code></td><td>promises</td></tr>
<tr><td><code>6</code></td><td><code>LANGSXP</code></td><td>language objects</td></tr>
<tr><td><code>7</code></td><td><code>SPECIALSXP</code></td><td>special functions</td></tr>
<tr><td><code>8</code></td><td><code>BUILTINSXP</code></td><td>builtin functions</td></tr>
<tr><td><code>9</code></td><td><code>CHARSXP</code></td><td>internal character strings</td></tr>
<tr><td><code>10</code></td><td><code>LGLSXP</code></td><td>logical vectors</td></tr>
<tr><td><code>13</code></td><td><code>INTSXP</code></td><td>integer vectors</td></tr>
<tr><td><code>14</code></td><td><code>REALSXP</code></td><td>numeric vectors</td></tr>
<tr><td><code>15</code></td><td><code>CPLXSXP</code></td><td>complex vectors</td></tr>
<tr><td><code>16</code></td><td><code>STRSXP</code></td><td>character vectors</td></tr>
<tr><td><code>17</code></td><td><code>DOTSXP</code></td><td>dot-dot-dot object</td></tr>
<tr><td><code>18</code></td><td><code>ANYSXP</code></td><td>make &ldquo;any&rdquo; args work</td></tr>
<tr><td><code>19</code></td><td><code>VECSXP</code></td><td>list (generic vector)</td></tr>
<tr><td><code>20</code></td><td><code>EXPRSXP</code></td><td>expression vector</td></tr>
<tr><td><code>21</code></td><td><code>BCODESXP</code></td><td>byte code</td></tr>
<tr><td><code>22</code></td><td><code>EXTPTRSXP</code></td><td>external pointer</td></tr>
<tr><td><code>23</code></td><td><code>WEAKREFSXP</code></td><td>weak reference</td></tr>
<tr><td><code>24</code></td><td><code>RAWSXP</code></td><td>raw vector</td></tr>
<tr><td><code>25</code></td><td><code>S4SXP</code></td><td>S4 classes not of simple type</td></tr>
</table>
</blockquote>

<a name="index-atomic-vector-type"></a>
<p>Many of these will be familiar from R level: the atomic vector types
are <code>LGLSXP</code>, <code>INTSXP</code>, <code>REALSXP</code>, <code>CPLXSP</code>,
<code>STRSXP</code> and <code>RAWSXP</code>.  Lists are <code>VECSXP</code> and names
(also known as symbols) are <code>SYMSXP</code>.  Pairlists (<code>LISTSXP</code>,
the name going back to the origins of R as a Scheme-like language)
are rarely seen at R level, but are for example used for argument
lists.  Character vectors are effectively lists all of whose elements
are <code>CHARSXP</code>, a type that is rarely visible at R level.
</p>
<a name="index-language-object"></a>
<a name="index-argument-list"></a>
<p>Language objects (<code>LANGSXP</code>) are calls (including formulae and so
on).  Internally they are pairlists with first element a
reference<a name="DOCF2" href="#FOOT2"><sup>2</sup></a> to the function to be called with remaining elements the
actual arguments for the call (and with the tags if present giving the
specified argument names).  Although this is not enforced, many places
in the code assume that the pairlist is of length one or more, often
without checking.
</p>
<a name="index-expression"></a>
<p>Expressions are of type <code>EXPRSXP</code>: they are a vector of (usually
language) objects most often seen as the result of <code>parse()</code>.
</p>
<a name="index-function"></a>
<p>The functions are of types <code>CLOSXP</code>, <code>SPECIALSXP</code> and
<code>BUILTINSXP</code>: where <code>SEXPTYPE</code>s are stored in an integer
these are sometimes lumped into a pseudo-type <code>FUNSXP</code> with code
99.  Functions defined via <code>function</code> are of type <code>CLOSXP</code> and
have formals, body and environment.
</p>
<a name="index-S4-type"></a>
<p>The <code>SEXPTYPE</code> <code>S4SXP</code> is for S4 objects which do not consist
solely of a simple type such as an atomic vector or function.
</p>

<hr>
<a name="Rest-of-header"></a>
<div class="header">
<p>
Next: <a href="#The-_0027data_0027" accesskey="n" rel="next">The 'data'</a>, Previous: <a href="#SEXPTYPEs" accesskey="p" rel="prev">SEXPTYPEs</a>, Up: <a href="#SEXPs" accesskey="u" rel="up">SEXPs</a> &nbsp; [<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="Rest-of-header-1"></a>
<h4 class="subsection">1.1.2 Rest of header</h4>

<p>The <code>sxpinfo</code> header is defined as a 32-bit C structure by
</p>
<div class="example">
<pre class="example">struct sxpinfo_struct {
    SEXPTYPE type      :  5;  /* <span class="roman">discussed above</span> */
    unsigned int obj   :  1;  /* <span class="roman">is this an object with a class attribute?</span> */
    unsigned int named :  2;  /* <span class="roman">used to control copying</span> */
    unsigned int gp    : 16;  /* <span class="roman">general purpose, see below</span> */
    unsigned int mark  :  1;  /* <span class="roman">mark object as &lsquo;in use&rsquo; in GC</span> */
    unsigned int debug :  1;
    unsigned int trace :  1;
    unsigned int spare :  1;  /* <span class="roman">debug once</span> */
    unsigned int gcgen :  1;  /* <span class="roman">generation for GC</span> */
    unsigned int gccls :  3;  /* <span class="roman">class of node for GC</span> */
};  /*              Tot: 32 */
</pre></div>

<a name="index-debug-bit"></a>
<p>The <code>debug</code> bit is used for closures and environments.  For
closures it is set by <code>debug()</code> and unset by <code>undebug()</code>, and
indicates that evaluations of the function should be run under the
browser.  For environments it indicates whether the browsing is in
single-step mode.
</p>
<a name="index-trace-bit"></a>
<p>The <code>trace</code> bit is used for functions for <code>trace()</code> and for
other objects when tracing duplications (see <code>tracemem</code>).
</p>
<a name="index-spare-bit"></a>
<p>The <code>spare</code> bit is used for closures to mark them for one
time debugging.
</p>
<a name="index-named-bit"></a>
<a name="index-NAMED"></a>
<a name="index-SET_005fNAMED"></a>
<a name="index-copying-semantics"></a>
<p>The <code>named</code> field is set and accessed by the <code>SET_NAMED</code> and
<code>NAMED</code> macros, and take values <code>0</code>, <code>1</code> and <code>2</code>.
R has a &lsquo;call by value&rsquo; illusion, so an assignment like
</p><div class="example">
<pre class="example">b &lt;- a
</pre></div>

<p>appears to make a copy of <code>a</code> and refer to it as <code>b</code>.
However, if neither <code>a</code> nor <code>b</code> are subsequently altered there
is no need to copy.  What really happens is that a new symbol <code>b</code>
is bound to the same value as <code>a</code> and the <code>named</code> field on the
value object is set (in this case to <code>2</code>).  When an object is about
to be altered, the <code>named</code> field is consulted.  A value of <code>2</code>
means that the object must be duplicated before being changed.  (Note
that this does not say that it is necessary to duplicate, only that it
should be duplicated whether necessary or not.)  A value of <code>0</code>
means that it is known that no other <code>SEXP</code> shares data with this
object, and so it may safely be altered.  A value of <code>1</code> is used
for situations like
</p>
<div class="example">
<pre class="example">dim(a) &lt;- c(7, 2)
</pre></div>

<p>where in principle two copies of <code>a</code> exist for the duration of the
computation as (in principle)
</p>
<div class="example">
<pre class="example">a &lt;- `dim&lt;-`(a, c(7, 2))
</pre></div>

<p>but for no longer, and so some primitive functions can be optimized to
avoid a copy in this case.
</p>
<p>The <code>gp</code> bits are by definition &lsquo;general purpose&rsquo;.  We label these
from 0 to 15.  Bits 0&ndash;5 and bits 14&ndash;15 have been used as described below
(mainly from detective work on the sources).
</p>
<a name="index-gp-bits"></a>
<a name="index-LEVELS"></a>
<a name="index-SETLEVELS"></a>
<p>The bits can be accessed and set by the <code>LEVELS</code> and
<code>SETLEVELS</code> macros, which names appear to date back to the internal
factor and ordered types and are now used in only a few places in the
code.  The <code>gp</code> field is serialized/unserialized for the
<code>SEXPTYPE</code>s other than <code>NILSXP</code>, <code>SYMSXP</code> and
<code>ENVSXP</code>.
</p>
<p>Bits 14 and 15 of <code>gp</code> are used for &lsquo;fancy bindings&rsquo;.  Bit 14 is
used to lock a binding or an environment, and bit 15 is used to indicate
an active binding.  (For the definition of an &lsquo;active binding&rsquo; see the
header comments in file <samp>src/main/envir.c</samp>.)  Bit 15 is used for an
environment to indicate if it participates in the global cache.
</p>
<a name="index-ARGSUSED"></a>
<a name="index-SET_005fARGUSED"></a>
<p>The macros <code>ARGUSED</code> and <code>SET_ARGUSED</code> are used when matching
actual and formal function arguments, and take the values 0, 1 and 2.
</p>
<a name="index-MISSING"></a>
<a name="index-SET_005fMISSING"></a>
<p>The macros <code>MISSING</code> and <code>SET_MISSING</code> are used for pairlists
of arguments.  Four bits are reserved, but only two are used (and
exactly what for is not explained).  It seems that bit 0 is used by
<code>matchArgs</code> to mark missingness on the returned argument list, and
bit 1 is used to mark the use of a default value for an argument copied
to the evaluation frame of a closure.
</p>
<a name="index-DDVAL"></a>
<a name="index-SET_005fDDVAL"></a>
<a name="index-_002e_002e_002e-argument"></a>
<p>Bit 0 is used by macros <code>DDVAL</code> and <code>SET_DDVAL</code>.  This
indicates that a <code>SYMSXP</code> is one of the symbols <code>..n</code> which
are implicitly created when <code>...</code> is processed, and so indicates
that it may need to be looked up in a <code>DOTSXP</code>.
</p>
<a name="index-PRSEEN"></a>
<a name="index-promise"></a>
<p>Bit 0 is used for <code>PRSEEN</code>, a flag to indicate if a promise has
already been seen during the evaluation of the promise (and so to avoid
recursive loops).
</p>
<p>Bit 0 is used for <code>HASHASH</code>, on the <code>PRINTNAME</code> of the
<code>TAG</code> of the frame of an environment. (This bit is not serialized
for <code>CHARSXP</code> objects.)
</p>
<p>Bits 0 and 1 are used for weak references (to indicate &lsquo;ready to
finalize&rsquo;, &lsquo;finalize on exit&rsquo;).
</p>
<p>Bit 0 is used by the condition handling system (on a <code>VECSXP</code>) to
indicate a calling handler.
</p>
<p>Bit 4 is turned on to mark S4 objects.
</p>
<p>Bits 1, 2, 3, 5 and 6 are used for a <code>CHARSXP</code> to denote its
encoding.  Bit 1 indicates that the <code>CHARSXP</code> should be treated as
a set of bytes, not necessarily representing a character in any known
encoding.  Bits 2, 3 and 6 are used to indicate that it is known to be
in Latin-1, UTF-8 or <acronym>ASCII</acronym> respectively.
</p>
<p>Bit 5 for a <code>CHARSXP</code> indicates that it is hashed by its address,
that is <code>NA_STRING</code> or is in the <code>CHARSXP</code> cache (this is not
serialized).  Only exceptionally is a <code>CHARSXP</code> not hashed, and
this should never happen in end-user code.
</p>
<hr>
<a name="The-_0027data_0027"></a>
<div class="header">
<p>
Next: <a href="#Allocation-classes" accesskey="n" rel="next">Allocation classes</a>, Previous: <a href="#Rest-of-header" accesskey="p" rel="prev">Rest of header</a>, Up: <a href="#SEXPs" accesskey="u" rel="up">SEXPs</a> &nbsp; [<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-_0060data_0027"></a>
<h4 class="subsection">1.1.3 The &lsquo;data&rsquo;</h4>

<p>A <code>SEXPREC</code> is a C structure containing the 32-bit header as
described above, three pointers (to the attributes, previous and next
node) and the node data, a union
</p>
<div class="example">
<pre class="example">union {
    struct primsxp_struct primsxp;
    struct symsxp_struct symsxp;
    struct listsxp_struct listsxp;
    struct envsxp_struct envsxp;
    struct closxp_struct closxp;
    struct promsxp_struct promsxp;
} u;
</pre></div>

<p>All of these alternatives apart from the first (an <code>int</code>) are three
pointers, so the union occupies three words.
</p>
<a name="index-vector-type"></a>
<p>The vector types are <code>RAWSXP</code>, <code>CHARSXP</code>, <code>LGLSXP</code>,
<code>INTSXP</code>, <code>REALSXP</code>, <code>CPLXSXP</code>, <code>STRSXP</code>,
<code>VECSXP</code>, <code>EXPRSXP</code> and <code>WEAKREFSXP</code>.  Remember that such
types are a <code>VECTOR_SEXPREC</code>, which again consists of the header
and the same three pointers, but followed by two integers giving the
length and &lsquo;true length&rsquo;<a name="DOCF3" href="#FOOT3"><sup>3</sup></a> of the vector, and then followed by the data (aligned as
required: on most 32-bit systems with a 24-byte <code>VECTOR_SEXPREC</code>
node the data can follow immediately after the node).  The data are a
block of memory of the appropriate length to store &lsquo;true length&rsquo;
elements (rounded up to a multiple of 8 bytes, with the 8-byte blocks
being the &lsquo;Vcells&rsquo; referred in the documentation for <code>gc()</code>).
</p>
<p>The &lsquo;data&rsquo; for the various types are given in the table below.  A lot of
this is interpretation, i.e. the types are not checked.
</p>
<dl compact="compact">
<dt><code>NILSXP</code></dt>
<dd><p>There is only one object of type <code>NILSXP</code>, <code>R_NilValue</code>, with
no data.
</p>
</dd>
<dt><code>SYMSXP</code></dt>
<dd><p>Pointers to three nodes, the name, value and internal, accessed by
<code>PRINTNAME</code> (a <code>CHARSXP</code>), <code>SYMVALUE</code> and
<code>INTERNAL</code>.  (If the symbol&rsquo;s value is a <code>.Internal</code> function,
the last is a pointer to the appropriate <code>SEXPREC</code>.)  Many symbols
have <code>SYMVALUE</code> <code>R_UnboundValue</code>.
</p>
</dd>
<dt><code>LISTSXP</code></dt>
<dd><p>Pointers to the CAR, CDR (usually a <code>LISTSXP</code> or <code>NULL</code>) and
TAG (a <code>SYMSXP</code> or <code>NULL</code>).
</p>
</dd>
<dt><code>CLOSXP</code></dt>
<dd><p>Pointers to the formals (a pairlist), the body and the environment.
</p>
</dd>
<dt><code>ENVSXP</code></dt>
<dd><p>Pointers to the frame, enclosing environment and hash table (<code>NULL</code> or a
<code>VECSXP</code>).  A frame is a tagged pairlist with tag the symbol and
CAR the bound value.
</p>
</dd>
<dt><code>PROMSXP</code></dt>
<dd><p>Pointers to the value, expression and environment (in which to evaluate
the expression).  Once an promise has been evaluated, the environment is
set to <code>NULL</code>.
</p>
</dd>
<dt><code>LANGSXP</code></dt>
<dd><p>A special type of <code>LISTSXP</code> used for function calls.  (The CAR
references the function (perhaps via a symbol or language object), and
the CDR the argument list with tags for named arguments.)  R-level
documentation references to &lsquo;expressions&rsquo; / &lsquo;language objects&rsquo; are
mainly <code>LANGSXP</code>s, but can be symbols (<code>SYMSXP</code>s) or
expression vectors (<code>EXPRSXP</code>s).
</p>
</dd>
<dt><code>SPECIALSXP</code></dt>
<dt><code>BUILTINSXP</code></dt>
<dd><p>An integer giving the offset into the table of
primitives/<code>.Internal</code>s.
</p>
</dd>
<dt><code>CHARSXP</code></dt>
<dd><p><code>length</code>, <code>truelength</code> followed by a block of bytes (allowing
for the <code>nul</code> terminator).
</p>
</dd>
<dt><code>LGLSXP</code></dt>
<dt><code>INTSXP</code></dt>
<dd><p><code>length</code>, <code>truelength</code> followed by a block of C <code>int</code>s
(which are 32 bits on all R platforms).
</p>
</dd>
<dt><code>REALSXP</code></dt>
<dd><p><code>length</code>, <code>truelength</code> followed by a block of C <code>double</code>s.
</p>
</dd>
<dt><code>CPLXSXP</code></dt>
<dd><p><code>length</code>, <code>truelength</code> followed by a block of C99 <code>double
complex</code>s.
</p>
</dd>
<dt><code>STRSXP</code></dt>
<dd><p><code>length</code>, <code>truelength</code> followed by a block of pointers
(<code>SEXP</code>s pointing to <code>CHARSXP</code>s).
</p>
</dd>
<dt><code>DOTSXP</code></dt>
<dd><p>A special type of <code>LISTSXP</code> for the value bound to a <code>...</code>
symbol: a pairlist of promises.
</p>
</dd>
<dt><code>ANYSXP</code></dt>
<dd><p>This is used as a place holder for any type: there are no actual objects
of this type.
</p>
</dd>
<dt><code>VECSXP</code></dt>
<dt><code>EXPRSXP</code></dt>
<dd><p><code>length</code>, <code>truelength</code> followed by a block of pointers.  These
are internally identical (and identical to <code>STRSXP</code>) but differ in
the interpretations placed on the elements.
</p>
</dd>
<dt><code>BCODESXP</code></dt>
<dd><p>For the &lsquo;byte-code&rsquo; objects generated by the compiler.
</p>
</dd>
<dt><code>EXTPTRSXP</code></dt>
<dd><p>Has three pointers, to the pointer, the protection value (an R object
which if alive protects this object) and a tag (a <code>SYMSXP</code>?).
</p>
</dd>
<dt><code>WEAKREFSXP</code></dt>
<dd><p>A <code>WEAKREFSXP</code> is a special <code>VECSXP</code> of length 4, with
elements &lsquo;<samp>key</samp>&rsquo;, &lsquo;<samp>value</samp>&rsquo;, &lsquo;<samp>finalizer</samp>&rsquo; and &lsquo;<samp>next</samp>&rsquo;.
The &lsquo;<samp>key</samp>&rsquo; is <code>NULL</code>, an environment or an external pointer,
and the &lsquo;<samp>finalizer</samp>&rsquo; is a function or <code>NULL</code>.
</p>
</dd>
<dt><code>RAWSXP</code></dt>
<dd><p><code>length</code>, <code>truelength</code> followed by a block of bytes.
</p>
</dd>
<dt><code>S4SXP</code></dt>
<dd><p>two unused pointers and a tag.
</p></dd>
</dl>

<hr>
<a name="Allocation-classes"></a>
<div class="header">
<p>
Previous: <a href="#The-_0027data_0027" accesskey="p" rel="prev">The 'data'</a>, Up: <a href="#SEXPs" accesskey="u" rel="up">SEXPs</a> &nbsp; [<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="Allocation-classes-1"></a>
<h4 class="subsection">1.1.4 Allocation classes</h4>

<a name="index-allocation-classes"></a>
<p>As we have seen, the field <code>gccls</code> in the header is three bits to
label up to 8 classes of nodes.  Non-vector nodes are of class 0, and
&lsquo;small&rsquo; vector nodes are of classes 1 to 5, with a class for custom
allocator vector nodes 6 and &lsquo;large&rsquo; vector nodes being of class 7.  The
&lsquo;small&rsquo; vector nodes are able to store vector data of up to 8, 16, 32,
64 and 128 bytes: larger vectors are <code>malloc</code>-ed individually
whereas the &lsquo;small&rsquo; nodes are allocated from pages of about 2000
bytes. Vector nodes allocated using custom allocators (via
<code>allocVector3</code>) are not counted in the gc memory usage statistics
since their memory semantics is not under R&rsquo;s control and may be
non-standard (e.g., memory could be partially shared across nodes).
</p>

<hr>
<a name="Environments-and-variable-lookup"></a>
<div class="header">
<p>
Next: <a href="#Attributes" accesskey="n" rel="next">Attributes</a>, Previous: <a href="#SEXPs" accesskey="p" rel="prev">SEXPs</a>, Up: <a href="#R-Internal-Structures" accesskey="u" rel="up">R Internal Structures</a> &nbsp; [<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="Environments-and-variable-lookup-1"></a>
<h3 class="section">1.2 Environments and variable lookup</h3>

<a name="index-environment"></a>
<a name="index-variable-lookup"></a>
<p>What users think of as &lsquo;variables&rsquo; are symbols which are bound to
objects in &lsquo;environments&rsquo;.  The word &lsquo;environment&rsquo; is used ambiguously
in R to mean <em>either</em> the frame of an <code>ENVSXP</code> (a pairlist
of symbol-value pairs) <em>or</em> an <code>ENVSXP</code>, a frame plus an
enclosure.
</p>
<a name="index-user-databases"></a>
<p>There are additional places that &lsquo;variables&rsquo; can be looked up, called
&lsquo;user databases&rsquo; in comments in the code.  These seem undocumented in
the R sources, but apparently refer to the <strong>RObjectTable</strong> package
at <a href="http://www.omegahat.org/RObjectTables/">http://www.omegahat.org/RObjectTables/</a>.
</p>
<a name="index-base-environment"></a>
<a name="index-environment_002c-base"></a>
<p>The base environment is special.  There is an <code>ENVSXP</code> environment
with enclosure the empty environment <code>R_EmptyEnv</code>, but the frame of
that environment is not used.  Rather its bindings are part of the
global symbol table, being those symbols in the global symbol table
whose values are not <code>R_UnboundValue</code>.  When R is started the
internal functions are installed (by C code) in the symbol table, with
primitive functions having values and <code>.Internal</code> functions having
what would be their values in the field accessed by the <code>INTERNAL</code>
macro.  Then <code>.Platform</code> and <code>.Machine</code> are computed and the
base package is loaded into the base environment followed by the system
profile.
</p>
<p>The frames of environments (and the symbol table) are normally hashed
for faster access (including insertion and deletion).
</p>
<p>By default R maintains a (hashed) global cache of &lsquo;variables&rsquo; (that
is symbols and their bindings) which have been found, and this refers
only to environments which have been marked to participate, which
consists of the global environment (aka the user workspace), the base
environment plus environments<a name="DOCF4" href="#FOOT4"><sup>4</sup></a> which have been <code>attach</code>ed.  When an environment is either
<code>attach</code>ed or <code>detach</code>ed, the names of its symbols are flushed
from the cache.  The cache is used whenever searching for variables from
the global environment (possibly as part of a recursive search).
</p>
<table summary="" class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">&bull; <a href="#Search-paths" accesskey="1">Search paths</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">&bull; <a href="#Namespaces" accesskey="2">Namespaces</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">&bull; <a href="#Hash-table" accesskey="3">Hash table</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
</table>

<hr>
<a name="Search-paths"></a>
<div class="header">
<p>
Next: <a href="#Namespaces" accesskey="n" rel="next">Namespaces</a>, Previous: <a href="#Environments-and-variable-lookup" accesskey="p" rel="prev">Environments and variable lookup</a>, Up: <a href="#Environments-and-variable-lookup" accesskey="u" rel="up">Environments and variable lookup</a> &nbsp; [<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="Search-paths-1"></a>
<h4 class="subsection">1.2.1 Search paths</h4>

<a name="index-search-path"></a>
<p>S has the notion of a &lsquo;search path&rsquo;: the lookup for a &lsquo;variable&rsquo;
leads (possibly through a series of frames) to the &lsquo;session frame&rsquo; the
&lsquo;working directory&rsquo; and then along the search path.  The search path is
a series of databases (as returned by <code>search()</code>) which contain the
system functions (but not necessarily at the end of the path, as by
default the equivalent of packages are added at the end).
</p>
<p>R has a variant on the S model.  There is a search path (also
returned by <code>search()</code>) which consists of the global environment
(aka user workspace) followed by environments which have been attached
and finally the base environment.  Note that unlike S it is not
possible to attach environments before the workspace nor after the base
environment.
</p>
<p>However, the notion of variable lookup is more general in R, hence
the plural in the title of this subsection.  Since environments have
enclosures, from any environment there is a search path found by looking
in the frame, then the frame of its enclosure and so on.  Since loops
are not allowed, this process will eventually terminate: it can
terminate at either the base environment or the empty environment.  (It
can be conceptually simpler to think of the search always terminating at
the empty environment, but with an optimization to stop at the base
environment.)  So the &lsquo;search path&rsquo; describes the chain of environments
which is traversed once the search reaches the global environment.
</p>
<hr>
<a name="Namespaces"></a>
<div class="header">
<p>
Next: <a href="#Hash-table" accesskey="n" rel="next">Hash table</a>, Previous: <a href="#Search-paths" accesskey="p" rel="prev">Search paths</a>, Up: <a href="#Environments-and-variable-lookup" accesskey="u" rel="up">Environments and variable lookup</a> &nbsp; [<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="Namespaces-1"></a>
<h4 class="subsection">1.2.2 Namespaces</h4>

<a name="index-namespace"></a>
<p>Namespaces are environments associated with packages (and once again
the base package is special and will be considered separately).  A
package <code><var>pkg</var></code> with a namespace defines two environments
<code>namespace:<var>pkg</var></code> and <code>package:<var>pkg</var></code>: it is
<code>package:<var>pkg</var></code> that can be <code>attach</code>ed and form part of
the search path.
</p>
<p>The objects defined by the R code in the package are symbols with
bindings in the <code>namespace:<var>pkg</var></code> environment.  The
<code>package:<var>pkg</var></code> environment is populated by selected symbols
from the <code>namespace:<var>pkg</var></code> environment (the exports).  The
enclosure of this environment is an environment populated with the
explicit imports from other namespaces, and the enclosure of
<em>that</em> environment is the base namespace.  (So the illusion of the
imports being in the namespace environment is created via the
environment tree.)  The enclosure of the base namespace is the global
environment, so the search from a package namespace goes via the
(explicit and implicit) imports to the standard &lsquo;search path&rsquo;.
</p>
<a name="index-base-namespace"></a>
<a name="index-namespace_002c-base"></a>
<a name="index-R_005fBaseNamespace"></a>
<p>The base namespace environment <code>R_BaseNamespace</code> is another
<code>ENVSXP</code> that is special-cased.  It is effectively the same thing
as the base environment <code>R_BaseEnv</code> <em>except</em> that its
enclosure is the global environment rather than the empty environment:
the internal code diverts lookups in its frame to the global symbol
table.
</p>
<hr>
<a name="Hash-table"></a>
<div class="header">
<p>
Previous: <a href="#Namespaces" accesskey="p" rel="prev">Namespaces</a>, Up: <a href="#Environments-and-variable-lookup" accesskey="u" rel="up">Environments and variable lookup</a> &nbsp; [<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="Hash-table-1"></a>
<h4 class="subsection">1.2.3 Hash table</h4>

<p>Environments in R usually have a hash table, and nowadays that is the
default in <code>new.env()</code>.  It is stored as a <code>VECSXP</code> where
<code>length</code> is used for the allocated size of the table and
<code>truelength</code> is the number of primary slots in use&mdash;the pointer to
the <code>VECSXP</code> is part of the header of a <code>SEXP</code> of type
<code>ENVSXP</code>, and this points to <code>R_NilValue</code> if the environment
is not hashed.
</p>
<p>For the pros and cons of hashing, see a basic text on Computer Science.
</p>
<p>The code to implement hashed environments is in <samp>src/main/envir.c</samp>.
Unless set otherwise (e.g. by the <code>size</code> argument of
<code>new.env()</code>) the initial table size is <code>29</code>.  The table will
be resized by a factor of 1.2 once the load factor (the proportion of
primary slots in use) reaches 85%.
</p>
<p>The hash chains are stored as pairlist elements of the <code>VECSXP</code>:
items are inserted at the front of the pairlist.  Hashing is principally
designed for fast searching of environments, which are from time to time
added to but rarely deleted from, so items are not actually deleted but
have their value set to <code>R_UnboundValue</code>.
</p>

<hr>
<a name="Attributes"></a>
<div class="header">
<p>
Next: <a href="#Contexts" accesskey="n" rel="next">Contexts</a>, Previous: <a href="#Environments-and-variable-lookup" accesskey="p" rel="prev">Environments and variable lookup</a>, Up: <a href="#R-Internal-Structures" accesskey="u" rel="up">R Internal Structures</a> &nbsp; [<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="Attributes-1"></a>
<h3 class="section">1.3 Attributes</h3>

<a name="index-attributes"></a>
<a name="index-ATTRIB"></a>
<a name="index-SET_005fATTRIB"></a>
<a name="index-DUPLICATE_005fATTRIB"></a>
<p>As we have seen, every <code>SEXPREC</code> has a pointer to the attributes of
the node (default <code>R_NilValue</code>).  The attributes can be
accessed/set by the macros/functions <code>ATTRIB</code> and
<code>SET_ATTRIB</code>, but such direct access is normally only used to check
if the attributes are <code>NULL</code> or to reset them.  Otherwise access
goes through the functions <code>getAttrib</code> and <code>setAttrib</code> which
impose restrictions on the attributes.  One thing to watch is that if
you copy attributes from one object to another you may (un)set the
<code>&quot;class&quot;</code> attribute and so need to copy the object and S4 bits as
well.  There is a macro/function <code>DUPLICATE_ATTRIB</code> to automate
this.
</p>
<p>Note that the &lsquo;attributes&rsquo; of a <code>CHARSXP</code> are used as part of the
management of the <code>CHARSXP</code> cache: of course <code>CHARSXP</code>&rsquo;s are
not user-visible but C-level code might look at their attributes.
</p>
<p>The code assumes that the attributes of a node are either
<code>R_NilValue</code> or a pairlist of non-zero length (and this is checked
by <code>SET_ATTRIB</code>).  The attributes are named (via tags on the
pairlist).  The replacement function <code>attributes&lt;-</code> ensures that
<code>&quot;dim&quot;</code> precedes <code>&quot;dimnames&quot;</code> in the pairlist.  Attribute
<code>&quot;dim&quot;</code> is one of several that is treated specially: the values are
checked, and any <code>&quot;names&quot;</code> and <code>&quot;dimnames&quot;</code> attributes are
removed.  Similarly, you cannot set <code>&quot;dimnames&quot;</code> without having set
<code>&quot;dim&quot;</code>, and the value assigned must be a list of the correct
length and with elements of the correct lengths (and all zero-length
elements are replaced by <code>NULL</code>).
</p>
<p>The other attributes which are given special treatment are
<code>&quot;names&quot;</code>, <code>&quot;class&quot;</code>, <code>&quot;tsp&quot;</code>, <code>&quot;comment&quot;</code> and
<code>&quot;row.names&quot;</code>.  For pairlist-like objects the names are not stored
as an attribute but (as symbols) as the tags: however the R interface
makes them look like conventional attributes, and for one-dimensional
arrays they are stored as the first element of the <code>&quot;dimnames&quot;</code>
attribute.  The C code ensures that the <code>&quot;tsp&quot;</code> attribute is an
<code>REALSXP</code>, the frequency is positive and the implied length agrees
with the number of rows of the object being assigned to.  Classes and
comments are restricted to character vectors, and assigning a
zero-length comment or class removes the attribute.  Setting or removing
a <code>&quot;class&quot;</code> attribute sets the object bit appropriately.  Integer
row names are converted to and from the internal compact representation.
</p>
<a name="index-copying-semantics-1"></a>
<p>Care needs to be taken when adding attributes to objects of the types
with non-standard copying semantics.  There is only one object of type
<code>NILSXP</code>, <code>R_NilValue</code>, and that should never have attributes
(and this is enforced in <code>installAttrib</code>).  For environments,
external pointers and weak references, the attributes should be relevant
to all uses of the object: it is for example reasonable to have a name
for an environment, and also a <code>&quot;path&quot;</code> attribute for those
environments populated from R code in a package.
</p>
<a name="index-attributes_002c-preserving"></a>
<a name="index-preserving-attributes"></a>
<p>When should attributes be preserved under operations on an object?
Becker, Chambers &amp; Wilks (1988, pp. 144&ndash;6) give some guidance.  Scalar
functions (those which operate element-by-element on a vector and whose
output is similar to the input) should preserve attributes (except
perhaps class, and if they do preserve class they need to preserve the
<code>OBJECT</code> and S4 bits).  Binary operations normally call
<a name="index-copyMostAttributes"></a>
<code>copyMostAttributes</code> to copy most attributes from the longer
argument (and if they are of the same length from both, preferring the
values on the first).  Here &lsquo;most&rsquo; means all except the <code>names</code>,
<code>dim</code> and <code>dimnames</code> which are set appropriately by the code
for the operator.
</p>
<p>Subsetting (other than by an empty index) generally drops all attributes
except <code>names</code>, <code>dim</code> and <code>dimnames</code> which are reset as
appropriate.  On the other hand, subassignment generally preserves such
attributes even if the length is changed.  Coercion drops all
attributes. For example:
</p>
<div class="example">
<pre class="example">&gt; x &lt;- structure(1:8, names=letters[1:8], comm=&quot;a comment&quot;)
&gt; x[]
a b c d e f g h
1 2 3 4 5 6 7 8
attr(,&quot;comm&quot;)
[1] &quot;a comment&quot;
&gt; x[1:3]
a b c
1 2 3
&gt; x[3] &lt;- 3
&gt; x
a b c d e f g h
1 2 3 4 5 6 7 8
attr(,&quot;comm&quot;)
[1] &quot;a comment&quot;
&gt; x[9] &lt;- 9
&gt; x
a b c d e f g h
1 2 3 4 5 6 7 8 9
attr(,&quot;comm&quot;)
[1] &quot;a comment&quot;
</pre></div>


<hr>
<a name="Contexts"></a>
<div class="header">
<p>
Next: <a href="#Argument-evaluation" accesskey="n" rel="next">Argument evaluation</a>, Previous: <a href="#Attributes" accesskey="p" rel="prev">Attributes</a>, Up: <a href="#R-Internal-Structures" accesskey="u" rel="up">R Internal Structures</a> &nbsp; [<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="Contexts-1"></a>
<h3 class="section">1.4 Contexts</h3>

<a name="index-context"></a>
<p><em>Contexts</em> are the internal mechanism used to keep track of where a
computation has got to (and from where), so that control-flow constructs
can work and reasonable information can be produced on error conditions
(such as <em>via</em> traceback), and otherwise (the <code>sys.<var>xxx</var></code>
functions).
</p>
<p>Execution contexts are a stack of C <code>structs</code>:
</p>
<div class="example">
<pre class="example">typedef struct RCNTXT {
    struct RCNTXT *nextcontext; /* <span class="roman">The next context up the chain</span> */
    int callflag;               /* <span class="roman">The context &lsquo;type&rsquo;</span> */
    JMP_BUF cjmpbuf;            /* <span class="roman">C stack and register information</span> */
    int cstacktop;              /* <span class="roman">Top of the pointer protection stack</span> */
    int evaldepth;              /* <span class="roman">Evaluation depth at inception</span> */
    SEXP promargs;              /* <span class="roman">Promises supplied to closure</span> */
    SEXP callfun;               /* <span class="roman">The closure called</span> */
    SEXP sysparent;             /* <span class="roman">Environment the closure was called from</span> */
    SEXP call;                  /* <span class="roman">The call that effected this context</span> */
    SEXP cloenv;                /* <span class="roman">The environment</span> */
    SEXP conexit;               /* <span class="roman">Interpreted <code>on.exit</code> code</span> */
    void (*cend)(void *);       /* <span class="roman">C <code>on.exit</code> thunk</span> */
    void *cenddata;             /* <span class="roman">Data for C <code>on.exit</code> thunk</span> */
    char *vmax;                 /* <span class="roman">Top of the <code>R_alloc</code> stack</span> */
    int intsusp;                /* <span class="roman">Interrupts are suspended</span> */
    SEXP handlerstack;          /* <span class="roman">Condition handler stack</span> */
    SEXP restartstack;          /* <span class="roman">Stack of available restarts</span> */
    struct RPRSTACK *prstack;   /* <span class="roman">Stack of pending promises</span> */
} RCNTXT, *context;
</pre></div>

<p>plus additional fields for the byte-code compiler.  The &lsquo;types&rsquo;
are from
</p>
<div class="example">
<pre class="example">enum {
    CTXT_TOPLEVEL = 0,  /* <span class="roman">toplevel context</span> */
    CTXT_NEXT     = 1,  /* <span class="roman">target for <code>next</code></span> */
    CTXT_BREAK    = 2,  /* <span class="roman">target for <code>break</code></span> */
    CTXT_LOOP     = 3,  /* <span class="roman"><code>break</code> or <code>next</code> target</span> */
    CTXT_FUNCTION = 4,  /* <span class="roman">function closure</span> */
    CTXT_CCODE    = 8,  /* <span class="roman">other functions that need error cleanup</span> */
    CTXT_RETURN   = 12, /* <span class="roman"><code>return()</code> from a closure</span> */
    CTXT_BROWSER  = 16, /* <span class="roman">return target on exit from browser</span> */
    CTXT_GENERIC  = 20, /* <span class="roman">rather, running an S3 method</span> */
    CTXT_RESTART  = 32, /* <span class="roman">a call to <code>restart</code> was made from a closure</span> */
    CTXT_BUILTIN  = 64  /* <span class="roman">builtin internal function</span> */
};
</pre></div>

<p>where the <code>CTXT_FUNCTION</code> bit is on wherever function closures are
involved.
</p>
<p>Contexts are created by a call to <code>begincontext</code> and ended by a
call to <code>endcontext</code>: code can search up the stack for a
particular type of context via <code>findcontext</code> (and jump there) or
jump to a specific context via <code>R_JumpToContext</code>.
<code>R_ToplevelContext</code> is the &lsquo;idle&rsquo; state (normally the command
prompt), and <code>R_GlobalContext</code> is the top of the stack.
</p>
<p>Note that whilst calls to closures and builtins set a context, those to special
internal functions never do.
</p>
<a name="index-UseMethod"></a>
<a name="index-method-dispatch"></a>
<p>Dispatching from a S3 generic (via <code>UseMethod</code> or its internal
equivalent) or calling <code>NextMethod</code> sets the context type to
<code>CTXT_GENERIC</code>.  This is used to set the <code>sysparent</code> of the
method call to that of the <code>generic</code>, so the method appears to have
been called in place of the generic rather than from the generic.
</p>
<p>The R <code>sys.frame</code> and <code>sys.call</code> functions work by counting
calls to closures (type <code>CTXT_FUNCTION</code>) from either end of the
context stack.
</p>
<p>Note that the <code>sysparent</code> element of the structure is not the same
thing as <code>sys.parent()</code>.  Element <code>sysparent</code> is primarily
used in managing changes of the function being evaluated, i.e. by
<code>Recall</code> and method dispatch.
</p>
<p><code>CTXT_CCODE</code> contexts are currently used in <code>cat()</code>,
<code>load()</code>, <code>scan()</code> and <code>write.table()</code> (to close the
connection on error), by <code>PROTECT</code>, serialization (to recover from
errors, e.g. free buffers) and within the error handling code (to
raise the C stack limit and reset some variables).
</p>

<hr>
<a name="Argument-evaluation"></a>
<div class="header">
<p>
Next: <a href="#Autoprinting" accesskey="n" rel="next">Autoprinting</a>, Previous: <a href="#Contexts" accesskey="p" rel="prev">Contexts</a>, Up: <a href="#R-Internal-Structures" accesskey="u" rel="up">R Internal Structures</a> &nbsp; [<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="Argument-evaluation-1"></a>
<h3 class="section">1.5 Argument evaluation</h3>

<a name="index-argument-evaluation"></a>
<p>As we have seen, functions in R come in three types, closures
(<code>SEXPTYPE</code> <code>CLOSXP</code>), specials (<code>SPECIALSXP</code>) and
builtins (<code>BUILTINSXP</code>).  In this section we consider when (and if)
the actual arguments of function calls are evaluated.  The rules are
different for the internal (special/builtin) and R-level functions
(closures).
</p>
<p>For a call to a closure, the actual and formal arguments are matched and
a matched call (another <code>LANGSXP</code>) is constructed.  This process
first replaces the actual argument list by a list of promises to the
values supplied.  It then constructs a new environment which contains
the names of the formal parameters matched to actual or default values:
all the matched values are promises, the defaults as promises to be
evaluated in the environment just created.  That environment is then
used for the evaluation of the body of the function, and promises will
be forced (and hence actual or default arguments evaluated) when they
are encountered.
<a name="index-NAMED-1"></a>
(Evaluating a promise sets <code>NAMED = 2</code> on its value, so if the
argument was a symbol its binding is regarded as having multiple
references during the evaluation of the closure call.)
</p>
<p>If the closure is an S3 generic (that is, contains a call to
<code>UseMethod</code>) the evaluation process is the same until the
<code>UseMethod</code> call is encountered.  At that point the argument on
which to do dispatch (normally the first) will be evaluated if it has
not been already.  If a method has been found which is a closure, a new
evaluation environment is created for it containing the matched
arguments of the method plus any new variables defined so far during the
evaluation of the body of the generic.  (Note that this means changes to
the values of the formal arguments in the body of the generic are
discarded when calling the method, but <em>actual</em> argument promises
which have been forced retain the values found when they were forced.
On the other hand, missing arguments have values which are promises to
use the default supplied by the method and not by the generic.)  If the
method found is a primitive it is called with the matched argument list
of promises (possibly already forced) used for the generic.
</p>
<a name="index-builtin-function"></a>
<a name="index-special-function"></a>
<a name="index-primitive-function"></a>
<a name="index-_002eInternal-function"></a>
<p>The essential difference<a name="DOCF5" href="#FOOT5"><sup>5</sup></a> between special and builtin functions is
that the arguments of specials are not evaluated before the C code is
called, and those of builtins are.  Note that being a special/builtin is
separate from being primitive or <code>.Internal</code>: <code>quote</code> is a
special primitive, <code>+</code> is a builtin primitive, <code>cbind</code> is a
special <code>.Internal</code> and <code>grep</code> is a builtin <code>.Internal</code>.
</p>
<a name="index-generic_002c-internal"></a>
<a name="index-DispatchOrEval"></a>
<p>Many of the internal functions are internal generics, which for specials
means that they do not evaluate their arguments on call, but the C code
starts with a call to <code>DispatchOrEval</code>.  The latter evaluates the
first argument, and looks for a method based on its class.  (If S4
dispatch is on, S4 methods are looked for first, even for S3 classes.)
If it finds a method, it dispatches to that method with a call based on
promises to evaluate the remaining arguments.  If no method is found,
the remaining arguments are evaluated before return to the internal
generic.
</p>
<a name="index-generic_002c-generic"></a>
<a name="index-DispatchGeneric"></a>
<p>The other way that internal functions can be generic is to be group
generic.  Most such functions are builtins (so immediately evaluate all
their arguments), and all contain a call to the C function
<code>DispatchGeneric</code>.  There are some peculiarities over the number of
arguments for the <code>&quot;Math&quot;</code> group generic, with some members
allowing only one argument, some having two (with a default for the
second) and <code>trunc</code> allows one or more but the default method only
accepts one.
</p>
<table summary="" class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">&bull; <a href="#Missingness" accesskey="1">Missingness</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">&bull; <a href="#Dot_002ddot_002ddot-arguments" accesskey="2">Dot-dot-dot arguments</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
</table>

<hr>
<a name="Missingness"></a>
<div class="header">
<p>
Next: <a href="#Dot_002ddot_002ddot-arguments" accesskey="n" rel="next">Dot-dot-dot arguments</a>, Previous: <a href="#Argument-evaluation" accesskey="p" rel="prev">Argument evaluation</a>, Up: <a href="#Argument-evaluation" accesskey="u" rel="up">Argument evaluation</a> &nbsp; [<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="Missingness-1"></a>
<h4 class="subsection">1.5.1 Missingness</h4>

<a name="index-missingness"></a>
<p>Actual arguments to (non-internal) R functions can be fewer than are
required to match the formal arguments of the function.  Having
unmatched formal arguments will not matter if the argument is never used
(by lazy evaluation),  but when the argument is evaluated, either its
default value is evaluated (within the evaluation environment of the
function) or an error is thrown with a message along the lines of
</p>
<div class="example">
<pre class="example">argument &quot;foobar&quot; is missing, with no default
</pre></div>

<a name="index-MISSING-1"></a>
<a name="index-R_005fMissingArg"></a>
<p>Internally missingness is handled by two mechanisms. The object
<code>R_MissingArg</code> is used to indicate that a formal argument has no
(default) value.  When matching the actual arguments to the formal
arguments, a new argument list is constructed from the formals all of
whose values are <code>R_MissingArg</code> with the first <code>MISSING</code> bit
set.  Then whenever a formal argument is matched to an actual argument,
the corresponding member of the new argument list has its value set to
that of the matched actual argument, and if that is not
<code>R_MissingArg</code> the missing bit is unset.
</p>
<p>This new argument list is used to form the evaluation frame for the
function, and if named arguments are subsequently given a new value
(before they are evaluated) the missing bit is cleared.
</p>
<p>Missingness of arguments can be interrogated via the <code>missing()</code>
function.  An argument is clearly missing if its missing bit is set or
if the value is <code>R_MissingArg</code>.  However, missingness can be passed
on from function to function, for using a formal argument as an actual
argument in a function call does not count as evaluation.  So
<code>missing()</code> has to examine the value (a promise) of a
non-yet-evaluated formal argument to see if it might be missing, which
might involve investigating a promise and so on &hellip;.
</p>
<p>Special primitives also need to handle missing arguments, and in some
case (e.g. <code>log</code>) that is why they are special and not
builtin.  This is usually done by testing if an argument&rsquo;s value is
<code>R_MissingArg</code>.
</p>
<hr>
<a name="Dot_002ddot_002ddot-arguments"></a>
<div class="header">
<p>
Previous: <a href="#Missingness" accesskey="p" rel="prev">Missingness</a>, Up: <a href="#Argument-evaluation" accesskey="u" rel="up">Argument evaluation</a> &nbsp; [<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="Dot_002ddot_002ddot-arguments-1"></a>
<h4 class="subsection">1.5.2 Dot-dot-dot arguments</h4>

<a name="index-_002e_002e_002e-argument-1"></a>
<p>Dot-dot-dot arguments are convenient when writing functions, but
complicate the internal code for argument evaluation.
</p>
<p>The formals of a function with a <code>...</code> argument represent that as a
single argument like any other argument, with tag the symbol
<code>R_DotsSymbol</code>.  When the actual arguments are matched to the
formals, the value of the <code>...</code> argument is of <code>SEXPTYPE</code>
<code>DOTSXP</code>, a pairlist of promises (as used for matched arguments)
but distinguished by the <code>SEXPTYPE</code>.
</p>
<p>Recall that the evaluation frame for a function initially contains the
<code><var>name</var>=<var>value</var></code> pairs from the matched call, and hence
this will be true for <code>...</code> as well.  The value of <code>...</code> is a
(special) pairlist whose elements are referred to by the special symbols
<code>..1</code>, <code>..2</code>, &hellip; which have the <code>DDVAL</code> bit set:
when one of these is encountered it is looked up (via <code>ddfindVar</code>)
in the value of the <code>...</code> symbol in the evaluation frame.
</p>
<p>Values of arguments matched to a <code>...</code> argument can be missing.
</p>
<p>Special primitives may need to handle <code>...</code> arguments: see for
example the internal code of <code>switch</code> in file
<samp>src/main/builtin.c</samp>.
</p>
<hr>
<a name="Autoprinting"></a>
<div class="header">
<p>
Next: <a href="#The-write-barrier" accesskey="n" rel="next">The write barrier</a>, Previous: <a href="#Argument-evaluation" accesskey="p" rel="prev">Argument evaluation</a>, Up: <a href="#R-Internal-Structures" accesskey="u" rel="up">R Internal Structures</a> &nbsp; [<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="Autoprinting-1"></a>
<h3 class="section">1.6 Autoprinting</h3>

<a name="index-autoprinting"></a>
<a name="index-R_005fVisible"></a>

<p>Whether the returned value of a top-level R expression is printed is
controlled by the global boolean variable <code>R_Visible</code>.  This is set
(to true or false) on entry to all primitive and internal functions
based on the <code>eval</code> column of the table in file
<samp>src/main/names.c</samp>: the appropriate setting can be extracted by the
macro <code>PRIMPRINT</code>.
<a name="index-PRIMPRINT"></a>
</p>
<a name="index-invisible"></a>
<p>The R primitive function <code>invisible</code> makes use of this
mechanism: it just sets <code>R_Visible = FALSE</code> before entry and
returns its argument.
</p>
<p>For most functions the intention will be that the setting of
<code>R_Visible</code> when they are entered is the setting used when they
return, but there need to be exceptions.  The R functions
<code>identify</code>, <code>options</code>, <code>system</code> and <code>writeBin</code>
determine whether the result should be visible from the arguments or
user action.  Other functions themselves dispatch functions which may
change the visibility flag: examples<a name="DOCF6" href="#FOOT6"><sup>6</sup></a> are
<code>.Internal</code>, <code>do.call</code>, <code>eval</code>, <code>withVisible</code>,
<code>if</code>, <code>NextMethod</code>, <code>Recall</code>, <code>recordGraphics</code>,
<code>standardGeneric</code>, <code>switch</code> and <code>UseMethod</code>.
</p>
<p>&lsquo;Special&rsquo; primitive and internal functions evaluate their arguments
internally <em>after</em> <code>R_Visible</code> has been set, and evaluation of
the arguments (e.g. an assignment as in PR#9263)) can change the value
of the flag.
</p>
<p>The <code>R_Visible</code> flag can also get altered during the evaluation of
a function, with comments in the code about <code>warning</code>,
<code>writeChar</code> and graphics functions calling <code>GText</code> (PR#7397).
(Since the C-level function <code>eval</code> sets <code>R_Visible</code>, this
could apply to any function calling it.  Since it is called when
evaluating promises, even object lookup can change <code>R_Visible</code>.)
Internal and primitive functions force the documented setting of
<code>R_Visible</code> on return, unless the C code is allowed to change it
(the exceptions above are indicated by <code>PRIMPRINT</code> having value 2).
</p>
<p>The actual autoprinting is done by <code>PrintValueEnv</code> in file
<samp>print.c</samp>.  If the object to be printed has the S4 bit set and S4
methods dispatch is on, <code>show</code> is called to print the object.
Otherwise, if the object bit is set (so the object has a
<code>&quot;class&quot;</code> attribute), <code>print</code> is called to dispatch methods:
for objects without a class the internal code of <code>print.default</code>
is called.
</p>

<hr>
<a name="The-write-barrier"></a>
<div class="header">
<p>
Next: <a href="#Serialization-Formats" accesskey="n" rel="next">Serialization Formats</a>, Previous: <a href="#Autoprinting" accesskey="p" rel="prev">Autoprinting</a>, Up: <a href="#R-Internal-Structures" accesskey="u" rel="up">R Internal Structures</a> &nbsp; [<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-write-barrier-and-the-garbage-collector"></a>
<h3 class="section">1.7 The write barrier and the garbage collector</h3>

<a name="index-write-barrier"></a>
<a name="index-garbage-collector"></a>
<p>R has long had a generational garbage collector, and bit <code>gcgen</code>
in the <code>sxpinfo</code> header is used in the implementation of this.
This is used in conjunction with the <code>mark</code> bit to identify two
previous generations.
</p>
<p>There are three levels of collections.  Level 0 collects only the
youngest generation, level 1 collects the two youngest generations and
level 2 collects all generations.  After 20 level-0 collections the next
collection is at level 1, and after 5 level-1 collections at level 2.
Further, if a level-<var>n</var> collection fails to provide 20% free space
(for each of nodes and the vector heap), the next collection will be at
level <var>n+1</var>.  (The R-level function <code>gc()</code> performs a
level-2 collection.)
</p>
<p>A generational collector needs to efficiently &lsquo;age&rsquo; the objects,
especially list-like objects (including <code>STRSXP</code>s).  This is done
by ensuring that the elements of a list are regarded as at least as old
as the list <em>when they are assigned</em>.  This is handled by the
functions <code>SET_VECTOR_ELT</code> and <code>SET_STRING_ELT</code>, which is why
they are functions and not macros.  Ensuring the integrity of such
operations is termed the <em>write barrier</em> and is done by making the
<code>SEXP</code> opaque and only providing access via functions (which cannot
be used as lvalues in assignments in C).
</p>
<p>All code in R extensions is by default behind the write barrier.  The
only way to obtain direct access to the internals of the <code>SEXPREC</code>s
is to define &lsquo;<samp>USE_RINTERNALS</samp>&rsquo; before including header file
<samp>Rinternals.h</samp>, which is normally defined in <samp>Defn.h</samp>.  To
enable a check on the way that the access is used, R can be compiled
with flag <samp>--enable-strict-barrier</samp> which ensures that header
<samp>Defn.h</samp> does not define &lsquo;<samp>USE_RINTERNALS</samp>&rsquo; and hence that
<code>SEXP</code> is opaque in most of R itself.  (There are some necessary
exceptions: foremost in file <samp>memory.c</samp> where the accessor
functions are defined and also in file <samp>size.c</samp> which needs access
to the sizes of the internal structures.)
</p>
<p>For background papers see
<a href="http://homepage.stat.uiowa.edu/~luke/R/barrier.html">http://homepage.stat.uiowa.edu/~luke/R/barrier.html</a> and
<a href="http://homepage.stat.uiowa.edu/~luke/R/gengcnotes.html">http://homepage.stat.uiowa.edu/~luke/R/gengcnotes.html</a>.
</p>
<hr>
<a name="Serialization-Formats"></a>
<div class="header">
<p>
Next: <a href="#Encodings-for-CHARSXPs" accesskey="n" rel="next">Encodings for CHARSXPs</a>, Previous: <a href="#The-write-barrier" accesskey="p" rel="prev">The write barrier</a>, Up: <a href="#R-Internal-Structures" accesskey="u" rel="up">R Internal Structures</a> &nbsp; [<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="Serialization-Formats-1"></a>
<h3 class="section">1.8 Serialization Formats</h3>

<a name="index-serialization"></a>
<p>Serialized versions of R objects are used by <code>load</code>/<code>save</code>
and also at a slightly lower level by <code>saveRDS</code>/<code>readRDS</code> (and
their earlier &lsquo;internal&rsquo; dot-name versions) and
<code>serialize</code>/<code>unserialize</code>.  These differ in what they
serialize to (a file, a connection, a raw vector) and whether they are
intended to serialize a single object or a collection of objects
(typically the workspace).  <code>save</code> writes a header at the beginning
of the file (a single LF-terminated line) which the lower-level versions
do not.
</p>
<p><code>save</code> and <code>saveRDS</code> allow various forms of compression, and
<code>gzip</code> compression is the default (except for <acronym>ASCII</acronym>
saves).  Compression is applied to the whole file stream, including the
headers, so serialized files can be uncompressed or re-compressed by
external programs.  Both <code>load</code> and <code>readRDS</code> can read
<code>gzip</code>, <code>bzip2</code> and <code>xz</code> forms of compression
when reading from a file, and <code>gzip</code> compression when reading
from a connection.
</p>
<p>R has used the same serialization format since R 1.4.0 in December
2001.  Earlier formats are still supported via <code>load</code> and
<code>save</code> but such formats are not described here. The current
serialization format is called &lsquo;version 2&rsquo;, and has been expanded in
back-compatible ways since its inception, for example to support
additional <code>SEXPTYPE</code>s.
</p>
<p><code>save</code> works by writing a single-line header (typically
<code>RDX2\n</code> for a binary save: the only other current value is
<code>RDA2\n</code> for <code>save(files=TRUE)</code>), then creating a tagged
pairlist of the objects to be saved and serializing that single object.
<code>load</code> reads the header line, unserializes a single object (a
pairlist or a vector list) and assigns the elements of the object in the
specified environment.  The header line serves two purposes in R: it
identifies the serialization format so <code>load</code> can switch to the
appropriate reader code, and the linefeed allows the detection of files
which have been subjected to a non-binary transfer which re-mapped line
endings.  It can also be thought of as a &lsquo;magic number&rsquo; in the sense
used by the <code>file</code> program (although R save files are not yet
by default known to that program).
</p>
<p>Serialization in R needs to take into account that objects may
contain references to environments, which then have enclosing
environments and so on.  (Environments recognized as package or name
space environments are saved by name.)  There are &lsquo;reference objects&rsquo;
which are not duplicated on copy and should remain shared on
unserialization.  These are weak references, external pointers and
environments other than those associated with packages, namespaces and
the global environment.  These are handled via a hash table, and
references after the first are written out as a reference marker indexed
by the table entry.
</p>
<p>Version-2 serialization first writes a header indicating the format
(normally &lsquo;<samp>X\n</samp>&rsquo; for an XDR format binary save, but &lsquo;<samp>A\n</samp>&rsquo;,
ASCII, and &lsquo;<samp>B\n</samp>&rsquo;, native word-order binary, can also occur) and
then three integers giving the version of the format and two R
versions (packed by the <code>R_Version</code> macro from <samp>Rversion.h</samp>).
(Unserialization interprets the two versions as the version of R
which wrote the file followed by the minimal version of R needed to
read the format.)  Serialization then writes out the object recursively
using function <code>WriteItem</code> in file <samp>src/main/serialize.c</samp>.
</p>
<p>Some objects are written as if they were <code>SEXPTYPE</code>s: such
pseudo-<code>SEXPTYPE</code>s cover <code>R_NilValue</code>, <code>R_EmptyEnv</code>,
<code>R_BaseEnv</code>, <code>R_GlobalEnv</code>, <code>R_UnboundValue</code>,
<code>R_MissingArg</code> and <code>R_BaseNamespace</code>.
</p>
<p>For all <code>SEXPTYPE</code>s except <code>NILSXP</code>, <code>SYMSXP</code> and
<code>ENVSXP</code> serialization starts with an integer with the
<code>SEXPTYPE</code> in bits 0:7<a name="DOCF7" href="#FOOT7"><sup>7</sup></a> followed by the object bit, two bits
indicating if there are any attributes and if there is a tag (for the
pairlist types), an unused bit and then the <code>gp</code>
field<a name="DOCF8" href="#FOOT8"><sup>8</sup></a> in
bits 12:27.  Pairlist-like objects write their attributes (if any), tag
(if any), CAR and then CDR (using tail recursion): other objects write
their attributes after themselves.  Atomic vector objects write their
length followed by the data: generic vector-list objects write their
length followed by a call to <code>WriteItem</code> for each element.  The
code for <code>CHARSXP</code>s special-cases <code>NA_STRING</code> and writes it as
length <code>-1</code> with no data.  Lengths no more than <code>2^31 - 1</code> are
written in that way and larger lengths (which only occur on 64-bit
systems) as <code>-1</code> followed by the upper and lower 32-bits as integers
(regarded as unsigned).
</p>
<p>Environments are treated in several ways: as we have seen, some are
written as specific pseudo-<code>SEXPTYPE</code>s.  Package and namespace
environments are written with pseudo-<code>SEXPTYPE</code>s followed by the
name.  &lsquo;Normal&rsquo; environments are written out as <code>ENVSXP</code>s with an
integer indicating if the environment is locked followed by the
enclosure, frame, &lsquo;tag&rsquo; (the hash table) and attributes.
</p>
<p>In the &lsquo;XDR&rsquo; format integers and doubles are written in bigendian order:
however the format is not fully XDR (as defined in RFC 1832) as byte
quantities (such as the contents of <code>CHARSXP</code> and <code>RAWSXP</code>
types) are written as-is and not padded to a multiple of four bytes.
</p>
<p>The &lsquo;ASCII&rsquo; format writes 7-bit characters.  Integers are formatted with
<code>%d</code> (except that <code>NA_integer_</code> is written as <code>NA</code>),
doubles formatted with <code>%.16g</code> (plus <code>NA</code>, <code>Inf</code> and
<code>-Inf</code>) and bytes with <code>%02x</code>.  Strings are written using
standard escapes (e.g. <code>\t</code> and <code>\013</code>) for non-printing and
non-<acronym>ASCII</acronym> bytes.
</p>
<hr>
<a name="Encodings-for-CHARSXPs"></a>
<div class="header">
<p>
Next: <a href="#The-CHARSXP-cache" accesskey="n" rel="next">The CHARSXP cache</a>, Previous: <a href="#Serialization-Formats" accesskey="p" rel="prev">Serialization Formats</a>, Up: <a href="#R-Internal-Structures" accesskey="u" rel="up">R Internal Structures</a> &nbsp; [<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="Encodings-for-CHARSXPs-1"></a>
<h3 class="section">1.9 Encodings for CHARSXPs</h3>

<p>Character data in R are stored in the sexptype <code>CHARSXP</code>.
</p>
<p>There is support for encodings other than that of the current locale, in
particular UTF-8 and the multi-byte encodings used on Windows for CJK
languages. A limited means to indicate the encoding of a <code>CHARSXP</code>
is <em>via</em> two of the &lsquo;general purpose&rsquo; bits which are used to declare
the encoding to be either Latin-1 or UTF-8.  (Note that it is possible
for a character vector to contain elements in different encodings.)
Both printing and plotting notice the declaration and convert the string
to the current locale (possibly using <code>&lt;xx&gt;</code> to display in
hexadecimal bytes that are not valid in the current locale).  Many (but
not all) of the character manipulation functions will either preserve
the declaration or re-encode the character string.
</p>
<p>Strings that refer to the OS such as file names need to be passed
through a wide-character interface on some OSes (e.g. Windows).
</p>
<p>When are character strings declared to be of known encoding?  One way is
to do so directly via <code>Encoding</code>.  The parser declares the encoding
if this is known, either via the <code>encoding</code> argument to
<code>parse</code> or from the locale within which parsing is being done at
the R command line.  (Other ways are recorded on the help page for
<code>Encoding</code>.)
</p>
<p>It is not necessary to declare the encoding of <acronym>ASCII</acronym> strings
as they will work in any locale.  <acronym>ASCII</acronym> strings should never
have a marked encoding, as any encoding will be ignored when entering
such strings into the <code>CHARSXP</code> cache.
</p>
<p>The rationale behind considering only UTF-8 and Latin-1 was that most
systems are capable of producing UTF-8 strings and this is the nearest
we have to a universal format.  For those that do not (for example those
lacking a powerful enough <code>iconv</code>), it is likely that they work in
Latin-1, the old R assumption. The the parser can return a
UTF-8-encoded string if it encounters a &lsquo;<samp>\uxxx</samp>&rsquo; escape for a
Unicode point that cannot be represented in the current charset.  (This
needs MBCS support, and was only enabled<a name="DOCF9" href="#FOOT9"><sup>9</sup></a> on
Windows.)  This is enabled for all platforms, and a &lsquo;<samp>\uxxx</samp>&rsquo; or
&lsquo;<samp>\Uxxxxxxxx</samp>&rsquo; escape ensures that the parsed string will be marked
as UTF-8.
</p>
<p>Most of the character manipulation functions now preserve UTF-8
encodings: there are some notes as to which at the top of file
<samp>src/main/character.c</samp> and in file
<samp>src/library/base/man/Encoding.Rd</samp>.
</p>
<p>Graphics devices are offered the possibility of handing UTF-8-encoded
strings without re-encoding to the native character set, by setting
<code>hasTextUTF8</code> to be &lsquo;<samp>TRUE</samp>&rsquo; and supplying functions
<code>textUTF8</code> and <code>strWidthUTF8</code> that expect UTF-8-encoded
inputs.  Normally the symbol font is encoded in Adobe Symbol encoding,
but that can be re-encoded to UTF-8 by setting <code>wantSymbolUTF8</code> to
&lsquo;<samp>TRUE</samp>&rsquo;.  The Windows&rsquo; port of cairographics has a rather peculiar
assumption: it wants the symbol font to be encoded in UTF-8 as if it
were encoded in Latin-1 rather than Adobe Symbol: this is selected by
<code>wantSymbolUTF8 = NA_LOGICAL</code>.
</p>
<p>Windows has no UTF-8 locales, but rather expects to work with
UCS-2<a name="DOCF10" href="#FOOT10"><sup>10</sup></a> strings.
R (being written in standard C) would not work internally with UCS-2
without extensive changes.  The <samp>Rgui</samp> console<a name="DOCF11" href="#FOOT11"><sup>11</sup></a> uses UCS-2 internally, but communicates with the R
engine in the native encoding.  To allow UTF-8 strings to be printed in
UTF-8 in <samp>Rgui.exe</samp>, an escape convention is used (see header file
<samp>rgui_UTF8.h</samp>) which is used by <code>cat</code>, <code>print</code> and
autoprinting.
</p>
<p>&lsquo;Unicode&rsquo; (UCS-2LE) files are common in the Windows world, and
<code>readLines</code> and <code>scan</code> will read them into UTF-8 strings on
Windows if the encoding is declared explicitly on an unopened
connection passed to those functions.
</p>
<hr>
<a name="The-CHARSXP-cache"></a>
<div class="header">
<p>
Next: <a href="#Warnings-and-errors" accesskey="n" rel="next">Warnings and errors</a>, Previous: <a href="#Encodings-for-CHARSXPs" accesskey="p" rel="prev">Encodings for CHARSXPs</a>, Up: <a href="#R-Internal-Structures" accesskey="u" rel="up">R Internal Structures</a> &nbsp; [<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-CHARSXP-cache-1"></a>
<h3 class="section">1.10 The CHARSXP cache</h3>

<a name="index-mkChar"></a>
<p>There is a global cache for <code>CHARSXP</code>s created by <code>mkChar</code> &mdash;
the cache ensures that most <code>CHARSXP</code>s with the same contents share
storage (&lsquo;contents&rsquo; including any declared encoding).  Not all
<code>CHARSXP</code>s are part of the cache &ndash; notably &lsquo;<samp>NA_STRING</samp>&rsquo; is
not. <code>CHARSXP</code>s reloaded from the <code>save</code> formats of R prior
to 0.99.0 are not cached (since the code used is frozen and very few
examples still exist).
</p>
<a name="index-mkCharLenCE"></a>
<p>The cache records the encoding of the string as well as the bytes: all
requests to create a <code>CHARSXP</code> should be <em>via</em> a call to
<code>mkCharLenCE</code>.  Any encoding given in <code>mkCharLenCE</code> call will
be ignored if the string&rsquo;s bytes are all <acronym>ASCII</acronym> characters.
</p>

<hr>
<a name="Warnings-and-errors"></a>
<div class="header">
<p>
Next: <a href="#S4-objects" accesskey="n" rel="next">S4 objects</a>, Previous: <a href="#The-CHARSXP-cache" accesskey="p" rel="prev">The CHARSXP cache</a>, Up: <a href="#R-Internal-Structures" accesskey="u" rel="up">R Internal Structures</a> &nbsp; [<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="Warnings-and-errors-1"></a>
<h3 class="section">1.11 Warnings and errors</h3>

<a name="index-warning"></a>
<a name="index-warningcall"></a>
<a name="index-error"></a>
<a name="index-errorcall"></a>

<p>Each of <code>warning</code> and <code>stop</code> have two C-level equivalents,
<code>warning</code>, <code>warningcall</code>, <code>error</code> and <code>errorcall</code>.
The relationship between the pairs is similar: <code>warning</code> tries to
fathom out a suitable call, and then calls <code>warningcall</code> with that
call as the first argument if it succeeds, and with <code>call =
R_NilValue</code> if it does not.  When <code>warningcall</code> is called, it
includes the deparsed call in its printout unless <code>call =
R_NilValue</code>.
</p>
<p><code>warning</code> and <code>error</code> look at the context stack.  If the
topmost context is not of type <code>CTXT_BUILTIN</code>, it is used to
provide the call, otherwise the next context provides the call.
This means that when these functions are called from a primitive or
<code>.Internal</code>, the imputed call will not be to
primitive/<code>.Internal</code> but to the function calling the
primitive/<code>.Internal</code> .  This is exactly what one wants for a
<code>.Internal</code>, as this will give the call to the closure wrapper.
(Further, for a <code>.Internal</code>, the call is the argument to
<code>.Internal</code>, and so may not correspond to any R function.)
However, it is unlikely to be what is needed for a primitive.
</p>
<p>The upshot is that that <code>warningcall</code> and <code>errorcall</code> should
normally be used for code called from a primitive, and <code>warning</code>
and <code>error</code> should be used for code called from a <code>.Internal</code>
(and necessarily from <code>.Call</code>, <code>.C</code> and so on, where the call
is not passed down).  However, there are two complications.  One is that
code might be called from either a primitive or a <code>.Internal</code>, in
which case probably <code>warningcall</code> is more appropriate.  The other
involves replacement functions, where the call was once of the form
</p><div class="example">
<pre class="example">&gt; length(x) &lt;- y ~ x
Error in &quot;length&lt;-&quot;(`*tmp*`, value = y ~ x) : invalid value
</pre></div>

<p>which is unpalatable to the end user.  For replacement functions there
will be a suitable context at the top of the stack, so <code>warning</code>
should be used.  (The results for <code>.Internal</code> replacement functions
such as <code>substr&lt;-</code> are not ideal.)
</p>


<hr>
<a name="S4-objects"></a>
<div class="header">
<p>
Next: <a href="#Memory-allocators" accesskey="n" rel="next">Memory allocators</a>, Previous: <a href="#Warnings-and-errors" accesskey="p" rel="prev">Warnings and errors</a>, Up: <a href="#R-Internal-Structures" accesskey="u" rel="up">R Internal Structures</a> &nbsp; [<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="S4-objects-1"></a>
<h3 class="section">1.12 S4 objects</h3>

<p>[This section is currently a preliminary draft and should not be taken
as definitive.  The description assumes that <code>R_NO_METHODS_TABLES</code>
has not been set.]
</p>
<table summary="" class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">&bull; <a href="#Representation-of-S4-objects" accesskey="1">Representation of S4 objects</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">&bull; <a href="#S4-classes" accesskey="2">S4 classes</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">&bull; <a href="#S4-methods" accesskey="3">S4 methods</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">&bull; <a href="#Mechanics-of-S4-dispatch" accesskey="4">Mechanics of S4 dispatch</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
</table>

<hr>
<a name="Representation-of-S4-objects"></a>
<div class="header">
<p>
Next: <a href="#S4-classes" accesskey="n" rel="next">S4 classes</a>, Previous: <a href="#S4-objects" accesskey="p" rel="prev">S4 objects</a>, Up: <a href="#S4-objects" accesskey="u" rel="up">S4 objects</a> &nbsp; [<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="Representation-of-S4-objects-1"></a>
<h4 class="subsection">1.12.1 Representation of S4 objects</h4>

<p>S4 objects can be of any <code>SEXPTYPE</code>.  They are either an object of
a simple type (such as an atomic vector or function) with S4 class
information or of type <code>S4SXP</code>.  In all cases, the &lsquo;S4 bit&rsquo; (bit 4
of the &lsquo;general purpose&rsquo; field) is set, and can be tested by the
macro/function <code>IS_S4_OBJECT</code>.
</p>
<p>S4 objects are created via <code>new()</code><a name="DOCF12" href="#FOOT12"><sup>12</sup></a> and thence via the C
function <code>R_do_new_object</code>.  This duplicates the prototype of the
class, adds a class attribute and sets the S4 bit.  All S4 class
attributes should be character vectors of length one with an attribute
giving (as a character string) the name of the package (or
<code>.GlobalEnv</code>) containing the class definition.  Since S4 objects
have a class attribute, the <code>OBJECT</code> bit is set.
</p>
<p>It is currently unclear what should happen if the class attribute is
removed from an S4 object, or if this should be allowed.
</p>
<hr>
<a name="S4-classes"></a>
<div class="header">
<p>
Next: <a href="#S4-methods" accesskey="n" rel="next">S4 methods</a>, Previous: <a href="#Representation-of-S4-objects" accesskey="p" rel="prev">Representation of S4 objects</a>, Up: <a href="#S4-objects" accesskey="u" rel="up">S4 objects</a> &nbsp; [<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="S4-classes-1"></a>
<h4 class="subsection">1.12.2 S4 classes</h4>

<p>S4 classes are stored as R objects in the environment in which they
are created, with names <code>.__C__<var>classname</var></code>: as such they are
not listed by default by <code>ls</code>.
</p>
<p>The objects are S4 objects of class <code>&quot;classRepresentation&quot;</code> which
is defined in the <strong>methods</strong> package.
</p>
<p>Since these are just objects, they are subject to the normal scoping
rules and can be imported and exported from namespaces like other
objects.  The directives <code>importClassesFrom</code> and
<code>exportClasses</code> are merely convenient ways to refer to class
objects without needing to know their internal &lsquo;metaname&rsquo; (although
<code>exportClasses</code> does a little sanity checking via <code>isClass</code>).
</p>
<hr>
<a name="S4-methods"></a>
<div class="header">
<p>
Next: <a href="#Mechanics-of-S4-dispatch" accesskey="n" rel="next">Mechanics of S4 dispatch</a>, Previous: <a href="#S4-classes" accesskey="p" rel="prev">S4 classes</a>, Up: <a href="#S4-objects" accesskey="u" rel="up">S4 objects</a> &nbsp; [<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="S4-methods-1"></a>
<h4 class="subsection">1.12.3 S4 methods</h4>

<p>Details of methods are stored in S4 objects of class
<code>&quot;MethodsList&quot;</code>.  They have a non-syntactic name of the form
<code>.__M__<var>generic</var>:<var>package</var></code> for all methods defined in the
current environment for the named generic derived from a specific
package (which might be <code>.GlobalEnv</code>).
</p>
<p>There is also environment <code>.__T__<var>generic</var>:<var>package</var></code> which
has names the signatures of the methods defined, and values the
corresponding method functions.  This is often referred to as a &lsquo;methods
table&rsquo;.
</p>
<p>When a package without a namespace is attached these objects become
visible on the search path.  <code>library</code> calls
<code>methods:::cacheMetaData</code> to update the internal tables.
</p>
<p>During an R session there is an environment associated with each
non-primitive generic containing objects <code>.AllMTable</code>,
<code>.Generic</code>, <code>.Methods</code>, <code>.MTable</code>, <code>.SigArgs</code> and
<code>.SigLength</code>.  <code>.MTable</code> and <code>AllMTable</code> are merged
methods tables containing all the methods defined directly and via
inheritance respectively.  <code>.Methods</code> is a merged methods list.
</p>
<p>Exporting methods from a namespace is more complicated than exporting a
class.  Note first that you do not export a method, but rather the
directive <code>exportMethods</code> will export all the methods defined in
the namespace for a specified generic: the code also adds to the list
of generics any that are exported directly.  For generics which are
listed via <code>exportMethods</code> or exported themselves, the
corresponding <code>&quot;MethodsList&quot;</code> and environment are exported and so
will appear (as hidden objects) in the package environment.
</p>
<p>Methods for primitives which are internally S4 generic (see below) are
always exported, whether mentioned in the <samp>NAMESPACE</samp> file or not.
</p>
<p>Methods can be imported either via the directive
<code>importMethodsFrom</code> or via importing a namespace by <code>import</code>.
Also, if a generic is imported via <code>importFrom</code>, its methods are
also imported.  In all cases the generic will be imported if it is in
the namespace, so <code>importMethodsFrom</code> is most appropriate for
methods defined on generics in other packages.  Since methods for a
generic could be imported from several different packages, the methods
tables are merged.
</p>
<p>When a package with a namespace is attached
<code>methods:::cacheMetaData</code> is called to update the internal tables:
only the visible methods will be cached.
</p>

<hr>
<a name="Mechanics-of-S4-dispatch"></a>
<div class="header">
<p>
Previous: <a href="#S4-methods" accesskey="p" rel="prev">S4 methods</a>, Up: <a href="#S4-objects" accesskey="u" rel="up">S4 objects</a> &nbsp; [<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="Mechanics-of-S4-dispatch-1"></a>
<h4 class="subsection">1.12.4 Mechanics of S4 dispatch</h4>

<p>This subsection does not discuss how S4 methods are chosen: see
<a href="https://developer.r-project.org/howMethodsWork.pdf">https://developer.r-project.org/howMethodsWork.pdf</a>.
</p>
<p>For all but primitive functions, setting a method on an existing
function that is not itself S4 generic creates a new object in the
current environment which is a call to <code>standardGeneric</code> with the
old definition as the default method.  Such S4 generics can also be
created <em>via</em> a call to <code>setGeneric</code><a name="DOCF13" href="#FOOT13"><sup>13</sup></a> and are standard closures
in the R language, with environment the environment within which they
are created.  With the advent of namespaces this is somewhat
problematic: if <code>myfn</code> was previously in a package with a name
space there will be two functions called <code>myfn</code> on the search
paths, and which will be called depends on which search path is in use.
This is starkest for functions in the base namespace, where the
original will be found ahead of the newly created function from any
other package with a namespace.
</p>
<p>Primitive functions are treated quite differently, for efficiency
reasons: this results in different semantics.  <code>setGeneric</code> is
disallowed for primitive functions.  The <strong>methods</strong> namespace
contains a list <code>.BasicFunsList</code> named by primitive functions:
the entries are either <code>FALSE</code> or a standard S4 generic showing
the effective definition.  When <code>setMethod</code> (or
<code>setReplaceMethod</code>) is called, it either fails (if the list entry
is <code>FALSE</code>) or a method is set on the effective generic given in
the list.
</p>
<p>Actual dispatch of S4 methods for almost all primitives piggy-backs on
the S3 dispatch mechanism, so S4 methods can only be dispatched for
primitives which are internally S3 generic.  When a primitive that is
internally S3 generic is called with a first argument which is an S4
object and S4 dispatch is on (that is, the <strong>methods</strong> namespace is
loaded), <code>DispatchOrEval</code> calls <code>R_possible_dispatch</code> (defined
in file <samp>src/main/objects.c</samp>).  (Members of the S3 group generics,
which includes all the generic operators, are treated slightly
differently: the first two arguments are checked and
<code>DispatchGroup</code> is called.)  <code>R_possible_dispatch</code> first
checks an internal table to see if any S4 methods are set for that
generic (and S4 dispatch is currently enabled for that generic), and if
so proceeds to S4 dispatch using methods stored in another internal
table.  All primitives are in the base namespace, and this mechanism
means that S4 methods can be set for (some) primitives and will always
be used, in contrast to setting methods on non-primitives.
</p>
<p>The exception is <code>%*%</code>, which is S4 generic but not S3 generic as
its C code contains a direct call to <code>R_possible_dispatch</code>.
</p>
<p>The primitive <code>as.double</code> is special, as <code>as.numeric</code> and
<code>as.real</code> are copies of it.  The <strong>methods</strong> package code partly
refers to generics by name and partly by function, and maps
<code>as.double</code> and <code>as.real</code> to <code>as.numeric</code> (since that is
the name used by packages exporting methods for it).
</p>
<p>Some elements of the language are implemented as primitives, for example
<code>}</code>.  This includes the subset and subassignment &lsquo;functions&rsquo; and
they are S4 generic, again piggybacking on S3 dispatch.
</p>
<p><code>.BasicFunsList</code> is generated when <strong>methods</strong> is installed, by
computing all primitives, initially disallowing methods on all and then
setting generics for members of <code>.GenericArgsEnv</code>, the S4 group
generics and a short exceptions list in file <samp>BasicFunsList.R</samp>: this
currently contains the subsetting and subassignment operators and an
override for <code>c</code>.
</p>
<hr>
<a name="Memory-allocators"></a>
<div class="header">
<p>
Next: <a href="#Internal-use-of-global-and-base-environments" accesskey="n" rel="next">Internal use of global and base environments</a>, Previous: <a href="#S4-objects" accesskey="p" rel="prev">S4 objects</a>, Up: <a href="#R-Internal-Structures" accesskey="u" rel="up">R Internal Structures</a> &nbsp; [<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="Memory-allocators-1"></a>
<h3 class="section">1.13 Memory allocators</h3>

<p>R&rsquo;s memory allocation is almost all done via routines in file
<samp>src/main/memory.c</samp>.  It is important to keep track of where memory
is allocated, as the Windows port (by default) makes use of a memory
allocator that differs from <code>malloc</code> etc as provided by MinGW.
Specifically, there are entry points <code>Rm_malloc</code>, <code>Rm_free</code>,
<code>Rm_calloc</code> and <code>Rm_free</code> provided by file
<samp>src/gnuwin32/malloc.c</samp>.  This was done for two reasons.  The
primary motivation was performance: the allocator provided by MSVCRT
<em>via</em> MinGW was far too slow at handling the many small allocations
that the allocation system for <code>SEXPREC</code>s uses.  As a side benefit,
we can set a limit on the amount of allocated memory: this is useful as
whereas Windows does provide virtual memory it is relatively far slower
than many other R platforms and so limiting R&rsquo;s use of swapping is
highly advantageous.  The high-performance allocator is only called from
<samp>src/main/memory.c</samp>, <samp>src/main/regex.c</samp>, <samp>src/extra/pcre</samp>
and <samp>src/extra/xdr</samp>: note that this means that it is not used in
packages.
</p>
<p>The rest of R should where possible make use of the allocators made
available by file <samp>src/main/memory.c</samp>, which are also the methods
recommended in
<a href="http://cran.r-project.org/doc/manuals/R-exts.html#Memory-allocation">Memory allocation</a> in <cite>Writing R Extensions</cite>
<a name="index-R_005falloc"></a>
<a name="index-Calloc"></a>
<a name="index-Realloc"></a>
<a name="index-Free"></a>
for use in R packages, namely the use of <code>R_alloc</code>,
<code>Calloc</code>, <code>Realloc</code> and <code>Free</code>.  Memory allocated by
<code>R_alloc</code> is freed by the garbage collector once the &lsquo;watermark&rsquo;
has been reset by calling
<a name="index-vmaxset"></a>
<code>vmaxset</code>.  This is done automatically by the wrapper code calling
primitives and <code>.Internal</code> functions (and also by the wrapper code
to <code>.Call</code> and <code>.External</code>), but
<a name="index-vmaxget"></a>
<code>vmaxget</code> and <code>vmaxset</code> can be used to reset the watermark
from within internal code if the memory is only required for a short
time.
</p>
<a name="index-alloca"></a>
<p>All of the methods of memory allocation mentioned so far are relatively
expensive.  All R platforms support <code>alloca</code>, and in almost all
cases<a name="DOCF14" href="#FOOT14"><sup>14</sup></a> this is managed by the
compiler, allocates memory on the C stack and is very efficient.
</p>
<p>There are two disadvantages in using <code>alloca</code>.  First, it is
fragile and care is needed to avoid writing (or even reading) outside
the bounds of the allocation block returned.  Second, it increases the
danger of overflowing the C stack.   It is suggested that it is only
used for smallish allocations (up to tens of thousands of bytes), and
that
</p>
<a name="index-R_005fCheckStack"></a>
<div class="example">
<pre class="example">    R_CheckStack();
</pre></div>

<p>is called immediately after the allocation (as R&rsquo;s stack checking
mechanism will warn far enough from the stack limit to allow for modest
use of alloca).  (<code>do_makeunique</code> in file <samp>src/main/unique.c</samp>
provides an example of both points.)
</p>
<p>There is an alternative check,
<a name="index-R_005fCheckStack2"></a>
</p><div class="example">
<pre class="example">    R_CheckStack2(size_t extra);
</pre></div>

<p>to be called immediately <em>before</em> trying an allocation of
<code>extra</code> bytes.
</p>
<p>An alternative strategy has been used for various functions which
require intermediate blocks of storage of varying but usually small
size, and this has been consolidated into the routines in the header
file <samp>src/main/RBufferUtils.h</samp>.  This uses a structure which
contains a buffer, the current size and the default size. A call to
<a name="index-R_005fAllocStringBuffer"></a>
</p><div class="example">
<pre class="example">    R_AllocStringBuffer(size_t blen, R_StringBuffer *buf);
</pre></div>

<p>sets <code>buf-&gt;data</code> to a memory area of at least <code>blen+1</code> bytes.
At least the default size is used, which means that for small
allocations the same buffer can be reused.  A call to
<a name="index-R_005fFreeStringBufferL"></a>
<a name="index-R_005fFreeStringBuffer"></a>
<code>R_FreeStringBufferL</code> releases memory if more than the default has
been allocated whereas a call to <code>R_FreeStringBuffer</code> frees any
memory allocated.
</p>
<p>The <code>R_StringBuffer</code> structure needs to be initialized, for example by
</p>
<div class="example">
<pre class="example">static R_StringBuffer ex_buff = {NULL, 0, MAXELTSIZE};
</pre></div>

<p>which uses a default size of <code>MAXELTSIZE = 8192</code> bytes.  Most
current uses have a static <code>R_StringBuffer</code> structure, which
allows the (default-sized) buffer to be shared between calls to e.g.
<code>grep</code> and even between functions: this will need to be changed if
R ever allows concurrent evaluation threads.  So the idiom is
</p>
<div class="example">
<pre class="example">static R_StringBuffer ex_buff = {NULL, 0, MAXELTSIZE};
...
    char *buf;
    for(i = 0; i &lt; n; i++) {
        compute len
        buf = R_AllocStringBuffer(len, &amp;ex_buff);
        use buf
    }
    /*  free allocation if larger than the default, but leave
        default allocated for future use */
   R_FreeStringBufferL(&amp;ex_buff);
</pre></div>


<table summary="" class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">&bull; <a href="#Internals-of-R_005falloc" accesskey="1">Internals of R_alloc</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
</table>

<hr>
<a name="Internals-of-R_005falloc"></a>
<div class="header">
<p>
Previous: <a href="#Memory-allocators" accesskey="p" rel="prev">Memory allocators</a>, Up: <a href="#Memory-allocators" accesskey="u" rel="up">Memory allocators</a> &nbsp; [<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="Internals-of-R_005falloc-1"></a>
<h4 class="subsection">1.13.1 Internals of R_alloc</h4>

<p>The memory used by <code>R_alloc</code> is allocated as R vectors, of type
<code>RAWSXP</code>.  Thus the allocation is in units of 8 bytes, and is
rounded up.  A request for zero bytes currently returns <code>NULL</code> (but
this should not be relied on).  For historical reasons, in all other
cases 1 byte is added before rounding up so the allocation is always
1&ndash;8 bytes more than was asked for: again this should not be relied on.
</p>
<p>The vectors allocated are protected via the setting of <code>R_VStack</code>,
as the garbage collector marks everything that can be reached from that
location.  When a vector is <code>R_alloc</code>ated, its <code>ATTRIB</code>
pointer is set to the current <code>R_VStack</code>, and <code>R_VStack</code> is
set to the latest allocation.  Thus <code>R_VStack</code> is a single-linked
chain of the vectors currently allocated via <code>R_alloc</code>.  Function
<code>vmaxset</code> resets the location <code>R_VStack</code>, and should be to a
value that has previously be obtained <em>via</em> <code>vmaxget</code>:
allocations after the value was obtained will no longer be protected and
hence available for garbage collection.
</p>
<hr>
<a name="Internal-use-of-global-and-base-environments"></a>
<div class="header">
<p>
Next: <a href="#Modules" accesskey="n" rel="next">Modules</a>, Previous: <a href="#Memory-allocators" accesskey="p" rel="prev">Memory allocators</a>, Up: <a href="#R-Internal-Structures" accesskey="u" rel="up">R Internal Structures</a> &nbsp; [<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="Internal-use-of-global-and-base-environments-1"></a>
<h3 class="section">1.14 Internal use of global and base environments</h3>

<p>This section notes known use by the system of these environments: the
intention is to minimize or eliminate such uses.
</p>
<table summary="" class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">&bull; <a href="#Base-environment" accesskey="1">Base environment</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">&bull; <a href="#Global-environment" accesskey="2">Global environment</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
</table>

<hr>
<a name="Base-environment"></a>
<div class="header">
<p>
Next: <a href="#Global-environment" accesskey="n" rel="next">Global environment</a>, Previous: <a href="#Internal-use-of-global-and-base-environments" accesskey="p" rel="prev">Internal use of global and base environments</a>, Up: <a href="#Internal-use-of-global-and-base-environments" accesskey="u" rel="up">Internal use of global and base environments</a> &nbsp; [<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="Base-environment-1"></a>
<h4 class="subsection">1.14.1 Base environment</h4>

<a name="index-base-environment-1"></a>
<a name="index-environment_002c-base-1"></a>
<a name="index-_002eDevice"></a>
<a name="index-_002eDevices"></a>
<p>The graphics devices system maintains two variables <code>.Device</code> and
<code>.Devices</code> in the base environment: both are always set.  The
variable <code>.Devices</code> gives a list of character vectors of the names
of open devices, and <code>.Device</code> is the element corresponding to the
currently active device.  The null device will always be open.
</p>
<a name="index-_002eOptions"></a>
<p>There appears to be a variable <code>.Options</code>, a pairlist giving the
current options settings.  But in fact this is just a symbol with a
value assigned, and so shows up as a base variable.
</p>
<a name="index-_002eLast_002evalue"></a>
<p>Similarly, the evaluator creates a symbol <code>.Last.value</code> which
appears as a variable in the base environment.
</p>
<a name="index-_002eTraceback"></a>
<a name="index-last_002ewarning"></a>
<p>Errors can give rise to objects <code>.Traceback</code> and
<code>last.warning</code> in the base environment.
</p>
<hr>
<a name="Global-environment"></a>
<div class="header">
<p>
Previous: <a href="#Base-environment" accesskey="p" rel="prev">Base environment</a>, Up: <a href="#Internal-use-of-global-and-base-environments" accesskey="u" rel="up">Internal use of global and base environments</a> &nbsp; [<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="Global-environment-1"></a>
<h4 class="subsection">1.14.2 Global environment</h4>

<a name="index-global-environment"></a>
<a name="index-environment_002c-global"></a>
<a name="index-_002eRandom_002eseed"></a>
<p>The seed for the random number generator is stored in object
<code>.Random.seed</code> in the global environment.
</p>
<a name="index-dump_002eframes"></a>
<p>Some error handlers may give rise to objects in the global environment:
for example <code>dump.frames</code> by default produces <code>last.dump</code>.
</p>
<a name="index-_002eSavedPlots"></a>
<p>The <code>windows()</code> device makes use of a variable <code>.SavedPlots</code>
to store display lists of saved plots for later display.  This is
regarded as a variable created by the user.
</p>

<hr>
<a name="Modules"></a>
<div class="header">
<p>
Next: <a href="#Visibility" accesskey="n" rel="next">Visibility</a>, Previous: <a href="#Internal-use-of-global-and-base-environments" accesskey="p" rel="prev">Internal use of global and base environments</a>, Up: <a href="#R-Internal-Structures" accesskey="u" rel="up">R Internal Structures</a> &nbsp; [<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="Modules-1"></a>
<h3 class="section">1.15 Modules</h3>

<a name="index-modules"></a>
<p>R makes use of a number of shared objects/DLLs stored in the
<samp>modules</samp> directory.  These are parts of the code which have been
chosen to be loaded &lsquo;on demand&rsquo; rather than linked as dynamic libraries
or incorporated into the main executable/dynamic library.
</p>
<p>For the remaining modules the motivation has been the amount of (often
optional) code they will bring in <em>via</em> libraries to which they are
linked.
</p>
<dl compact="compact">
<dt><code>internet</code></dt>
<dd><p>The internal HTTP and FTP clients and socket support, which link to
system-specific support libraries.  This may load <code>libcurl</code> and on
Windows will load <samp>wininet.dll</samp> and <samp>ws2_32.dll</samp>.
</p>
</dd>
<dt><code>lapack</code></dt>
<dd><p>The code which makes use of the LAPACK library, and is linked to
<samp>libRlapack</samp> or an external LAPACK library.
</p>
</dd>
<dt><code>X11</code></dt>
<dd><p>(Unix-alikes only.)  The <code>X11()</code>, <code>jpeg()</code>, <code>png()</code> and
<code>tiff()</code> devices. These are optional, and links to some or all of
the <code>X11</code>, <code>pango</code>, <code>cairo</code>, <code>jpeg</code>, <code>libpng</code>
and <code>libtiff</code> libraries.
</p></dd>
</dl>

<hr>
<a name="Visibility"></a>
<div class="header">
<p>
Next: <a href="#Lazy-loading" accesskey="n" rel="next">Lazy loading</a>, Previous: <a href="#Modules" accesskey="p" rel="prev">Modules</a>, Up: <a href="#R-Internal-Structures" accesskey="u" rel="up">R Internal Structures</a> &nbsp; [<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="Visibility-1"></a>
<h3 class="section">1.16 Visibility</h3>
<a name="index-visibility"></a>

<table summary="" class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">&bull; <a href="#Hiding-C-entry-points" accesskey="1">Hiding C entry points</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">&bull; <a href="#Variables-in-Windows-DLLs" accesskey="2">Variables in Windows DLLs</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
</table>

<hr>
<a name="Hiding-C-entry-points"></a>
<div class="header">
<p>
Next: <a href="#Variables-in-Windows-DLLs" accesskey="n" rel="next">Variables in Windows DLLs</a>, Previous: <a href="#Visibility" accesskey="p" rel="prev">Visibility</a>, Up: <a href="#Visibility" accesskey="u" rel="up">Visibility</a> &nbsp; [<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="Hiding-C-entry-points-1"></a>
<h4 class="subsection">1.16.1 Hiding C entry points</h4>

<p>We make use of the visibility mechanisms discussed in
<a href="http://cran.r-project.org/doc/manuals/R-exts.html#Controlling-visibility">Controlling visibility</a> in <cite>Writing R Extensions</cite>,
C entry points not needed outside the main R executable/dynamic
library (and in particular in no package nor module) should be prefixed
by <code>attribute_hidden</code>.
<a name="index-attribute_005fhidden"></a>
Minimizing the visibility of symbols in the R dynamic library will
speed up linking to it (which packages will do) and reduce the
possibility of linking to the wrong entry points of the same name.  In
addition, on some platforms reducing the number of entry points allows
more efficient versions of PIC to be used: somewhat over half the entry
points are hidden.  A convenient way to hide variables (as distinct from
functions) is to declare them <code>extern0</code> in header file <samp>Defn.h</samp>.
</p>
<p>The visibility mechanism used is only available with some compilers and
platforms, and in particular not on Windows, where an alternative
mechanism is used.  Entry points will not be made available in
<samp>R.dll</samp> if they are listed in the file
<samp>src/gnuwin32/Rdll.hide</samp>.
<a name="index-Rdll_002ehide"></a>
Entries in that file start with a space and must be strictly in
alphabetic order in the C locale (use <code>sort</code> on the file to
ensure this if you change it).  It is possible to hide Fortran as well
as C entry points via this file: the former are lower-cased and have an
underline as suffix, and the suffixed name should be included in the
file.  Some entry points exist only on Windows or need to be visible
only on Windows, and some notes on these are provided in file
<samp>src/gnuwin32/Maintainters.notes</samp>.
</p>
<p>Because of the advantages of reducing the number of visible entry
points, they should be declared <code>attribute_hidden</code> where possible.
Note that this only has an effect on a shared-R-library build, and so
care is needed not to hide entry points that are legitimately used by
packages.  So it is best if the decision on visibility is made when a
new entry point is created, including the decision if it should be
included in header file <samp>Rinternals.h</samp>.  A list of the visible
entry points on shared-R-library build on a reasonably standard
Unix-alike can be made by something like
</p>
<div class="example">
<pre class="example">nm -g libR.so | grep ‘ [BCDT] ’ | cut -b20-
</pre></div>

<hr>
<a name="Variables-in-Windows-DLLs"></a>
<div class="header">
<p>
Previous: <a href="#Hiding-C-entry-points" accesskey="p" rel="prev">Hiding C entry points</a>, Up: <a href="#Visibility" accesskey="u" rel="up">Visibility</a> &nbsp; [<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="Variables-in-Windows-DLLs-1"></a>
<h4 class="subsection">1.16.2 Variables in Windows DLLs</h4>

<p>Windows is unique in that it conventionally treats importing variables
differently from functions: variables that are imported from a DLL need
to be specified  by a prefix (often &lsquo;<samp>_imp_</samp>&rsquo;) when being linked to
(&lsquo;imported&rsquo;) but not when being linked from (&lsquo;exported&rsquo;).  The details
depend on the compiler system, and have changed for MinGW during the
lifetime of that port.  They are in the main hidden behind some macros
defined in header file <samp>R_ext/libextern.h</samp>.
</p>
<p>A (non-function) variable in the main R sources that needs to be
referred to outside <samp>R.dll</samp> (in a package, module or another DLL
such as <samp>Rgraphapp.dll</samp>) should be declared with prefix
<code>LibExtern</code>.  The main use is in <samp>Rinternals.h</samp>, but it needs
to be considered for any public header and also <samp>Defn.h</samp>.
</p>
<p>It would nowadays be possible to make use of the &lsquo;auto-import&rsquo; feature
of the MinGW port of <code>ld</code> to fix up imports from DLLs (and if
R is built for the Cygwin platform this is what happens).  However,
this was not possible when the MinGW build of R was first constructed
in ca 1998, allows less control of visibility and would not work for
other Windows compiler suites.
</p>
<p>It is only possible to check if this has been handled correctly by
compiling the R sources on Windows.
</p>
<hr>
<a name="Lazy-loading"></a>
<div class="header">
<p>
Previous: <a href="#Visibility" accesskey="p" rel="prev">Visibility</a>, Up: <a href="#R-Internal-Structures" accesskey="u" rel="up">R Internal Structures</a> &nbsp; [<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="Lazy-loading-1"></a>
<h3 class="section">1.17 Lazy loading</h3>

<p>Lazy loading is always used for code in packages but is optional
(selected by the package maintainer) for datasets in packages.  When a
package/namespace which uses it is loaded, the package/namespace
environment is populated with promises for all the named objects: when
these promises are evaluated they load the actual code from a database.
</p>
<p>There are separate databases for code and data, stored in the <samp>R</samp>
and <samp>data</samp> subdirectories.  The database consists of two files,
<samp><var>name</var>.rdb</samp> and <samp><var>name</var>.rdx</samp>.  The <samp>.rdb</samp> file
is a concatenation of serialized objects, and the <samp>.rdx</samp> file
contains an index.  The objects are stored in (usually) a
<code>gzip</code>-compressed format with a 4-byte header giving the
uncompressed serialized length (in XDR, that is big-endian, byte order)
and read by a call to the primitive <code>lazyLoadDBfetch</code>.  (Note that
this makes lazy-loading unsuitable for really large objects: the
unserialized length of an R object can exceed 4GB.)
</p>
<p>The index or &lsquo;map&rsquo; file <samp><var>name</var>.rdx</samp> is a compressed serialized
R object to be read by <code>readRDS</code>.  It is a list with three
elements <code>variables</code>, <code>references</code> and <code>compressed</code>.  The
first two are named lists of integer vectors of length 2 giving the
offset and length of the serialized object in the <samp><var>name</var>.rdb</samp>
file.  Element <code>variables</code> has an entry for each named object:
<code>references</code> serializes a temporary environment used when named
environments are added to the database.  <code>compressed</code> is a logical
indicating if the serialized objects were compressed: compression is
always used nowadays. We later added the values <code>compressed = 2</code>
and <code>3</code> for <code>bzip2</code> and <code>xz</code> compression (with the
possibility of future expansion to other methods): these formats add a
fifth byte to the header for the type of compression, and store
serialized objects uncompressed if compression expands them.
</p>
<p>The loader for a lazy-load database of code or data is function
<code>lazyLoad</code> in the <strong>base</strong> package, but note that there is a
separate copy to load <strong>base</strong> itself in file
<samp>R_HOME/base/R/base</samp>.
</p>
<p>Lazy-load databases are created by the code in
<samp>src/library/tools/R/makeLazyLoad.R</samp>: the main tool is the
unexported function <code>makeLazyLoadDB</code> and the insertion of database
entries is done by calls to <code>.Call(&quot;R_lazyLoadDBinsertValue&quot;,
...)</code>.
</p>
<p>Lazy-load databases of less than 10MB are cached in memory at first use:
this was found necessary when using file systems with high latency
(removable devices and network-mounted file systems on Windows).
</p>
<p>Lazy-load databases are loaded into the exports for a package, but not
into the namespace environment itself.  Thus they are visible when the
package is <em>attached</em>, and also <em>via</em> the <code>::</code> operator.
This was a deliberate design decision, as packages mostly make datasets
available for use by the end user (or other packages), and they should
not be found preferentially from functions in the package, surprising
users who expected the normal search path to be used.  (There is an
alternative mechanism, <samp>sysdata.rda</samp>, for &lsquo;system datasets&rsquo; that
are intended primarily to be used within the package.)
</p>
<p>The same database mechanism is used to store parsed <samp>Rd</samp> files.
One or all of the parsed objects is fetched by a call to
<code>tools:::fetchRdDB</code>.
</p>
<hr>
<a name="g_t_002eInternal-vs-_002ePrimitive"></a>
<div class="header">
<p>
Next: <a href="#Internationalization-in-the-R-sources" accesskey="n" rel="next">Internationalization in the R sources</a>, Previous: <a href="#R-Internal-Structures" accesskey="p" rel="prev">R Internal Structures</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> &nbsp; [<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_t_002eInternal-vs-_002ePrimitive-1"></a>
<h2 class="chapter">2 <code>.Internal</code> vs <code>.Primitive</code></h2>

<a name="index-_002eInternal"></a>
<a name="index-_002ePrimitive"></a>
<p>C code compiled into R at build time can be called directly in what
are termed <em>primitives</em> or via the <code>.Internal</code> interface,
which is very similar to the <code>.External</code> interface except in
syntax.  More precisely, R maintains a table of R function names and
corresponding C functions to call, which by convention all start with
&lsquo;<samp>do_</samp>&rsquo; and return a <code>SEXP</code>.  This table (<code>R_FunTab</code> in
file <samp>src/main/names.c</samp>) also specifies how many arguments to a
function are required or allowed, whether or not the arguments are to be
evaluated before calling, and whether the function is &lsquo;internal&rsquo; in
the sense that it must be accessed via the <code>.Internal</code> interface,
or directly accessible in which case it is printed in R as
<code>.Primitive</code>.
</p>
<p>Functions using <code>.Internal()</code> wrapped in a closure are in general
preferred as this ensures standard handling of named and default
arguments.  For example, <code>grep</code> is defined as
</p>
<div class="example">
<pre class="example">grep &lt;-
function (pattern, x, ignore.case = FALSE, perl = FALSE, value = FALSE,
         fixed = FALSE, useBytes = FALSE, invert = FALSE)
{
    if (!is.character(x)) x &lt;- structure(as.character(x), names = names(x))
    .Internal(grep(as.character(pattern), x, ignore.case, value,
                   perl, fixed, useBytes, invert))
}

</pre></div>
<p>and the use of <code>as.character</code> allows methods to be dispatched (for
example, for factors).
</p>
<p>However, for reasons of convenience and also efficiency (as there is
some overhead in using the <code>.Internal</code> interface wrapped in a
function closure), the primitive functions are exceptions that can be
accessed directly.  And of course, primitive functions are needed for
basic operations&mdash;for example <code>.Internal</code> is itself a primitive.
Note that primitive functions make no use of R code, and hence are
very different from the usual interpreted functions.  In particular,
<code>formals</code> and <code>body</code> return <code>NULL</code> for such objects, and
argument matching can be handled differently.  For some primitives
(including <code>call</code>, <code>switch</code>, <code>.C</code> and <code>.subset</code>)
positional matching is important to avoid partial matching of the first
argument.
</p>
<p>The list of primitive functions is subject to change; currently, it
includes the following.
</p>
<ol>
<li> &ldquo;Special functions&rdquo; which really are <em>language</em> elements, but
implemented as primitive functions:

<div class="example">
<pre class="example">{       (         if     for      while  repeat  break  next
return  function  quote  switch
</pre></div>

</li><li> Language elements and basic <em>operator</em>s (i.e., functions usually
<em>not</em> called as <code>foo(a, b, ...)</code>) for subsetting, assignment,
arithmetic, comparison and logic:

<div class="example">
<pre class="example">               [    [[    $    @
&lt;-   &lt;&lt;-  =    [&lt;-  [[&lt;-  $&lt;-  @&lt;-

+    -    *    /     ^    %%   %*%  %/%
&lt;    &lt;=   ==   !=    &gt;=   &gt;
|    ||   &amp;    &amp;&amp;    !
</pre></div>

<p>When the arithmetic, comparison and logical operators are called as
functions, any argument names are discarded so positional matching is used.
</p>
</li><li> &ldquo;Low level&rdquo; 0&ndash; and 1&ndash;argument functions which belong to one of the
following groups of functions:

<ol>
<li> Basic mathematical functions with a single argument, i.e.,

<div class="example">
<pre class="example">abs     sign    sqrt
floor   ceiling
</pre><pre class="example">
</pre><pre class="example">exp     expm1
log2    log10   log1p
cos     sin     tan
acos    asin    atan
cosh    sinh    tanh
acosh   asinh   atanh
cospi   sinpi   tanpi
</pre><pre class="example">
</pre><pre class="example">gamma   lgamma  digamma trigamma
</pre><pre class="example">
</pre><pre class="example">cumsum  cumprod cummax  cummin
</pre><pre class="example">
</pre><pre class="example">Im  Re  Arg  Conj  Mod
</pre></div>

<p><code>log</code> is a primitive function of one or two arguments with named
argument matching.
</p>
<p><code>trunc</code> is a difficult case: it is a primitive that can have one
or more arguments: the default method handled in the primitive has
only one.
</p>
</li><li> Functions rarely used outside of &ldquo;programming&rdquo; (i.e., mostly used
inside other functions), such as

<div class="example">
<pre class="example">nargs          missing        on.exit        interactive
as.call        as.character   as.complex     as.double
as.environment as.integer     as.logical     as.raw
is.array       is.atomic      is.call        is.character
is.complex     is.double      is.environment is.expression
is.finite      is.function    is.infinite    is.integer
is.language    is.list        is.logical     is.matrix
is.na          is.name        is.nan         is.null
is.numeric     is.object      is.pairlist    is.raw
is.real        is.recursive   is.single      is.symbol
baseenv        emptyenv       globalenv      pos.to.env
unclass        invisible      seq_along      seq_len
</pre></div>

</li><li> The programming and session management utilities

<div class="example">
<pre class="example">browser  proc.time  gc.time tracemem retracemem untracemem
</pre></div>

</li></ol>

</li><li> The following basic replacement and extractor functions

<div class="example">
<pre class="example">length      length&lt;-
class       class&lt;-
oldClass    oldCLass&lt;-
attr        attr&lt;-
attributes  attributes&lt;-
names       names&lt;-
dim         dim&lt;-
dimnames    dimnames&lt;-
            environment&lt;-
            levels&lt;-
            storage.mode&lt;-
</pre></div>

<a name="index-NAMED-2"></a>
<p>Note that optimizing <code>NAMED = 1</code> is only effective within a
primitive (as the closure wrapper of a <code>.Internal</code> will set
<code>NAMED = 2</code> when the promise to the argument is evaluated) and
hence replacement functions should where possible be primitive to avoid
copying (at least in their default methods).
</p>
</li><li> The following functions are primitive for efficiency reasons:

<div class="example">
<pre class="example">:          ~          c           list
call       expression substitute
UseMethod  standardGeneric
.C         .Fortran   .Call       .External
round      signif      rep        seq.int
</pre></div>

<p>as well as the following internal-use-only functions
</p>
<div class="example">
<pre class="example">.Primitive     .Internal
.Call.graphics .External.graphics
.subset        .subset2
.primTrace     .primUntrace
lazyLoadDBfetch
</pre></div>

</li></ol>


<p>The multi-argument primitives
</p><div class="example">
<pre class="example">call       switch
.C         .Fortran   .Call       .External
</pre></div>

<p>intentionally use positional matching, and need to do so to avoid
partial matching to their first argument.  They do check that the first
argument is unnamed or for the first two, partially matches the formal
argument name.  On the other hand,
</p>
<div class="example">
<pre class="example">attr       attr&lt;-     browser     rememtrace substitute  UseMethod
log        round      signif      rep        seq.int
</pre></div>

<p>manage their own argument matching and do work in the standard way.
</p>
<p>All the one-argument primitives check that if they are called with a
named argument that this (partially) matches the name given in the
documentation: this is also done for replacement functions with one
argument plus <code>value</code>.
</p>
<p>The net effect is that argument matching for primitives intended for
end-user use <em>as functions</em> is done in the same way as for
interpreted functions except for the six exceptions where positional
matching is required.
</p>
<table summary="" class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">&bull; <a href="#Special-primitives" accesskey="1">Special primitives</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">&bull; <a href="#Special-internals" accesskey="2">Special internals</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">&bull; <a href="#Prototypes-for-primitives" accesskey="3">Prototypes for primitives</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">&bull; <a href="#Adding-a-primitive" accesskey="4">Adding a primitive</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
</table>

<hr>
<a name="Special-primitives"></a>
<div class="header">
<p>
Next: <a href="#Special-internals" accesskey="n" rel="next">Special internals</a>, Previous: <a href="#g_t_002eInternal-vs-_002ePrimitive" accesskey="p" rel="prev">.Internal vs .Primitive</a>, Up: <a href="#g_t_002eInternal-vs-_002ePrimitive" accesskey="u" rel="up">.Internal vs .Primitive</a> &nbsp; [<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="Special-primitives-1"></a>
<h3 class="section">2.1 Special primitives</h3>

<p>A small number of primitives are <em>specials</em> rather than
<em>builtins</em>, that is they are entered with unevaluated arguments.
This is clearly necessary for the language constructs and the assignment
operators, as well as for <code>&amp;&amp;</code> and <code>||</code> which conditionally
evaluate their second argument, and <code>~</code>, <code>.Internal</code>,
<code>call</code>, <code>expression</code>, <code>missing</code>, <code>on.exit</code>,
<code>quote</code> and <code>substitute</code> which do not evaluate some of their
arguments.
</p>
<p><code>rep</code> and <code>seq.int</code> are special as they evaluate some of their
arguments conditional on which are non-missing.
</p>
<p><code>log</code>, <code>round</code> and <code>signif</code> are special to allow default
values to be given to missing arguments.
</p>
<p>The subsetting, subassignment and <code>@</code> operators are all special.
(For both extraction and replacement forms, <code>$</code> and <code>@</code>
take a symbol argument, and <code>[</code> and <code>[[</code> allow missing
arguments.)
</p>
<p><code>UseMethod</code> is special to avoid the additional contexts added to
calls to builtins.
</p>
<hr>
<a name="Special-internals"></a>
<div class="header">
<p>
Next: <a href="#Prototypes-for-primitives" accesskey="n" rel="next">Prototypes for primitives</a>, Previous: <a href="#Special-primitives" accesskey="p" rel="prev">Special primitives</a>, Up: <a href="#g_t_002eInternal-vs-_002ePrimitive" accesskey="u" rel="up">.Internal vs .Primitive</a> &nbsp; [<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="Special-internals-1"></a>
<h3 class="section">2.2 Special internals</h3>

<p>There are also special <code>.Internal</code> functions: <code>NextMethod</code>,
<code>Recall</code>, <code>withVisible</code>, <code>cbind</code>, <code>rbind</code> (to allow
for the <code>deparse.level</code> argument), <code>eapply</code>, <code>lapply</code> and
<code>vapply</code>.
</p>
<hr>
<a name="Prototypes-for-primitives"></a>
<div class="header">
<p>
Next: <a href="#Adding-a-primitive" accesskey="n" rel="next">Adding a primitive</a>, Previous: <a href="#Special-internals" accesskey="p" rel="prev">Special internals</a>, Up: <a href="#g_t_002eInternal-vs-_002ePrimitive" accesskey="u" rel="up">.Internal vs .Primitive</a> &nbsp; [<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="Prototypes-for-primitives-1"></a>
<h3 class="section">2.3 Prototypes for primitives</h3>

<p>Prototypes are available for the primitive functions and operators, and
these are used for printing, <code>args</code> and package checking (e.g. by
<code>tools::checkS3methods</code> and by package <a href="https://CRAN.R-project.org/package=codetools"><strong>codetools</strong></a>).  There are
two environments in the <strong>base</strong> package (and namespace),
&lsquo;<samp>.GenericArgsEnv</samp>&rsquo; for those primitives which are internal S3
generics, and &lsquo;<samp>.ArgsEnv</samp>&rsquo; for the rest.  Those environments contain
closures with the same names as the primitives, formal arguments derived
(manually) from the help pages, a body which is a suitable call to
<code>UseMethod</code> or <code>NULL</code> and environment the base namespace.
</p>
<p>The C code for <code>print.default</code> and <code>args</code> uses the closures in
these environments in preference to the definitions in base (as
primitives).
</p>
<p>The QC function <code>undoc</code> checks that all the functions prototyped in
these environments are currently primitive, and that the primitives not
included are better thought of as language elements (at the time of
writing
</p>
<div class="example">
<pre class="example">$  $&lt;-  &amp;&amp;  (  :  @  @&lt;-  [  [[  [[&lt;-  [&lt;-  {  ||  ~  &lt;-  &lt;&lt;-  =
break  for function  if  next  repeat  return  while
</pre></div>

<p>).  One could argue about <code>~</code>, but it is known to the parser and has
semantics quite unlike a normal function.  And <code>:</code> is documented
with different argument names in its two meanings.)
</p>
<p>The QC functions <code>codoc</code> and <code>checkS3methods</code> also make use of
these environments (effectively placing them in front of base in the
search path), and hence the formals of the functions they contain are
checked against the help pages by <code>codoc</code>.  However, there are two
problems with the generic primitives.  The first is that many of the
operators are part of the S3 group generic <code>Ops</code> and that defines
their arguments to be <code>e1</code> and <code>e2</code>: although it would be very
unusual, an operator could be called as e.g. <code>&quot;+&quot;(e1=a, e2=b)</code>
and if method dispatch occurred to a closure, there would be an argument
name mismatch.  So the definitions in environment <code>.GenericArgsEnv</code>
have to use argument names <code>e1</code> and <code>e2</code> even though the
traditional documentation is in terms of <code>x</code> and <code>y</code>:
<code>codoc</code> makes the appropriate adjustment via
<code>tools:::.make_S3_primitive_generic_env</code>.  The second discrepancy
is with the <code>Math</code> group generics, where the group generic is
defined with argument list <code>(x, ...)</code>, but most of the members only
allow one argument when used as the default method (and <code>round</code> and
<code>signif</code> allow two as default methods): again fix-ups are used.
</p>
<p>Those primitives which are in <code>.GenericArgsEnv</code> are checked (via
<samp>tests/primitives.R</samp>) to be generic <em>via</em> defining methods for
them, and a check is made that the remaining primitives are probably not
generic, by setting a method and checking it is not dispatched to (but
this can fail for other reasons).  However, there is no certain way to
know that if other <code>.Internal</code> or primitive functions are not
internally generic except by reading the source code.
</p>
<hr>
<a name="Adding-a-primitive"></a>
<div class="header">
<p>
Previous: <a href="#Prototypes-for-primitives" accesskey="p" rel="prev">Prototypes for primitives</a>, Up: <a href="#g_t_002eInternal-vs-_002ePrimitive" accesskey="u" rel="up">.Internal vs .Primitive</a> &nbsp; [<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="Adding-a-primitive-1"></a>
<h3 class="section">2.4 Adding a primitive</h3>

<p>[For R-core use: reverse this procedure to remove a primitive.  Most
commonly this is done by changing a <code>.Internal</code> to a primitive or
<em>vice versa</em>.]
</p>
<p>Primitives are listed in the table <code>R_FunTab</code> in
<samp>src/main/names.c</samp>: primitives have &lsquo;<samp>Y = 0</samp>&rsquo; in the &lsquo;<samp>eval</samp>&rsquo;
field.
</p>
<p>There needs to be an &lsquo;<samp>\alias</samp>&rsquo; entry in a help file in the <strong>base</strong>
package, and the primitive needs to be added to one of the lists at the
start of this section.
</p>
<p>Some primitives are regarded as language elements (the current ones are
listed above).  These need to be added to two lists of exceptions,
<code>langElts</code> in <code>undoc()</code> (in file
<samp>src/library/tools/R/QC.R</samp>) and <code>lang_elements</code> in
<samp>tests/primitives.R</samp>.
</p>
<p>All other primitives are regarded as functions and should be listed in
one of the environments defined in <samp>src/library/base/R/zzz.R</samp>,
either <code>.ArgsEnv</code> or <code>.GenericArgsEnv</code>: internal generics also
need to be listed in the character vector <code>.S3PrimitiveGenerics</code>.
Note too the discussion about argument matching above: if you add a
primitive function with more than one argument by converting a
<code>.Internal</code> you need to add argument matching to the C code, and
for those with a single argument, add argument-name checking.
</p>
<p>Do ensure that <code>make check-devel</code> has been run: that tests most
of these requirements.
</p>
<hr>
<a name="Internationalization-in-the-R-sources"></a>
<div class="header">
<p>
Next: <a href="#Package-Structure" accesskey="n" rel="next">Package Structure</a>, Previous: <a href="#g_t_002eInternal-vs-_002ePrimitive" accesskey="p" rel="prev">.Internal vs .Primitive</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> &nbsp; [<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-in-the-R-sources-1"></a>
<h2 class="chapter">3 Internationalization in the R sources</h2>

<p>The process of marking messages (errors, warnings etc) for translation
in an R package is described in
<a href="http://cran.r-project.org/doc/manuals/R-exts.html#Internationalization">Internationalization</a> in <cite>Writing R Extensions</cite>,
and the standard packages included with R have (with an exception in
<strong>grDevices</strong> for the menus of the <code>windows()</code> device) been
internationalized in the same way as other packages.
</p>
<table summary="" class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">&bull; <a href="#R-code" accesskey="1">R code</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">&bull; <a href="#Main-C-code" accesskey="2">Main C code</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">&bull; <a href="#Windows_002dGUI_002dspecific-code" accesskey="3">Windows-GUI-specific code</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">&bull; <a href="#OS-X-GUI" accesskey="4">OS X GUI</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">&bull; <a href="#Updating" accesskey="5">Updating</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
</table>

<hr>
<a name="R-code"></a>
<div class="header">
<p>
Next: <a href="#Main-C-code" accesskey="n" rel="next">Main C code</a>, Previous: <a href="#Internationalization-in-the-R-sources" accesskey="p" rel="prev">Internationalization in the R sources</a>, Up: <a href="#Internationalization-in-the-R-sources" accesskey="u" rel="up">Internationalization in the R sources</a> &nbsp; [<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-code-1"></a>
<h3 class="section">3.1 R code</h3>

<p>Internationalization for R code is done in exactly the same way as
for extension packages.  As all standard packages which have R code
also have a namespace, it is never necessary to specify <code>domain</code>,
but for efficiency calls to <code>message</code>, <code>warning</code> and
<code>stop</code> should include <code>domain = NA</code> when the message is
constructed <em>via</em> <code>gettextf</code>, <code>gettext</code> or
<code>ngettext</code>.
</p>
<p>For each package, the extracted messages and translation sources are
stored under package directory <samp>po</samp> in the source package, and
compiled translations under <samp>inst/po</samp> for installation to package
directory <samp>po</samp> in the installed package.  This also applies to C
code in packages.
</p>
<hr>
<a name="Main-C-code"></a>
<div class="header">
<p>
Next: <a href="#Windows_002dGUI_002dspecific-code" accesskey="n" rel="next">Windows-GUI-specific code</a>, Previous: <a href="#R-code" accesskey="p" rel="prev">R code</a>, Up: <a href="#Internationalization-in-the-R-sources" accesskey="u" rel="up">Internationalization in the R sources</a> &nbsp; [<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="Main-C-code-1"></a>
<h3 class="section">3.2 Main C code</h3>

<p>The main C code (e.g. that in files <samp>src/*/*.c</samp> and in
the modules) is where R is closest to the sort of application for
which &lsquo;<samp>gettext</samp>&rsquo; was written.  Messages in the main C code are in
domain <code>R</code> and stored in the top-level directory <samp>po</samp> with
compiled translations under <samp>share/locale</samp>.
</p>
<p>The list of files covered by the R domain is specified in file
<samp>po/POTFILES.in</samp>.
</p>
<p>The normal way to mark messages for translation is via <code>_(&quot;msg&quot;)</code>
just as for packages.  However, sometimes one needs to mark passages for
translation without wanting them translated at the time, for example
when declaring string constants.  This is the purpose of the <code>N_</code>
macro, for example
</p>
<div class="example">
<pre class="example">{ ERROR_ARGTYPE,           N_(&quot;invalid argument type&quot;)},
</pre></div>

<p>from file <samp>src/main/errors.c</samp>.
</p>
<p>The <code>P_</code> macro
</p>
<div class="example">
<pre class="example">#ifdef ENABLE_NLS
#define P_(StringS, StringP, N) ngettext (StringS, StringP, N)
#else
#define P_(StringS, StringP, N) (N &gt; 1 ? StringP: StringS)
#endif
</pre></div>

<p>may be used
as a wrapper for <code>ngettext</code>: however in some cases the preferred
approach has been to conditionalize (on <code>ENABLE_NLS</code>) code using
<code>ngettext</code>.
</p>
<p>The macro <code>_(&quot;msg&quot;)</code> can safely be used in directory
<samp>src/appl</samp>; the header for standalone &lsquo;<samp>nmath</samp>&rsquo; skips possible
translation.  (This does not apply to <code>N_</code> or <code>P_</code>).
</p>

<hr>
<a name="Windows_002dGUI_002dspecific-code"></a>
<div class="header">
<p>
Next: <a href="#OS-X-GUI" accesskey="n" rel="next">OS X GUI</a>, Previous: <a href="#Main-C-code" accesskey="p" rel="prev">Main C code</a>, Up: <a href="#Internationalization-in-the-R-sources" accesskey="u" rel="up">Internationalization in the R sources</a> &nbsp; [<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_002dGUI_002dspecific-code-1"></a>
<h3 class="section">3.3 Windows-GUI-specific code</h3>

<p>Messages for the Windows GUI are in a separate domain &lsquo;<samp>RGui</samp>&rsquo;.  This
was done for two reasons:
</p>
<ul>
<li> The translators for the Windows version of R might be separate from
those for the rest of R (familiarity with the GUI helps), and

</li><li> Messages for Windows are most naturally handled in the native charset
for the language, and in the case of CJK languages the charset is
Windows-specific.  (It transpires that as the <code>iconv</code> we ported
works well under Windows, this is less important than anticipated.)
</li></ul>

<p>Messages for the &lsquo;<samp>RGui</samp>&rsquo; domain are marked by <code>G_(&quot;msg&quot;)</code>, a
macro that is defined in header file <samp>src/gnuwin32/win-nls.h</samp>.  The
list of files that are considered is hardcoded in the
<code>RGui.pot-update</code> target of file <samp>po/Makefile.in.in</samp>: note
that this includes <samp>devWindows.c</samp> as the menus on the
<code>windows</code> device are considered to be part of the GUI.  (There is
also <code>GN_(&quot;msg&quot;)</code>, the analogue of <code>N_(&quot;msg&quot;)</code>.)
</p>
<p>The template and message catalogs for the &lsquo;<samp>RGui</samp>&rsquo; domain are in the
top-level <samp>po</samp> directory.
</p>

<hr>
<a name="OS-X-GUI"></a>
<div class="header">
<p>
Next: <a href="#Updating" accesskey="n" rel="next">Updating</a>, Previous: <a href="#Windows_002dGUI_002dspecific-code" accesskey="p" rel="prev">Windows-GUI-specific code</a>, Up: <a href="#Internationalization-in-the-R-sources" accesskey="u" rel="up">Internationalization in the R sources</a> &nbsp; [<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-GUI-1"></a>
<h3 class="section">3.4 OS X GUI</h3>

<p>This is handled separately: see
<a href="https://developer.r-project.org/Translations30.html">https://developer.r-project.org/Translations30.html</a>.
</p>

<hr>
<a name="Updating"></a>
<div class="header">
<p>
Previous: <a href="#OS-X-GUI" accesskey="p" rel="prev">OS X GUI</a>, Up: <a href="#Internationalization-in-the-R-sources" accesskey="u" rel="up">Internationalization in the R sources</a> &nbsp; [<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-1"></a>
<h3 class="section">3.5 Updating</h3>

<p>See file <samp>po/README</samp> for how to update the message templates and catalogs.
</p>
<hr>
<a name="Package-Structure"></a>
<div class="header">
<p>
Next: <a href="#Files" accesskey="n" rel="next">Files</a>, Previous: <a href="#Internationalization-in-the-R-sources" accesskey="p" rel="prev">Internationalization in the R sources</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> &nbsp; [<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="Structure-of-an-Installed-Package"></a>
<h2 class="chapter">4 Structure of an Installed Package</h2>

<table summary="" class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">&bull; <a href="#Metadata" accesskey="1">Metadata</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">&bull; <a href="#Help" accesskey="2">Help</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
</table>

<p>The structure of a <em>source</em> packages is described in <a href="http://cran.r-project.org/doc/manuals/R-exts.html#Creating-R-packages">Creating R packages</a> in <cite>Writing R Extensions</cite>: this
chapter is concerned with the structure of <em>installed</em> packages.
</p>
<p>An installed package has a top-level file <samp>DESCRIPTION</samp>, a copy of
the file of that name in the package sources with a &lsquo;<samp>Built</samp>&rsquo; field
appended, and file <samp>INDEX</samp>, usually describing the objects on which
help is available, a file <samp>NAMESPACE</samp> if the package has a name
space, optional files such as <samp>CITATION</samp>, <samp>LICENCE</samp> and
<samp>NEWS</samp>, and any other files copied in from <samp>inst</samp>.  It will
have directories <samp>Meta</samp>, <samp>help</samp> and <samp>html</samp> (even if the
package has no help pages), almost always has a directory <samp>R</samp> and
often has a directory <samp>libs</samp> to contain compiled code.  Other
directories with known meaning to R are <samp>data</samp>, <samp>demo</samp>,
<samp>doc</samp> and <samp>po</samp>.
</p>
<p>Function <code>library</code> looks for a namespace and if one is found
passes control to <code>loadNamespace</code>.  Then <code>library</code> or
<code>loadNamespace</code> looks for file <samp>R/<var>pkgname</var></samp>, warns if it
is not found and otherwise sources the code (using <code>sys.source</code>)
into the package&rsquo;s environment, then lazy-loads a database
<samp>R/sysdata</samp> if present.  So how R code gets loaded depends on
the contents of  <samp>R/<var>pkgname</var></samp>: a standard template to load
lazy-load databases are provided in <samp>share/R/nspackloader.R</samp>.
</p>
<p>Compiled code is usually loaded when the package&rsquo;s namespace is loaded
by a <code>useDynlib</code> directive in a <samp>NAMESPACE</samp> file or by the
package&rsquo;s <code>.onLoad</code> function.  Conventionally compiled code is
loaded by a call to <code>library.dynam</code> and this looks in directory
<samp>libs</samp> (and in an appropriate sub-directory if sub-architectures
are in use) for a shared object (Unix-alike) or DLL (Windows).
</p>
<p>Subdirectory <samp>data</samp> serves two purposes. In a package using
lazy-loading of data, it contains a lazy-load database <samp>Rdata</samp>,
plus a file <samp>Rdata.rds</samp> which contain a named character vector used
by <code>data()</code> in the (unusual) event that it is used for such a
package.  Otherwise it is a copy of the <samp>data</samp> directory in the
sources, with saved images re-compressed if <code>R CMD INSTALL
--resave-data</code> was used.
</p>
<p>Subdirectory <samp>demo</samp> supports the <code>demo</code> function, and is
copied from the sources.
</p>
<p>Subdirectory <samp>po</samp> contains (in subdirectories) compiled message
catalogs.
</p>
<hr>
<a name="Metadata"></a>
<div class="header">
<p>
Next: <a href="#Help" accesskey="n" rel="next">Help</a>, Previous: <a href="#Package-Structure" accesskey="p" rel="prev">Package Structure</a>, Up: <a href="#Package-Structure" accesskey="u" rel="up">Package Structure</a> &nbsp; [<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="Metadata-1"></a>
<h3 class="section">4.1 Metadata</h3>

<p>Directory <samp>Meta</samp> contains several files in <code>.rds</code> format, that
is serialized R objects written by <code>saveRDS</code>.  All packages
have files <samp>Rd.rds</samp>, <samp>hsearch.rds</samp>, <samp>links.rds</samp> and
<samp>package.rds</samp>.  Packages with namespaces have a file
<samp>nsInfo.rds</samp>, and those with data, demos or vignettes have
<samp>data.rds</samp>, <samp>demo.rds</samp> or <samp>vignette.rds</samp> files.
</p>
<p>The structure of these files (and their existence and names) is private
to R, so the description here is for those trying to follow the R
sources: there should be no reference to these files in non-base
packages.
</p>
<p>File <samp>package.rds</samp> is a dump of information extracted from the
<samp>DESCRIPTION</samp> file.  It is a list of several components.  The
first, &lsquo;<samp>DESCRIPTION</samp>&rsquo;, is a character vector, the <samp>DESCRIPTION</samp>
file as read by <code>read.dcf</code>.  Further elements &lsquo;<samp>Depends</samp>&rsquo;,
&lsquo;<samp>Suggests</samp>&rsquo;, &lsquo;<samp>Imports</samp>&rsquo;, &lsquo;<samp>Rdepends</samp>&rsquo; and &lsquo;<samp>Rdepends2</samp>&rsquo;
record the &lsquo;<samp>Depends</samp>&rsquo;, &lsquo;<samp>Suggests</samp>&rsquo; and &lsquo;<samp>Imports</samp>&rsquo; fields.
These are all lists, and can be empty.  The first three have an entry
for each package named, each entry being a list of length 1 or 3, which
element &lsquo;<samp>name</samp>&rsquo; (the package name) and optional elements &lsquo;<samp>op</samp>&rsquo;
(a character string) and &lsquo;<samp>version</samp>&rsquo; (an object of class
&lsquo;<samp>&quot;package_version&quot;</samp>&rsquo;).  Element &lsquo;<samp>Rdepends</samp>&rsquo; is used for the
first version dependency on R, and &lsquo;<samp>Rdepends2</samp>&rsquo; is a list of zero
or more R version dependencies&mdash;each is a three-element list of the
form described for packages.  Element &lsquo;<samp>Rdepends</samp>&rsquo; is no longer used,
but it is still potentially needed so R &lt; 2.7.0 can detect that the
package was not installed for it.
</p>
<p>File <samp>nsInfo.rds</samp> records a list, a parsed version of the
<samp>NAMESPACE</samp> file.
</p>
<p>File <samp>Rd.rds</samp> records a data frame with one row for each help file.
The columns are &lsquo;<samp>File</samp>&rsquo; (the file name with extension), &lsquo;<samp>Name</samp>&rsquo;
(the &lsquo;<samp>\name</samp>&rsquo; section), &lsquo;<samp>Type</samp>&rsquo; (from the optional
&lsquo;<samp>\docType</samp>&rsquo; section), &lsquo;<samp>Title</samp>&rsquo;, &lsquo;<samp>Encoding</samp>&rsquo;, &lsquo;<samp>Aliases</samp>&rsquo;,
&lsquo;<samp>Concepts</samp>&rsquo; and &lsquo;<samp>Keywords</samp>&rsquo;.  All columns are character vectors
apart from &lsquo;<samp>Aliases</samp>&rsquo;, which is a list of character vectors.
</p>
<p>File <samp>hsearch.rds</samp> records the information to be used by
&lsquo;<samp>help.search</samp>&rsquo;.  This is a list of four unnamed elements which are
character matrices for help files, aliases, keywords and concepts.  All
the matrices have columns &lsquo;<samp>ID</samp>&rsquo; and &lsquo;<samp>Package</samp>&rsquo; which are used to
tie the aliases, keywords and concepts (the remaining column of the last
three elements) to a particular help file.  The first element has
further columns &lsquo;<samp>LibPath</samp>&rsquo; (stored as <code>&quot;&quot;</code> and filled in what
the file is loaded), &lsquo;<samp>name</samp>&rsquo;, &lsquo;<samp>title</samp>&rsquo;, &lsquo;<samp>topic</samp>&rsquo; (the first
alias, used when presenting the results as
&lsquo;<samp><var>pkgname</var>::<var>topic</var></samp>&rsquo;) and &lsquo;<samp>Encoding</samp>&rsquo;.
</p>
<p>File <samp>links.rds</samp> records a named character vector, the names being
aliases and the values character strings of the form
</p><div class="example">
<pre class="example">&quot;../../<var>pkgname</var>/html/<var>filename</var>.html&quot;
</pre></div>

<p>File <samp>data.rds</samp> records a two-column character matrix with columns
of dataset names and titles from the corresponding help file.  File
<samp>demo.rds</samp> has the same structure for package demos.
</p>
<p>File <samp>vignette.rds</samp> records a data frame with one row for each
&lsquo;vignette&rsquo; (<samp>.[RS]nw</samp> file in <samp>inst/doc</samp>) and with columns
&lsquo;<samp>File</samp>&rsquo; (the full file path in the sources), &lsquo;<samp>Title</samp>&rsquo;,
&lsquo;<samp>PDF</samp>&rsquo; (the pathless file name of the installed PDF version, if
present), &lsquo;<samp>Depends</samp>&rsquo;, &lsquo;<samp>Keywords</samp>&rsquo; and &lsquo;<samp>R</samp>&rsquo; (the pathless
file name of the installed R code, if present).
</p>

<hr>
<a name="Help"></a>
<div class="header">
<p>
Previous: <a href="#Metadata" accesskey="p" rel="prev">Metadata</a>, Up: <a href="#Package-Structure" accesskey="u" rel="up">Package Structure</a> &nbsp; [<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-1"></a>
<h3 class="section">4.2 Help</h3>

<p>All installed packages, whether they had any <samp>.Rd</samp> files or not,
have <samp>help</samp> and <samp>html</samp> directories. The latter normally only
contains the single file <samp>00Index.html</samp>, the package index which
has hyperlinks to the help topics (if any).
</p>
<p>Directory <samp>help</samp> contains files <samp>AnIndex</samp>, <samp>paths.rds</samp>
and <samp><var>pkgname</var>.rd[bx]</samp>.  The latter two files are a lazy-load
database of parsed <samp>.Rd</samp> files, accessed by
<code>tools:::fetchRdDB</code>.  File <samp>paths.rds</samp> is a saved character
vector of the original path names of the <samp>.Rd</samp> files, used when
updating the database.
</p>
<p>File <samp>AnIndex</samp> is a two-column tab-delimited file: the first column
contains the aliases defined in the help files and the second the
basename (without the <samp>.Rd</samp> or <samp>.rd</samp> extension) of the file
containing that alias.  It is read by <code>utils:::index.search</code> to
search for files matching a topic (alias), and read by <code>scan</code> in
<code>utils:::matchAvailableTopics</code>, part of the completion system.
</p>
<p>File <samp>aliases.rds</samp> is the same information as <samp>AnIndex</samp> as a
named character vector (names the topics, values the file basename), for
faster access.
</p>
<hr>
<a name="Files"></a>
<div class="header">
<p>
Next: <a href="#Graphics-Devices" accesskey="n" rel="next">Graphics Devices</a>, Previous: <a href="#Package-Structure" accesskey="p" rel="prev">Package Structure</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> &nbsp; [<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="Files-1"></a>
<h2 class="chapter">5 Files</h2>

<p>R provides many functions to work with files and directories: many of
these have been added relatively recently to facilitate scripting in
R and in particular the replacement of Perl scripts by R scripts
in the management of R itself.
</p>
<p>These functions are implemented by standard C/POSIX library calls,
except on Windows.  That means that filenames must be encoded in the
current locale as the OS provides no other means to access the file
system: increasingly filenames are stored in UTF-8 and the OS will
translate filenames to UTF-8 in other locales.  So using a UTF-8 locale
gives transparent access to the whole file system.
</p>
<p>Windows is another story.  There the internal view of filenames is in
UTF-16LE (so-called &lsquo;Unicode&rsquo;), and standard C library calls can only
access files whose names can be expressed in the current codepage.  To
circumvent that restriction, there is a parallel set of Windows-specific
calls which take wide-character arguments for filepaths.  Much of the
file-handling in R has been moved over to using these functions, so
filenames can be manipulated in R as UTF-8 encoded character strings,
converted to wide characters (which on Windows are UTF-16LE) and passed
to the OS.  The utilities <code>RC_fopen</code> and <code>filenameToWchar</code>
help this process.  Currently <code>file.copy</code> to a directory,
<code>list.files</code>, <code>list.dirs</code> and <code>path.expand</code> work only
with filepaths encoded in the current codepage.
</p>
<p>All these functions do tilde expansion, in the same way as
<code>path.expand</code>, with the deliberate exception of <code>Sys.glob</code>.
</p>
<p>File names may be case sensitive or not: the latter is the norm on
Windows and OS X, the former on other Unix-alikes.  Note that this
is a property of both the OS and the file system: it is often possible
to map names to upper or lower case when mounting the file system.  This
can affect the matching of patterns in <code>list.files</code> and
<code>Sys.glob</code>.
</p>
<p>File names commonly contain spaces on Windows and OS X but not
elsewhere.  As file names are handled as character strings by R,
spaces are not usually a concern unless file names are passed to other
process, e.g. by a <code>system</code> call.
</p>
<p>Windows has another couple of peculiarities.  Whereas a POSIX file
system has a single root directory (and other physical file systems are
mounted onto logical directories under that root), Windows has separate
roots for each physical or logical file system (&lsquo;volume&rsquo;), organized
under <em>drives</em> (with file paths starting <code>D:</code> for an
<acronym>ASCII</acronym> letter, case-insensitively) and <em>network shares</em>
(with paths like <code>\netname\topdir\myfiles\a file</code>.  There is a
current drive, and path names without a drive part are relative to the
current drive.  Further, each drive has a current directory, and
relative paths are relative to that current directory, on a particular
drive if one is specified.  So <samp>D:dir\file</samp> and <samp>D:</samp> are valid
path specifications (the last being the current directory on drive
<samp>D:</samp>).
</p>


<hr>
<a name="Graphics-Devices"></a>
<div class="header">
<p>
Next: <a href="#GUI-consoles" accesskey="n" rel="next">GUI consoles</a>, Previous: <a href="#Files" accesskey="p" rel="prev">Files</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> &nbsp; [<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="Graphics"></a>
<h2 class="chapter">6 Graphics</h2>

<p>R&rsquo;s graphics internals were re-designed to enable multiple graphics
systems to be installed on top on the graphics &lsquo;engine&rsquo; &ndash; currently
there are two such systems, one supporting &lsquo;base&rsquo; graphics (based on
that in S and whose R code<a name="DOCF15" href="#FOOT15"><sup>15</sup></a> is in package
<strong>graphics</strong>) and one implemented in package <strong>grid</strong>.
</p>
<p>Some notes on the historical changes can be found at
<a href="https://www.stat.auckland.ac.nz/~paul/R/basegraph.html">https://www.stat.auckland.ac.nz/~paul/R/basegraph.html</a> and
<a href="https://www.stat.auckland.ac.nz/~paul/R/graphicsChanges.html">https://www.stat.auckland.ac.nz/~paul/R/graphicsChanges.html</a>.
</p>
<p>At the lowest level is a graphics device, which manages a plotting
surface (a screen window or a representation to be written to a file).
This implements a set of graphics primitives, to &lsquo;draw&rsquo;
</p>
<ul>
<li> a circle, optionally filled
</li><li> a rectangle, optionally filled
</li><li> a line
</li><li> a set of connected lines
</li><li> a polygon, optionally filled
</li><li> a paths, optionally filled using a winding rule
</li><li> text
</li><li> a raster image (optional)
</li><li> and to set a clipping rectangle
</li></ul>

<p>as well as requests for information such as
</p>
<ul>
<li> the width of a string if plotted
</li><li> the metrics (width, ascent, descent) of a single character
</li><li> the current size of the plotting surface
</li></ul>

<p>and requests/opportunities to take action such as
</p>
<ul>
<li> start a new &lsquo;page&rsquo;, possibly after responding to a request to ask
the user for confirmation.
</li><li> return the position of the device pointer (if any).
</li><li> when a device become the current device or stops being the current
device (this is usually used to change the window title on a screen
device).
</li><li> when drawing starts or finishes (e.g. used to flush graphics to
the screen when drawing stops).
</li><li> wait for an event, for example a mouse click or keypress.
</li><li> an &lsquo;onexit&rsquo; action, to clean up if plotting is interrupted (by an
error or by the user).
</li><li> capture the current contents of the device as a raster image.
</li><li> close the device.
</li></ul>

<p>The device also sets a number of variables, mainly Boolean flags
indicating its capabilities.  Devices work entirely in &lsquo;device units&rsquo;
which are up to its developer: they can be in pixels, big points (1/72
inch), twips, &hellip;, and can differ<a name="DOCF16" href="#FOOT16"><sup>16</sup></a> in the
&lsquo;<samp>x</samp>&rsquo; and &lsquo;<samp>y</samp>&rsquo; directions.
</p>
<p>The next layer up is the graphics &lsquo;engine&rsquo; that is the main interface to
the device (although the graphics subsystems do talk directly to
devices).  This is responsible for clipping lines, rectangles and
polygons, converting the <code>pch</code> values <code>0...26</code> to sets of
lines/circles, centring (and otherwise adjusting) text, rendering
mathematical expressions (&lsquo;plotmath&rsquo;) and mapping colour descriptions
such as names to the internal representation.
</p>

<p>Another function of the engine is to manage display lists and snapshots.
Some but not all instances of graphics devices maintain display lists, a
&lsquo;list&rsquo; of operations that have been performed on the device to produce
the current plot (since the device was opened or the plot was last
cleared, e.g. by <code>plot.new</code>).  Screen devices generally maintain
a display list to handle repaint and resize events whereas file-based
formats do not&mdash;display lists are also used to implement
<code>dev.copy()</code> and friends.  The display list is a pairlist of
<code>.Internal</code> (base graphics) or <code>.Call.graphics</code> (grid
graphics) calls, which means that the C code implementing a graphics
operation will be re-called when the display list is replayed: apart
from the part which records the operation if successful.
</p>
<p>Snapshots of the current graphics state are taken by
<code>GEcreateSnapshot</code> and replayed later in the session by
<code>GEplaySnapshot</code>.  These are used by <code>recordPlot()</code>,
<code>replayPlot()</code> and the GUI menus of the <code>windows()</code> device.
The &lsquo;state&rsquo; includes the display list.
</p>

<p>The top layer comprises the graphics subsystems. Although there is
provision for 24 subsystems since about 2001, currently still only two
exist, &lsquo;base&rsquo; and
&lsquo;grid&rsquo;.  The base subsystem is registered with the engine when R is
initialized, and unregistered (via <code>KillAllDevices</code>) when an R
session is shut down.  The grid subsystem is registered in its
<code>.onLoad</code> function and unregistered in the <code>.onUnload</code>
function.  The graphics subsystem may also have &lsquo;state&rsquo; information
saved in a snapshot (currently base does and grid does not).
</p>
<p>Package <strong>grDevices</strong> was originally created to contain the basic
graphics devices (although <code>X11</code> is in a separate load-on-demand
module because of the volume of external libraries it brings in).  Since
then it has been used for other functionality that was thought desirable
for use with <strong>grid</strong>, and hence has been transferred from package
<strong>graphics</strong> to <strong>grDevices</strong>.  This is principally concerned with
the handling of colours and recording and replaying plots.
</p>
<table summary="" class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">&bull; <a href="#Graphics-devices" accesskey="1">Graphics devices</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">&bull; <a href="#Colours" accesskey="2">Colours</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">&bull; <a href="#Base-graphics" accesskey="3">Base graphics</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">&bull; <a href="#Grid-graphics" accesskey="4">Grid graphics</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
</table>

<hr>
<a name="Graphics-devices"></a>
<div class="header">
<p>
Next: <a href="#Colours" accesskey="n" rel="next">Colours</a>, Previous: <a href="#Graphics-Devices" accesskey="p" rel="prev">Graphics Devices</a>, Up: <a href="#Graphics-Devices" accesskey="u" rel="up">Graphics Devices</a> &nbsp; [<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="Graphics-Devices-1"></a>
<h3 class="section">6.1 Graphics Devices</h3>

<p>R ships with several graphics devices, and there is support for
third-party packages to provide additional devices&mdash;several packages
now do.  This section describes the device internals from the viewpoint
of a would-be writer of a graphics device.
</p>
<table summary="" class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">&bull; <a href="#Device-structures" accesskey="1">Device structures</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">&bull; <a href="#Device-capabilities" accesskey="2">Device capabilities</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">&bull; <a href="#Handling-text" accesskey="3">Handling text</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">&bull; <a href="#Conventions" accesskey="4">Conventions</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">&bull; <a href="#g_t_0027Mode_0027" accesskey="5">'Mode'</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">&bull; <a href="#Graphics-events" accesskey="6">Graphics events</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">&bull; <a href="#Specific-devices" accesskey="7">Specific devices</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
</table>

<hr>
<a name="Device-structures"></a>
<div class="header">
<p>
Next: <a href="#Device-capabilities" accesskey="n" rel="next">Device capabilities</a>, Previous: <a href="#Graphics-devices" accesskey="p" rel="prev">Graphics devices</a>, Up: <a href="#Graphics-devices" accesskey="u" rel="up">Graphics devices</a> &nbsp; [<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="Device-structures-1"></a>
<h4 class="subsection">6.1.1 Device structures</h4>

<p>There are two types used internally which are pointers to structures
related to graphics devices.
</p>
<p>The <code>DevDesc</code> type is a structure defined in the header file
<samp>R_ext/GraphicsDevice.h</samp> (which is included by
<samp>R_ext/GraphicsEngine.h</samp>).  This describes the physical
characteristics of a device, the capabilities of the device driver and
contains a set of callback functions that will be used by the graphics
engine to obtain information about the device and initiate actions
(e.g. a new page, plotting a line or some text).  Type <code>pDevDesc</code>
is a pointer to this type.
</p>
<p>The following callbacks can be omitted (or set to the null pointer,
their default value) when appropriate default behaviour will be taken by
the graphics engine: <code>activate</code>, <code>cap</code>, <code>deactivate</code>,
<code>locator</code>, <code>holdflush</code> (API version 9), <code>mode</code>,
<code>newFrameConfirm</code>, <code>path</code>, <code>raster</code> and <code>size</code>.
</p>
<p>The relationship of device units to physical dimensions is set by the
element <code>ipr</code> of the <code>DevDesc</code> structure: a &lsquo;<samp>double</samp>&rsquo;
array of length 2.
</p>

<p>The <code>GEDevDesc</code> type is a structure defined in
<samp>R_ext/GraphicsEngine.h</samp> (with comments in the file) as
</p>
<div class="example">
<pre class="example">typedef struct _GEDevDesc GEDevDesc;
struct _GEDevDesc {
    pDevDesc dev;
    Rboolean displayListOn;
    SEXP displayList;
    SEXP DLlastElt;
    SEXP savedSnapshot;
    Rboolean dirty;
    Rboolean recordGraphics;
    GESystemDesc *gesd[MAX_GRAPHICS_SYSTEMS];
    Rboolean ask;
}
</pre></div>

<p>So this is essentially a device structure plus information about the
device maintained by the graphics engine and normally<a name="DOCF17" href="#FOOT17"><sup>17</sup></a> visible to the engine
and not to the device.  Type <code>pGEDevDesc</code> is a pointer to this
type.
</p>
<p>The graphics engine maintains an array of devices, as pointers to
<code>GEDevDesc</code> structures.  The array is of size 64 but the first
element is always occupied by the <code>&quot;null device&quot;</code> and the final
element is kept as NULL as a sentinel.<a name="DOCF18" href="#FOOT18"><sup>18</sup></a>  This array is reflected in the R variable
&lsquo;<samp>.Devices</samp>&rsquo;.  Once a device is killed its element becomes available
for reallocation (and its name will appear as <code>&quot;&quot;</code> in
&lsquo;<samp>.Devices</samp>&rsquo;).  Exactly one of the devices is &lsquo;active&rsquo;: this is the
the null device if no other device has been opened and not killed.
</p>
<p>Each instance of a graphics device needs to set up a <code>GEDevDesc</code>
structure by code very similar to
</p>
<div class="example">
<pre class="example">    pGEDevDesc gdd;

    R_GE_checkVersionOrDie(R_GE_version);
    R_CheckDeviceAvailable();
    BEGIN_SUSPEND_INTERRUPTS {
        pDevDesc dev;
        /* Allocate and initialize the device driver data */
        if (!(dev = (pDevDesc) calloc(1, sizeof(DevDesc))))
            return 0; /* or error() */
        /* set up device driver or free ‘dev’ and error() */
        gdd = GEcreateDevDesc(dev);
        GEaddDevice2(gdd, &quot;dev_name&quot;);
    } END_SUSPEND_INTERRUPTS;
</pre></div>

<p>The <code>DevDesc</code> structure contains a <code>void *</code> pointer
&lsquo;<samp>deviceSpecific</samp>&rsquo; which is used to store data specific to the
device.  Setting up the device driver includes initializing all the
non-zero elements of the <code>DevDesc</code> structure.
</p>
<p>Note that the device structure is zeroed when allocated: this provides
some protection against future expansion of the structure since the
graphics engine can add elements that need to be non-NULL/non-zero to be
&lsquo;on&rsquo; (and the structure ends with 64 reserved bytes which will be zeroed
and allow for future expansion).
</p>
<p>Rather more protection is provided by the version number of the
engine/device API, <code>R_GE_version</code> defined in
<samp>R_ext/GraphicsEngine.h</samp> together with access functions
</p>
<div class="example">
<pre class="example">int R_GE_getVersion(void);
void R_GE_checkVersionOrDie(int version);
</pre></div>

<p>If a graphics device calls <code>R_GE_checkVersionOrDie(R_GE_version)</code>
it can ensure it will only be used in versions of R which provide the
API it was designed for and compiled against.
</p>
<hr>
<a name="Device-capabilities"></a>
<div class="header">
<p>
Next: <a href="#Handling-text" accesskey="n" rel="next">Handling text</a>, Previous: <a href="#Device-structures" accesskey="p" rel="prev">Device structures</a>, Up: <a href="#Graphics-devices" accesskey="u" rel="up">Graphics devices</a> &nbsp; [<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="Device-capabilities-1"></a>
<h4 class="subsection">6.1.2 Device capabilities</h4>

<p>The following &lsquo;capabilities&rsquo; can be defined for the device&rsquo;s
<code>DevDesc</code> structure.
</p>
<ul>
<li> <code>canChangeGamma</code> &ndash;
<code>Rboolean</code>: can the display gamma be adjusted?  This is now
ignored, as gamma support has been removed.
</li><li> <code>canHadj</code> &ndash;
<code>integer</code>: can the device do horizontal adjustment of text
<em>via</em> the <code>text</code> callback, and if so, how precisely? 0 = no
adjustment, 1 = {0, 0.5, 1} (left, centre, right justification) or 2 =
continuously variable (in [0,1]) between left and right justification.
</li><li> <code>canGenMouseDown</code> &ndash;
<code>Rboolean</code>: can the device handle mouse down events?  This
flag and the next three are not currently used by R, but are maintained
for back compatibility.
</li><li> <code>canGenMouseMove</code> &ndash;
<code>Rboolean</code>: ditto for mouse move events.
</li><li> <code>canGenMouseUp</code> &ndash;
<code>Rboolean</code>: ditto for mouse up events.
</li><li> <code>canGenKeybd</code> &ndash;
<code>Rboolean</code>: ditto for keyboard events.
</li><li> <code>hasTextUTF8</code> &ndash;
<code>Rboolean</code>: should non-symbol text be sent (in UTF-8) to the
<code>textUTF8</code> and <code>strWidthUTF8</code> callbacks, and sent as Unicode
points (negative values) to the <code>metricInfo</code> callback?
</li><li> <code>wantSymbolUTF8</code> &ndash;
<code>Rboolean</code>: should symbol text be handled in UTF-8 in the same way
as other text?  Requires <code>textUTF8 = TRUE</code>.
</li><li> <code>haveTransparency</code>:
does the device support semi-transparent colours?
</li><li> <code>haveTransparentBg</code>:
can the background be fully or semi-transparent?
</li><li> <code>haveRaster</code>:
is there support for rendering raster images?
</li><li> <code>haveCapture</code>:
is there support for <code>grid::grid.cap</code>?
</li><li> <code>haveLocator</code>:
is there an interactive locator?
</li></ul>

<p>The last three can often be deduced to be false from the presence of
<code>NULL</code> entries instead of the corresponding functions.
</p>
<hr>
<a name="Handling-text"></a>
<div class="header">
<p>
Next: <a href="#Conventions" accesskey="n" rel="next">Conventions</a>, Previous: <a href="#Device-capabilities" accesskey="p" rel="prev">Device capabilities</a>, Up: <a href="#Graphics-devices" accesskey="u" rel="up">Graphics devices</a> &nbsp; [<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="Handling-text-1"></a>
<h4 class="subsection">6.1.3 Handling text</h4>

<p>Handling text is probably the hardest task for a graphics device, and
the design allows for the device to optionally indicate that it has
additional capabilities.  (If the device does not, these will if
possible be handled in the graphics engine.)
</p>
<p>The three callbacks for handling text that must be in all graphics
devices are <code>text</code>, <code>strWidth</code> and <code>metricInfo</code> with
declarations
</p>
<div class="example">
<pre class="example">void text(double x, double y, const char *str, double rot, double hadj,
          pGgcontext gc, pDevDesc dd);

double strWidth(const char *str, pGEcontext gc, pDevDesc dd);

void metricInfo(int c, pGEcontext gc,
               double* ascent, double* descent, double* width,
               pDevDesc dd);
</pre></div>

<p>The &lsquo;<samp>gc</samp>&rsquo; parameter provides the graphics context, most importantly
the current font and fontsize, and &lsquo;<samp>dd</samp>&rsquo; is a pointer to the active
device&rsquo;s structure.
</p>
<p>The <code>text</code> callback should plot &lsquo;<samp>str</samp>&rsquo; at &lsquo;<samp>(x,
y)</samp>&rsquo;<a name="DOCF19" href="#FOOT19"><sup>19</sup></a> with an anti-clockwise rotation of
&lsquo;<samp>rot</samp>&rsquo; degrees.  (For &lsquo;<samp>hadj</samp>&rsquo; see below.)  The interpretation
for horizontal text is that the baseline is at <code>y</code> and the start is
a <code>x</code>, so any left bearing for the first character will start at
<code>x</code>.
</p>
<p>The <code>strWidth</code> callback computes the width of the string which it
would occupy if plotted horizontally in the current font.  (Width here
is expected to include both (preferably) or neither of left and right
bearings.)
</p>
<p>The <code>metricInfo</code> callback computes the size of a single
character: <code>ascent</code> is the distance it extends above the baseline
and <code>descent</code> how far it extends below the baseline.
<code>width</code> is the amount by which the cursor should be advanced when
the character is placed.  For <code>ascent</code> and <code>descent</code> this is
intended to be the bounding box of the &lsquo;ink&rsquo; put down by the glyph and
not the box which might be used when assembling a line of conventional
text (it needs to be for e.g. <code>hat(beta)</code> to work correctly).
However, the <code>width</code> is used in plotmath to advance to the next
character, and so needs to include left and right bearings.
</p>
<p>The <em>interpretation</em> of &lsquo;<samp>c</samp>&rsquo; depends on the locale.  In a
single-byte locale values <code>32...255</code> indicate the corresponding
character in the locale (if present).  For the symbol font (as used by
&lsquo;<samp>graphics::par(font=5)</samp>&rsquo;, &lsquo;<samp>grid::gpar(fontface=5</samp>&rsquo;) and by
&lsquo;plotmath&rsquo;), values <code>32...126, 161...239, 241...254</code> indicate
glyphs in the Adobe Symbol encoding.  In a multibyte locale, <code>c</code>
represents a Unicode point (except in the symbol font).  So the function
needs to include code like
</p>
<div class="example">
<pre class="example">    Rboolean Unicode = mbcslocale &amp;&amp; (gc-&gt;fontface != 5);
    if (c &lt; 0) { Unicode = TRUE; c = -c; }
    if(Unicode) UniCharMetric(c, ...); else CharMetric(c, ...);
</pre></div>

<p>In addition, if device capability <code>hasTextUTF8</code> (see below) is
true, Unicode points will be passed as negative values: the code snippet
above shows how to handle this.  (This applies to the symbol font only
if device capability <code>wantSymbolUTF8</code> is true.)
</p>
<p>If possible, the graphics device should handle clipping of text.  It
indicates this by the structure element <code>canClip</code> which if true
will result in calls to the callback <code>clip</code> to set the clipping
region. If this is not done, the engine will clip very crudely (by
omitting any text that does not appear to be wholly inside the clipping
region).
</p>
<p>The device structure has an integer element <code>canHadj</code>, which
indicates if the device can do horizontal alignment of text.  If this is
one, argument &lsquo;<samp>hadj</samp>&rsquo; to <code>text</code> will be called as <code>0 ,0.5,
1</code> to indicate left-, centre- and right-alignment at the indicated
position.  If it is two, continuous values in the range <code>[0, 1]</code>
are assumed to be supported.
</p>
<p>Capability <code>hasTextUTF8</code> if true, it has two consequences.
First, there are callbacks <code>textUTF8</code> and <code>strWidthUTF8</code> that
should behave identically to <code>text</code> and <code>strWidth</code> except that
&lsquo;<samp>str</samp>&rsquo; is assumed to be in UTF-8 rather than the current locale&rsquo;s
encoding.  The graphics engine will call these for all text except in
the symbol font.  Second, Unicode points will be passed to the
<code>metricInfo</code> callback as negative integers.  If your device would
prefer to have UTF-8-encoded symbols, define <code>wantSymbolUTF8</code> as
well as <code>hasTextUTF8</code>.  In that case text in the symbol font is
sent to <code>textUTF8</code> and <code>strWidthUTF8</code>.
</p>
<p>Some devices can produce high-quality rotated text, but those based on
bitmaps often cannot.  Those which can should set
<code>useRotatedTextInContour</code> to be true from graphics API version 4.
</p>
<p>Several other elements relate to the precise placement of text by the
graphics engine:
</p>
<div class="example">
<pre class="example">double xCharOffset;
double yCharOffset;
double yLineBias;
double cra[2];
</pre></div>

<p>These are more than a little mysterious.  Element <code>cra</code> provides an
indication of the character size, <code>par(&quot;cra&quot;)</code> in base graphics, in
device units.  The mystery is what is meant by &lsquo;character size&rsquo;: which
character, which font at which size?  Some help can be obtained by
looking at what this is used for.  The first element, &lsquo;width&rsquo;, is not
used by R except to set the graphical parameters.  The second,
&lsquo;height&rsquo;, is use to set the line spacing, that is the relationship
between <code>par(&quot;mai&quot;)</code> and <code>par(&quot;mai&quot;)</code> and so on.  It is
suggested that a good choice is
</p>
<div class="example">
<pre class="example">dd-&gt;cra[0] = 0.9 * fnsize;
dd-&gt;cra[1] = 1.2 * fnsize;
</pre></div>

<p>where &lsquo;<samp>fnsize</samp>&rsquo; is the &lsquo;size&rsquo; of the standard font (<code>cex=1</code>)
on the device, in device units.  So for a 12-point font (the usual
default for graphics devices), &lsquo;<samp>fnsize</samp>&rsquo; should be 12 points in
device units.
</p>
<p>The remaining elements are yet more mysterious.  The <code>postscript()</code>
device says
</p>
<div class="example">
<pre class="example">    /* Character Addressing Offsets */
    /* These offsets should center a single */
    /* plotting character over the plotting point. */
    /* Pure guesswork and eyeballing ... */

    dd-&gt;xCharOffset =  0.4900;
    dd-&gt;yCharOffset =  0.3333;
    dd-&gt;yLineBias = 0.2;
</pre></div>

<p>It seems that <code>xCharOffset</code> is not currently used, and
<code>yCharOffset</code> is used by the base graphics system to set vertical
alignment in <code>text()</code> when <code>pos</code> is specified, and in
<code>identify()</code>.  It is occasionally used by the graphic engine when
attempting exact centring of text, such as character string values of
<code>pch</code> in <code>points()</code> or <code>grid.points()</code>&mdash;however, it is
only used when precise character metric information is not available or
for multi-line strings.
</p>
<p><code>yLineBias</code> is used in the base graphics system in <code>axis()</code> and
<code>mtext()</code> to provide a default for their &lsquo;<samp>padj</samp>&rsquo; argument.
</p>
<hr>
<a name="Conventions"></a>
<div class="header">
<p>
Next: <a href="#g_t_0027Mode_0027" accesskey="n" rel="next">'Mode'</a>, Previous: <a href="#Handling-text" accesskey="p" rel="prev">Handling text</a>, Up: <a href="#Graphics-devices" accesskey="u" rel="up">Graphics devices</a> &nbsp; [<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="Conventions-1"></a>
<h4 class="subsection">6.1.4 Conventions</h4>

<p>The aim is to make the (default) output from graphics devices as similar
as possible.  Generally people follow the model of the <code>postscript</code>
and <code>pdf</code> devices (which share most of their internal code).
</p>
<p>The following conventions have become established:
</p>
<ul>
<li> The default size of a device should be 7 inches square.

</li><li> There should be a &lsquo;<samp>pointsize</samp>&rsquo; argument which defaults to 12, and it
should give the pointsize in big points (1/72 inch).  How exactly this
is interpreted is font-specific, but it should use a font which works
with lines packed 1/6 inch apart, and looks good with lines 1/5 inch
apart (that is with 2pt leading).

</li><li> The default font family should be a sans serif font, e.g Helvetica or
similar (e.g. Arial on Windows).

</li><li> <code>lwd = 1</code> should correspond to a line width of 1/96 inch.  This
will be a problem with pixel-based devices, and generally there is a
minimum line width of 1 pixel (although this may not be appropriate
where anti-aliasing of lines is used, and <code>cairo</code> prefers a minimum
of 2 pixels).

</li><li> Even very small circles should be visible, e.g. by using a minimum
radius of 1 pixel or replacing very small circles by a single filled
pixel.

</li><li> How RGB colour values will be interpreted should be documented, and
preferably be sRGB.

</li><li> The help page should describe its policy on these conventions.

</li></ul>

<p>These conventions are less clear-cut for bitmap devices, especially
where the bitmap format does not have a design resolution.
</p>
<p>The interpretation of the line texture (<code>par(&quot;lty&quot;</code>) is described
in the header <samp>GraphicsEngine.h</samp> and in the help for <code>par</code>: note that the
&lsquo;scale&rsquo; of the pattern should be proportional to the line width (at
least for widths above the default).
</p>

<hr>
<a name="g_t_0027Mode_0027"></a>
<div class="header">
<p>
Next: <a href="#Graphics-events" accesskey="n" rel="next">Graphics events</a>, Previous: <a href="#Conventions" accesskey="p" rel="prev">Conventions</a>, Up: <a href="#Graphics-devices" accesskey="u" rel="up">Graphics devices</a> &nbsp; [<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_t_0060Mode_0027"></a>
<h4 class="subsection">6.1.5 &lsquo;Mode&rsquo;</h4>

<p>One of the device callbacks is a function <code>mode</code>, documented in
the header as
</p>
<div class="example">
<pre class="example">     * device_Mode is called whenever the graphics engine
     * starts drawing (mode=1) or stops drawing (mode=0)
     * GMode (in graphics.c) also says that
     * mode = 2 (graphical input on) exists.
     * The device is not required to do anything
</pre></div>

<p>Since <code>mode = 2</code> has only recently been documented at device level.
It could be used to change the graphics cursor, but devices currently do
that in the <code>locator</code> callback.  (In base graphics the mode is set
for the duration of a <code>locator</code> call, but if <code>type != &quot;n&quot;</code> is
switched back for each point whilst annotation is being done.)
</p>
<p>Many devices do indeed do nothing on this call, but some screen devices
ensure that drawing is flushed to the screen when called with <code>mode
= 0</code>.  It is tempting to use it for some sort of buffering, but note
that &lsquo;drawing&rsquo; is interpreted at quite a low level and a typical single
figure will stop and start drawing many times.  The buffering introduced
in the <code>X11()</code> device makes use of <code>mode = 0</code> to indicate
activity: it updates the screen after <em>ca</em> 100ms of inactivity.
</p>
<p>This callback need not be supplied if it does nothing.
</p>
<hr>
<a name="Graphics-events"></a>
<div class="header">
<p>
Next: <a href="#Specific-devices" accesskey="n" rel="next">Specific devices</a>, Previous: <a href="#g_t_0027Mode_0027" accesskey="p" rel="prev">'Mode'</a>, Up: <a href="#Graphics-devices" accesskey="u" rel="up">Graphics devices</a> &nbsp; [<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="Graphics-events-1"></a>
<h4 class="subsection">6.1.6 Graphics events</h4>

<p>Graphics devices may be designed to handle user interaction: not all are.
</p>
<p>Users may use <code>grDevices::setGraphicsEventEnv</code> to set the
<code>eventEnv</code> environment in the device driver to hold event
handlers. When the user calls <code>grDevices::getGraphicsEvent</code>, R will
take three steps.  First, it sets the device driver member
<code>gettingEvent</code> to <code>true</code> for each device with a
non-<code>NULL</code> <code>eventEnv</code> entry, and calls <code>initEvent(dd,
true)</code> if the callback is defined.  It then enters an event loop.  Each
time through the loop R will process events once, then check whether any
device has set the <code>result</code> member of <code>eventEnv</code> to a
non-<code>NULL</code> value, and will save the first such value found to be
returned.  C functions <code>doMouseEvent</code> and <code>doKeybd</code> are
provided to call the R event handlers <code>onMouseDown</code>,
<code>onMouseMove</code>, <code>onMouseUp</code>, and <code>onKeybd</code> and set
<code>eventEnv$result</code> during this step.  Finally, <code>initEvent</code> is
called again with <code>init=false</code> to inform the devices that the
loop is done, and the result is returned to the user.
</p>
<hr>
<a name="Specific-devices"></a>
<div class="header">
<p>
Previous: <a href="#Graphics-events" accesskey="p" rel="prev">Graphics events</a>, Up: <a href="#Graphics-devices" accesskey="u" rel="up">Graphics devices</a> &nbsp; [<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="Specific-devices-1"></a>
<h4 class="subsection">6.1.7 Specific devices</h4>

<p>Specific devices are mostly documented by comments in their sources,
although for devices of many years&rsquo; standing those comments can be in
need of updating.  This subsection is a repository of notes on design
decisions.
</p>
<table summary="" class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">&bull; <a href="#X11_0028_0029" accesskey="1">X11()</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">&bull; <a href="#windows_0028_0029" accesskey="2">windows()</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
</table>

<hr>
<a name="X11_0028_0029"></a>
<div class="header">
<p>
Next: <a href="#windows_0028_0029" accesskey="n" rel="next">windows()</a>, Previous: <a href="#Specific-devices" accesskey="p" rel="prev">Specific devices</a>, Up: <a href="#Specific-devices" accesskey="u" rel="up">Specific devices</a> &nbsp; [<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_0028_0029-1"></a>
<h4 class="subsubsection">6.1.7.1 X11()</h4>

<p>The <code>X11(type=&quot;Xlib&quot;)</code> device dates back to the mid 1990&rsquo;s and was
written then in <code>Xlib</code>, the most basic X11 toolkit.  It has since
optionally made use of a few features from other toolkits: <code>libXt</code>
is used to read X11 resources, and <code>libXmu</code> is used in the handling
of clipboard selections.
</p>
<p>Using basic <code>Xlib</code> code makes drawing fast, but is limiting.  There
is no support of translucent colours (that came in the <code>Xrender</code>
toolkit of 2000) nor for rotated text (which R implements by
rendering text to a bitmap and rotating the latter).
</p>
<p>The hinting for the X11 window asks for backing store to be used, and
some windows managers may use it to handle repaints, but it seems that
most repainting is done by replaying the display list (and here the fast
drawing is very helpful).
</p>
<p>There are perennial problems with finding fonts.  Many users fail to
realize that fonts are a function of the X server and not of the machine
that R is running on.  After many difficulties, R tries first to
find the nearest size match in the sizes provided for Adobe fonts in the
standard 75dpi and 100dpi X11 font packages&mdash;even that will fail to
work when users of near-100dpi screens have only the 75dpi set
installed.  The 75dpi set allows sizes down to 6 points on a 100dpi
screen, but some users do try to use smaller sizes and even 6 and 8
point bitmapped fonts do not look good.
</p>
<p>Introduction of UTF-8 locales has caused another wave of difficulties.
X11 has very few genuine UTF-8 fonts, and produces composite fontsets
for the <code>iso10646-1</code> encoding.  Unfortunately these seem to have
low coverage apart from a few monospaced fonts in a few sizes (which are
not suitable for graph annotation), and where glyphs are missing what is
plotted is often quite unsatisfactory.
</p>
<p>The current approach is to make use of more modern toolkits, namely
<code>cairo</code> for rendering and <code>Pango</code> for font
management&mdash;because these are associated with <code>Gtk+2</code> they are
widely available.  Cairo supports translucent colours and alpha-blending
(<em>via</em> <code>Xrender</code>), and anti-aliasing for the display of lines
and text.  Pango&rsquo;s font management is based on <code>fontconfig</code> and
somewhat mysterious, but it seems mainly to use Type 1 and TrueType
fonts on the machine running R and send grayscale bitmaps to cairo.
</p>

<hr>
<a name="windows_0028_0029"></a>
<div class="header">
<p>
Previous: <a href="#X11_0028_0029" accesskey="p" rel="prev">X11()</a>, Up: <a href="#Specific-devices" accesskey="u" rel="up">Specific devices</a> &nbsp; [<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_0028_0029-1"></a>
<h4 class="subsubsection">6.1.7.2 windows()</h4>

<p>The <code>windows()</code> device is a family of devices: it supports plotting
to Windows (enhanced) metafiles, <code>BMP</code>, <code>JPEG</code>, <code>PNG</code> and
<code>TIFF</code> files as well as to Windows printers.
</p>
<p>In most of these cases the primary plotting is to a bitmap: this is used
for the (default) buffering of the screen device, which also enables the
current plot to be saved to BMP, JPEG, PNG or TIFF (it is the internal
bitmap which is copied to the file in the appropriate format).
</p>
<p>The device units are pixels (logical ones on a metafile device).
</p>
<p>The code was originally written by Guido Masarotto with extensive use of
macros, which can make it hard to disentangle.
</p>
<p>For a screen device, <code>xd-&gt;gawin</code> is the canvas of the screen, and
<code>xd-&gt;bm</code> is the off-screen bitmap.  So macro <code>DRAW</code> arranges
to plot to <code>xd-&gt;bm</code>, and if buffering is off, also to
<code>xd-&gt;gawin</code>.  For all other device, <code>xd-&gt;gawin</code> is the canvas,
a bitmap for the <code>jpeg()</code> and <code>png()</code> device, and an internal
representation of a Windows metafile for the <code>win.metafile()</code> and
<code>win.print</code> device.  Since &lsquo;plotting&rsquo; is done by Windows GDI calls
to the appropriate canvas, its precise nature is hidden by the GDI
system.
</p>
<p>Buffering on the screen device is achieved by running a timer, which
when it fires copies the internal bitmap to the screen.  This is set to
fire every 500ms (by default) and is reset to 100ms after plotting
activity.
</p>
<p>Repaint events are handled by copying the internal bitmap to the screen
canvas (and then reinitializing the timer), unless there has been a resize.
Resizes are handled by replaying the display list: this might not be
necessary if a fixed canvas with scrollbars is being used, but that is
the least popular of the three forms of resizing.
</p>
<p>Text on the device has moved to &lsquo;Unicode&rsquo; (UCS-2) in recent years.
UTF-8 is requested (<code>hasTextUTF8 = TRUE</code>) for standard text, and
converted to UCS-2 in the plotting functions in file
<samp>src/extra/graphapp/gdraw.c</samp>.  However, GDI has no support for
Unicode symbol fonts, and symbols are handled in Adobe Symbol encoding.
</p>
<p>There is support for translucent colours (with alpha channel between 0
and 255) was introduced on the screen device and bitmap
devices.<a name="DOCF20" href="#FOOT20"><sup>20</sup></a> This is done by drawing on a further internal bitmap,
<code>xd-&gt;bm2</code>, in the opaque version of the colour then alpha-blending
that bitmap to <code>xd-&gt;bm</code>.  The alpha-blending routine is in a
separate DLL, <samp>msimg32.dll</samp>, which is loaded on first use.  As
small a rectangular region as reasonably possible is alpha-blended (this
is rectangle <code>r</code> in the code), but things like mitre joins make
estimation of a tight bounding box too much work for lines and polygonal
boundaries.  Translucent-coloured lines are not common, and the
performance seems acceptable.
</p>
<p>The support for a transparent background in <code>png()</code> predates full
alpha-channel support in <code>libpng</code> (let alone in PNG viewers), so
makes use of the limited transparency support in earlier versions of
PNG.  Where 24-bit colour is used, this is done by marking a single
colour to be rendered as transparent.  R chose &lsquo;<samp>#fdfefd</samp>&rsquo;, and
uses this as the background colour (in <code>GA_NewPage</code> if the
specified background colour is transparent (and all non-opaque
background colours are treated as transparent).  So this works by
marking that colour in the PNG file, and viewers without transparency
support see a slightly-off-white background, as if there were a
near-white canvas.  Where a palette is used in the PNG file (if less
than 256 colours were used) then this colour is recorded with full
transparency and the remaining colours as opaque.  If 32-bit colour were
available then we could add a full alpha channel, but this is dependent
on the graphics hardware and undocumented properties of GDI.
</p>

<hr>
<a name="Colours"></a>
<div class="header">
<p>
Next: <a href="#Base-graphics" accesskey="n" rel="next">Base graphics</a>, Previous: <a href="#Graphics-devices" accesskey="p" rel="prev">Graphics devices</a>, Up: <a href="#Graphics-Devices" accesskey="u" rel="up">Graphics Devices</a> &nbsp; [<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="Colours-1"></a>
<h3 class="section">6.2 Colours</h3>

<p>Devices receive colours as a <code>typedef</code> <code>rcolor</code> (an
<code>unsigned int</code>) defined in the header
<samp>R_ext/GraphicsEngine.h</samp>).  The 4 bytes are <em>R</em> ,<em>G</em>,
<em>B</em> and <em>alpha</em> from least to most significant. So each of RGB
has 256 levels of luminosity from 0 to 255.  The alpha byte represents
opacity, so value 255 is fully opaque and 0 fully transparent: many but
not all devices handle semi-transparent colours.
</p>
<p>Colors can be created in C via the macro <code>R_RGBA</code>, and a set of
macros are defined in <samp>R_ext/GraphicsDevice.h</samp> to extract the
various components.
</p>
<p>Colours in the base graphics system were originally adopted from S (and
before that the GRZ library from Bell Labs), with the concept of a
(variable-sized) palette of colours referenced by numbers
&lsquo;<samp>1...<var>N</var></samp>&rsquo; plus &lsquo;<samp>0</samp>&rsquo; (the background colour of the current
device).  R introduced the idea of referring to colours by character
strings, either in the forms &lsquo;<samp>#RRGGBB</samp>&rsquo; or &lsquo;<samp>#RRGGBBAA</samp>&rsquo;
(representing the bytes in hex) as given by function <code>rgb()</code> or via
names: the 657 known names are given in the character vector
<code>colors</code> and in a table in file <samp>colors.c</samp> in package
<strong>grDevices</strong>.  Note that semi-transparent colours are not
&lsquo;premultiplied&rsquo;, so 50% transparent white is &lsquo;<samp>#ffffff80</samp>&rsquo;.
</p>
<p>Integer or character <code>NA</code> colours are mapped internally to
transparent white, as is the character string <code>&quot;NA&quot;</code>.
</p>
<p>The handling of negative colour numbers was undefined (and inconsistent)
prior to R 3.0.0, which made them an error.  Colours greater than
&lsquo;<samp><var>N</var></samp>&rsquo; are wrapped around, so that for example with the default
palette of size 8, colour &lsquo;<samp>10</samp>&rsquo; is colour &lsquo;<samp>2</samp>&rsquo; in the palette.
</p>
<p>Integer colours have been used more widely than the base graphics
sub-system, as they are supported by package <strong>grid</strong> and hence by
<a href="https://CRAN.R-project.org/package=lattice"><strong>lattice</strong></a> and <a href="https://CRAN.R-project.org/package=ggplot2"><strong>ggplot2</strong></a>.  (They are also used by package
<a href="https://CRAN.R-project.org/package=rgl"><strong>rgl</strong></a>.)  <strong>grid</strong> did re-define colour &lsquo;<samp>0</samp>&rsquo; to be
transparent white, but <a href="https://CRAN.R-project.org/package=rgl"><strong>rgl</strong></a> used <code>col2rgb</code> and hence the
background colour of base graphics.
</p>
<p>Note that positive integer colours refer to the current palette and
colour &lsquo;<samp>0</samp>&rsquo; to the current device (and a device is opened if needs
be).  These are mapped to type <code>rcolor</code> at the time of use: this
matters when re-playing the display list, e.g. when a device is
resized or <code>dev.copy</code> is used.  The palette should be thought of as
per-session: it is stored in package <strong>grDevices</strong>.
</p>
<p>The convention is that devices use the colorspace &lsquo;sRGB&rsquo;. This is an
industry standard: it is used by Web browsers and JPEGs from all but
high-end digital cameras.  The interpretation is a matter for graphics
devices and for code that manipulates colours, but not for the graphics
engine or subsystems.
</p>
<p>R uses a painting model similar to PostScript and PDF.  This means
that where shapes (circles, rectangles and polygons) can both be filled
and have a stroked border, the fill should be painted first and then the
border (or otherwise only half the border will be visible).  Where both
the fill and the border are semi-transparent there is some room for
interpretation of the intention.  Most devices first paint the fill and
then the border, alpha-blending at each step.  However, PDF does some
automatic grouping of objects, and <em>when the fill and the border
have the same alpha</em>, they are painted onto the same layer and then
alpha-blended in one step.  (See p. 569 of the PDF Reference Sixth
Edition, version 1.7.  Unfortunately, although this is what the PDF
standard says should happen, it is not correctly implemented by some
viewers.)
</p>
<p>The mapping from colour numbers to type <code>rcolor</code> is primarily done
by function <code>RGBpar3</code>: this is exported from the R binary but
linked to code in package <strong>grDevices</strong>.  The first argument is a
<code>SEXP</code> pointing to a character, integer or double vector, and the
second is the <code>rcolor</code> value for colour <code>0</code> (or <code>&quot;0&quot;</code>).
C entry point <code>RGBpar</code> is a wrapper that takes <code>0</code> to be
transparent white: it is often used to set colour defaults for devices.
The R-level wrapper is <code>col2rgb</code>.
</p>
<p>There is also <code>R_GE_str2col</code> which takes a C string and converts to
type <code>rcolor</code>: <code>&quot;0'</code> is converted to transparent white.
</p>
<p>There is a R-level conversion of colours to &lsquo;<samp>##RRGGBBAA</samp>&rsquo; by
<code>image.default(useRaster = TRUE)</code>.
</p>
<p>The other color-conversion entry point in the API is <code>name2col</code>
which takes a colour name (a C string) and returns a value of type
<code>rcolor</code>.  This handles <code>&quot;NA&quot;</code>, <code>&quot;transparent&quot;</code> and the
657 colours known to the R function <code>colors()</code>.
</p>
<hr>
<a name="Base-graphics"></a>
<div class="header">
<p>
Next: <a href="#Grid-graphics" accesskey="n" rel="next">Grid graphics</a>, Previous: <a href="#Colours" accesskey="p" rel="prev">Colours</a>, Up: <a href="#Graphics-Devices" accesskey="u" rel="up">Graphics Devices</a> &nbsp; [<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="Base-graphics-1"></a>
<h3 class="section">6.3 Base graphics</h3>

<p>The base graphics system was migrated to package <strong>graphics</strong> in R
3.0.0: it was previously implemented in files in <samp>src/main</samp>.
</p>
<p>For historical reasons it is largely implemented in two layers.
Files <samp>plot.c</samp>, <code>plot3d.c</code> and <code>par.c</code> contain the code
for the around 30 <code>.External</code> calls that implement the basic
graphics operations.  This code then calls functions with names starting
with <code>G</code> and declared in header <samp>Rgraphics.h</samp> in file
<samp>graphics.c</samp>, which in turn call the graphics engine (whose
functions almost all have names starting with <code>GE</code>).
</p>
<p>A large part of the infrastructure of the base graphics subsystem are
the graphics parameters (as set/read by <code>par()</code>).  These are stored
in a <code>GPar</code> structure declared in the private header
<samp>Graphics.h</samp>.  This structure has two variables (<code>state</code> and
<code>valid</code>) tracking the state of the base subsystem on the device,
and many variables recording the graphics parameters and functions of
them.
</p>
<p>The base system state is contained in <code>baseSystemState</code> structure
defined in <samp>R_ext/GraphicsBase.h</samp>.  This contains three <code>GPar</code>
structures and a Boolean variable used to record if <code>plot.new()</code>
(or <code>persp</code>) has been used successfully on the device.
</p>
<p>The three copies of the <code>GPar</code> structure are used to store the
current parameters (accessed via <code>gpptr</code>), the &lsquo;device copy&rsquo;
(accessed via <code>dpptr</code>) and space for a saved copy of the &lsquo;device
copy&rsquo; parameters.  The current parameters are, clearly, those currently
in use and are copied from the &lsquo;device copy&rsquo; whenever <code>plot.new()</code>
is called (whether or not that advances to the next &lsquo;page&rsquo;). The saved
copy keeps the state when the device was last completely cleared (e.g.
when <code>plot.new()</code> was called with <code>par(new=TRUE)</code>), and is
used to replay the display list.
</p>
<p>The separation is not completely clean: the &lsquo;device copy&rsquo; is altered if
a plot with log scale(s) is set up via <code>plot.window()</code>.
</p>
<p>There is yet another copy of most of the graphics parameters in
<code>static</code> variables in <samp>graphics.c</samp> which are used to preserve
the current parameters across the processing of inline parameters in
high-level graphics calls (handled by <code>ProcessInlinePars</code>).
</p>
<p>Snapshots of the base subsystem record the &lsquo;saved device copy&rsquo; of the
<code>GPar</code> structure.
</p>
<table summary="" class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">&bull; <a href="#Arguments-and-parameters" accesskey="1">Arguments and parameters</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
</table>

<hr>
<a name="Arguments-and-parameters"></a>
<div class="header">
<p>
Previous: <a href="#Base-graphics" accesskey="p" rel="prev">Base graphics</a>, Up: <a href="#Base-graphics" accesskey="u" rel="up">Base graphics</a> &nbsp; [<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="Arguments-and-parameters-1"></a>
<h4 class="subsection">6.3.1 Arguments and parameters</h4>

<p>There is an unfortunate confusion between some of the graphical
parameters (as set by <code>par</code>) and arguments to base graphic
functions of the same name.  This description may help set the record
straight.
</p>
<p>Most of the high-level plotting functions accept graphical parameters as
additional arguments, which are then often passed to lower-level
functions if not already named arguments (which is the main source of
confusion).
</p>
<p>Graphical parameter <code>bg</code> is the background colour of the plot.
Argument <code>bg</code> refers to the fill colour for the filled symbols
<code>21</code> to <code>25</code>.  It is an argument to the function
<code>plot.xy</code>, but normally passed by the default method of
<code>points</code>, often from a <code>plot</code> method.
</p>
<p>Graphics parameters <code>cex</code>, <code>col</code>, <code>lty</code>, <code>lwd</code> and
<code>pch</code> also appear as arguments of <code>plot.xy</code> and so are often
passed as arguments from higher-level plot functions such as
<code>lines</code>, <code>points</code> and <code>plot</code> methods.  They appear as
arguments of <code>legend</code>, <code>col</code>, <code>lty</code> and <code>lwd</code> are
arguments of <code>arrows</code> and <code>segments</code>.  When used as arguments
they can be vectors, recycled to control the various lines, points and
segments.  When set a graphical parameters they set the default
rendering: in addition <code>par(cex=)</code> sets the overall character
expansion which subsequent calls (as arguments or on-line graphical
parameters) multiply.
</p>
<p>The handling of missing values differs in the two classes of uses.
Generally these are errors when used in <code>par</code> but cause the
corresponding element of the plot to be omitted when used as an element
of a vector argument.  Originally the interpretation of arguments was
mainly left to the device, but as from R 3.0.0 some of this is
pre-empted in the graphics engine (but for example the handling of
<code>lwd = 0</code> remains device-specific, with some interpreting it as a
&lsquo;thinnest possible&rsquo; line).
</p>
<hr>
<a name="Grid-graphics"></a>
<div class="header">
<p>
Previous: <a href="#Base-graphics" accesskey="p" rel="prev">Base graphics</a>, Up: <a href="#Graphics-Devices" accesskey="u" rel="up">Graphics Devices</a> &nbsp; [<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="Grid-graphics-1"></a>
<h3 class="section">6.4 Grid graphics</h3>

<p>[At least pointers to documentation.]
</p>
<hr>
<a name="GUI-consoles"></a>
<div class="header">
<p>
Next: <a href="#Tools" accesskey="n" rel="next">Tools</a>, Previous: <a href="#Graphics-Devices" accesskey="p" rel="prev">Graphics Devices</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> &nbsp; [<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="GUI-consoles-1"></a>
<h2 class="chapter">7 GUI consoles</h2>

<p>The standard R front-ends are programs which run in a terminal, but
there are several ways to provide a GUI console.
</p>
<p>This can be done by a package which is loaded from terminal-based R
and launches a console as part of its startup code or by the user
running a specific function: package <a href="https://CRAN.R-project.org/package=Rcmdr"><strong>Rcmdr</strong></a> is a well-known
example with a Tk-based GUI.
</p>
<p>There used to be a Gtk-based console invoked by <code>R --gui=GNOME</code>:
this relied on special-casing in the front-end shell script to launch a
different executable.  There still is <code>R --gui=Tk</code>, which starts
terminal-based R and runs <code>tcltk::tkStartGui()</code> as part of the
modified startup sequence.
</p>
<p>However, the main way to run a GUI console is to launch a separate
program which runs embedded R: this is done by <code>Rgui.exe</code> on
Windows and <code>R.app</code> on OS X.  The first is an integral part
of R and the code for the console is currently in <samp>R.dll</samp>.
</p>
<table summary="" class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">&bull; <a href="#R_002eapp" accesskey="1">R.app</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
</table>

<hr>
<a name="R_002eapp"></a>
<div class="header">
<p>
Previous: <a href="#GUI-consoles" accesskey="p" rel="prev">GUI consoles</a>, Up: <a href="#GUI-consoles" accesskey="u" rel="up">GUI consoles</a> &nbsp; [<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_002eapp-1"></a>
<h3 class="section">7.1 R.app</h3>

<p><code>R.app</code> is a OS X application which provides a console.  Its
sources are a separate project<a name="DOCF21" href="#FOOT21"><sup>21</sup></a>, and its binaries
link to an R installation which it runs as a dynamic library
<samp>libR.dylib</samp>.  The standard <acronym>CRAN</acronym> distribution of R for
OS X bundles the GUI and R itself, but installing the GUI is optional
and either component can be updated separately.
</p>
<p><code>R.app</code> relies on <samp>libR.dylib</samp> being in a specific place,
and hence on R having been built and installed as a Mac OS X
&lsquo;framework&rsquo;.  Specifically, it uses
<samp>/Library/Frameworks/R.framework/R</samp>.  This is a symbolic link, as
frameworks can contain multiple versions of R.  It eventually
resolves to
<samp>/Library/Frameworks/R.framework/Versions/Current/Resources/lib/libR.dylib</samp>,
which is (in the <acronym>CRAN</acronym> distribution) a &lsquo;fat&rsquo; binary containing
multiple sub-architectures.
</p>
<p>OS X applications are directory trees: each <code>R.app</code> contains
a front-end written in Objective-C for one sub-architecture: in the
standard distribution there are separate applications for 32- and 64-bit
Intel architectures.
</p>
<p>Originally the R sources contained quite a lot of code used only by
the OS X GUI, but by R 3.0.0 this was been migrated to the
<code>R.app</code> sources.
</p>
<p><code>R.app</code> starts R as an embedded application with a
command-line which includes <samp>--gui=aqua</samp> (see below).  It uses
most of the interface pointers defined in the header
<samp>Rinterface.h</samp>, plus a private interface pointer in file
<samp>src/main/sysutils.c</samp>.  It adds an environment
it names <code>tools:RGUI</code> to the second position in the search path.
This contains a number of utility functions used to support the menu
items, for example <code>package.manager()</code>, plus functions <code>q()</code>
and <code>quit()</code> which mask those in package <strong>base</strong>&mdash;the custom
versions save the history in a way specific to <code>R.app</code>.
</p>
<p>There is a <code>configure</code> option <samp>--with-aqua</samp> for R
which customizes the way R is built: this is distinct from the
<samp>--enable-R-framework</samp> option which causes <code>make install</code>
to install R as the framework needed for use with <code>R.app</code>.  (The
option <samp>--with-aqua</samp> is the default on OS X.)  It sets the
macro <code>HAVE_AQUA</code> in <samp>config.h</samp> and the make variable
<code>BUILD_AQUA_TRUE</code>.  These have several consequences:
</p>
<ul>
<li> The <code>quartz()</code> device is built (other than as a stub) in package
<strong>grDevices</strong>: this needs an Objective-C compiler.  Then
<code>quartz()</code> can be used with terminal R provided the latter has
access to the OS X screen.

</li><li> File <samp>src/unix/aqua.c</samp> is compiled.  This now only contains an
interface pointer for the <code>quartz()</code> device(s).

</li><li> <code>capabilities(&quot;aqua&quot;)</code> is set to <code>TRUE</code>.

</li><li> The default path for a personal library directory is set as
<samp>~/Library/R/x.y/library</samp>.

</li><li> There is support for setting a &lsquo;busy&rsquo; indicator whilst waiting for
<code>system()</code> to return.

</li><li> <code>R_ProcessEvents</code> is inhibited in a forked child from package
<strong>parallel</strong>.  The associated callback in <code>R.app</code> does things
which should not be done in a child, and forking forks the whole process
including the console.

</li><li> There is support for starting the embedded R with the option
<samp>--gui=aqua</samp>: when this is done the global C variable
<code>useaqua</code> is set to a true value.  This has consequences:

<ul>
<li> The R session is asserted to be interactive <em>via</em> <code>R_Interactive</code>.

</li><li> <code>.Platform$GUI</code> is set to <code>&quot;AQUA&quot;</code>.  That has consequences:
<ul>
<li> The environment variable <code>DISPLAY</code> is set to &lsquo;<samp>:0</samp>&rsquo; if not
already set.

</li><li> <samp>/usr/local/bin</samp> is appended to <code>PATH</code> since that is where
<code>gfortran</code> is installed.

</li><li> The default <acronym>HTML</acronym> browser is switched to the one in <code>R.app</code>.

</li><li> Various widgets are switched to the versions provided in
<code>R.app</code>: these include graphical menus, the data editor (but not
the data viewer used by <code>View()</code>) and the workspace browser invoked
by <code>browseEnv()</code>.

</li><li> The <strong>grDevices</strong> package when loaded knows that it is being run
under <code>R.app</code> and so informs any <code>quartz</code> devices that a
Quartz event loop is already running.
</li></ul>

</li><li> The use of the OS&rsquo;s <code>system</code> function (including by <code>system()</code>
and <code>system2()</code>, and to launch editors and pagers) is replaced by a
version in <code>R.app</code> (which by default just calls the OS&rsquo;s
<code>system</code> with various signal handlers reset).

</li></ul>

</li><li> If either R was started by <samp>--gui=aqua</samp> or R is running in
a terminal which is not of type &lsquo;<samp>dumb</samp>&rsquo;, the standard output to
files <samp>stdout</samp> and <samp>stderr</samp> is directed through the C function
<code>Rstd_WriteConsoleEx</code>.  This uses ANSI terminal escapes to render
lines sent to <code>stderr</code> as bold on <code>stdout</code>.

</li><li> For historical reasons the startup option <code>-psn</code> is allowed but
ignored.  (It seems that in 2003, &lsquo;<samp>r27492</samp>&rsquo;, this was added by Finder.)

</li></ul>



<hr>
<a name="Tools"></a>
<div class="header">
<p>
Next: <a href="#R-coding-standards" accesskey="n" rel="next">R coding standards</a>, Previous: <a href="#GUI-consoles" accesskey="p" rel="prev">GUI consoles</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> &nbsp; [<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="Tools-1"></a>
<h2 class="chapter">8 Tools</h2>

<p>The behavior of <code>R CMD check</code> can be controlled through a
variety of command line arguments and environment variables.
</p>
<p>There is an internal <samp>--install=<var>value</var></samp> command line
argument not shown by <code>R CMD check --help</code>, with possible values
</p>
<dl compact="compact">
<dt><code>check:<var>file</var></code></dt>
<dd><p>Assume that installation was already performed with stdout/stderr to
<var>file</var>, the contents of which need to be checked (without repeating
the installation).  This is useful for checks applied by repository
maintainers: it reduces the check time by the installation time given
that the package has already been installed.  In this case, one also
needs to specify <em>where</em> the package was installed to using command
line option <samp>--library</samp>.
</p></dd>
<dt><code>fake</code></dt>
<dd><p>Fake installation, and turn off the run-time tests.
</p></dd>
<dt><code>skip</code></dt>
<dd><p>Skip installation, e.g., when testing recommended packages bundled with
R.
</p></dd>
<dt><code>no</code></dt>
<dd><p>The same as <samp>--no-install</samp> : turns off installation and the tests
which require the package to be installed.
</p></dd>
</dl>

<p>The following environment variables can be used to customize the
operation of <code>check</code>: a convenient place to set these is the
check environment file (default, <samp>~/.R/check.Renviron</samp>).
</p>
<dl compact="compact">
<dt><code>_R_CHECK_ALL_NON_ISO_C_</code>
<a name="index-_005fR_005fCHECK_005fALL_005fNON_005fISO_005fC_005f"></a>
</dt>
<dd><p>If true, do not ignore compiler (typically GCC) warnings about non ISO C
code in <em>system</em> headers.  Note that this may also show additional
ISO C++ warnings.
Default: false.
</p></dd>
<dt><code>_R_CHECK_FORCE_SUGGESTS_</code>
<a name="index-_005fR_005fCHECK_005fFORCE_005fSUGGESTS_005f"></a>
</dt>
<dd><p>If true, give an error if suggested packages are not available.
Default: true (but false for CRAN submission checks).
</p></dd>
<dt><code>_R_CHECK_RD_CONTENTS_</code>
<a name="index-_005fR_005fCHECK_005fRD_005fCONTENTS_005f"></a>
</dt>
<dd><p>If true, check <samp>Rd</samp> files for auto-generated content which needs
editing, and missing argument documentation.
Default: true.
</p></dd>
<dt><code>_R_CHECK_RD_LINE_WIDTHS_</code>
<a name="index-_005fR_005fCHECK_005fRD_005fLINE_005fWIDTHS_005f"></a>
</dt>
<dd><p>If true, check <samp>Rd</samp> line widths in usage and examples sections.
Default: false (but true for CRAN submission checks).
</p></dd>
<dt><code>_R_CHECK_RD_STYLE_</code>
<a name="index-_005fR_005fCHECK_005fRD_005fSTYLE_005f"></a>
</dt>
<dd><p>If true, check whether <samp>Rd</samp> usage entries for S3 methods use the full
function name rather than the appropriate <code>\method</code> markup.
Default: true.
</p></dd>
<dt><code>_R_CHECK_RD_XREFS_</code>
<a name="index-_005fR_005fCHECK_005fRD_005fXREFS_005f"></a>
</dt>
<dd><p>If true, check the cross-references in <samp>.Rd</samp> files.
Default: true.
</p></dd>
<dt><code>_R_CHECK_SUBDIRS_NOCASE_</code>
<a name="index-_005fR_005fCHECK_005fSUBDIRS_005fNOCASE_005f"></a>
</dt>
<dd><p>If true, check the case of directories such as <samp>R</samp> and <samp>man</samp>.
Default: true.
</p></dd>
<dt><code>_R_CHECK_SUBDIRS_STRICT_</code>
<a name="index-_005fR_005fCHECK_005fSUBDIRS_005fSTRICT_005f"></a>
</dt>
<dd><p>Initial setting for <samp>--check-subdirs</samp>.
Default: &lsquo;<samp>default</samp>&rsquo; (which checks only tarballs, and checks in the
<samp>src</samp> only if there is no <samp>configure</samp> file).
</p></dd>
<dt><code>_R_CHECK_USE_CODETOOLS_</code>
<a name="index-_005fR_005fCHECK_005fUSE_005fCODETOOLS_005f"></a>
</dt>
<dd><p>If true, make use of the <a href="https://CRAN.R-project.org/package=codetools"><strong>codetools</strong></a> package, which provides a
detailed analysis of visibility of objects (but may give false
positives).
Default: true (if recommended packages are installed).
</p></dd>
<dt><code>_R_CHECK_USE_INSTALL_LOG_</code>
<a name="index-_005fR_005fCHECK_005fUSE_005fINSTALL_005fLOG_005f"></a>
</dt>
<dd><p>If true, record the output from installing a package as part of its
check to a log file (<samp>00install.out</samp> by default), even when running
interactively.
Default: true.
</p></dd>
<dt><code>_R_CHECK_VIGNETTES_NLINES_</code>
<a name="index-_005fR_005fCHECK_005fVIGNETTES_005fNLINES_005f"></a>
</dt>
<dd><p>Maximum number of lines to show at the bottom of the output when reporting
errors in running or re-building vignettes.
Default: 10 for running, 25 for re-building.
</p></dd>
<dt><code>_R_CHECK_CODOC_S4_METHODS_</code>
<a name="index-_005fR_005fCHECK_005fCODOC_005fS4_005fMETHODS_005f"></a>
</dt>
<dd><p>Control whether <code>codoc()</code> testing is also performed on S4 methods.
Default: true.
</p></dd>
<dt><code>_R_CHECK_DOT_INTERNAL_</code>
<a name="index-_005fR_005fCHECK_005fDOT_005fINTERNAL_005f"></a>
</dt>
<dd><p>Control whether the package code is scanned for <code>.Internal</code> calls,
which should only be used by base (and occasionally by recommended) packages.
Default: true.
</p></dd>
<dt><code>_R_CHECK_EXECUTABLES_</code>
<a name="index-_005fR_005fCHECK_005fEXECUTABLES_005f"></a>
</dt>
<dd><p>Control checking for executable (binary) files.
Default: true.
</p></dd>
<dt><code>_R_CHECK_EXECUTABLES_EXCLUSIONS_</code>
<a name="index-_005fR_005fCHECK_005fEXECUTABLES_005fEXCLUSIONS_005f"></a>
</dt>
<dd><p>Control whether checking for executable (binary) files ignores files
listed in the package&rsquo;s <samp>BinaryFiles</samp> file.
Default: true (but false for CRAN submission checks).
However, most likely this package-level override mechanism will be
removed eventually.
</p></dd>
<dt><code>_R_CHECK_PERMISSIONS_</code>
<a name="index-_005fR_005fCHECK_005fPERMISSIONS_005f"></a>
</dt>
<dd><p>Control whether permissions of files should be checked.
Default: true iff <code>.Platform$OS.type == &quot;unix&quot;</code>.
</p></dd>
<dt><code>_R_CHECK_FF_CALLS_</code>
<a name="index-_005fR_005fCHECK_005fFF_005fCALLS_005f"></a>
</dt>
<dd><p>Allows turning off <code>checkFF()</code> testing. If set to
&lsquo;<samp>registration</samp>&rsquo;, checks the registration information (number of
arguments, correct choice of <code>.C/.Fortran/.Call/.External</code>) for
such calls provided the package is installed.
Default: true.
</p></dd>
<dt><code>_R_CHECK_FF_DUP_</code>
<a name="index-_005fR_005fCHECK_005fFF_005fDUP_005f"></a>
</dt>
<dd><p>Controls <code>checkFF(check_DUP)</code>
Default: true (and forced to be true for CRAN submission checks).
</p></dd>
<dt><code>_R_CHECK_LICENSE_</code>
<a name="index-_005fR_005fCHECK_005fLICENSE_005f"></a>
</dt>
<dd><p>Control whether/how license checks are performed. A possible value is
&lsquo;<samp>maybe</samp>&rsquo; (warn in case of problems, but not about standardizable
non-standard license specs).
Default: true.
</p></dd>
<dt><code>_R_CHECK_RD_EXAMPLES_T_AND_F_</code>
<a name="index-_005fR_005fCHECK_005fRD_005fEXAMPLES_005fT_005fAND_005fF_005f"></a>
</dt>
<dd><p>Control whether <code>check_T_and_F()</code> also looks for &ldquo;bad&rdquo; (global)
&lsquo;<samp>T</samp>&rsquo;/&lsquo;<samp>F</samp>&rsquo; uses in examples.
Off by default because this can result in false positives.
</p></dd>
<dt><code>_R_CHECK_RD_CHECKRD_MINLEVEL_</code>
<a name="index-_005fR_005fCHECK_005fRD_005fCHECKRD_005fMINLEVEL_005f"></a>
</dt>
<dd><p>Controls the minimum level for reporting warnings from <code>checkRd</code>.
Default: -1.
</p></dd>
<dt><code>_R_CHECK_XREFS_REPOSITORIES_</code>
<a name="index-_005fR_005fCHECK_005fXREFS_005fREPOSITORIES_005f"></a>
</dt>
<dd><p>If set to a non-empty value, a space-separated list of repositories to
use to determine known packages.  Default: empty, when the CRAN,
Omegahat and Bioconductor repositories known to R is used.
</p></dd>
<dt><code>_R_CHECK_SRC_MINUS_W_IMPLICIT_</code>
<a name="index-_005fR_005fCHECK_005fSRC_005fMINUS_005fW_005fIMPLICIT_005f"></a>
</dt>
<dd><p>Control whether installation output is checked for compilation warnings
about implicit function declarations (as spotted by GCC with command
line option <samp>-Wimplicit-function-declaration</samp>, which is implied
by <samp>-Wall</samp>).
Default: false.
</p></dd>
<dt><code>_R_CHECK_SRC_MINUS_W_UNUSED_</code>
<a name="index-_005fR_005fCHECK_005fSRC_005fMINUS_005fW_005fUNUSED_005f"></a>
</dt>
<dd><p>Control whether installation output is checked for compilation warnings
about unused code constituents (as spotted by GCC with command line
option <samp>-Wunused</samp>, which is implied by <samp>-Wall</samp>).
Default: true.
</p></dd>
<dt><code>_R_CHECK_WALL_FORTRAN_</code>
<a name="index-_005fR_005fCHECK_005fWALL_005fFORTRAN_005f"></a>
</dt>
<dd><p>Control whether gfortran 4.0 or later <samp>-Wall</samp> warnings are used in
the analysis of installation output.
Default: false, even though the warnings are justifiable.
</p></dd>
<dt><code>_R_CHECK_ASCII_CODE_</code>
<a name="index-_005fR_005fCHECK_005fASCII_005fCODE_005f"></a>
</dt>
<dd><p>If true, check R code for non-ascii characters.
Default: true.
</p></dd>
<dt><code>_R_CHECK_ASCII_DATA_</code>
<a name="index-_005fR_005fCHECK_005fASCII_005fDATA_005f"></a>
</dt>
<dd><p>If true, check data for non-ascii characters.
Default: true.
</p></dd>
<dt><code>_R_CHECK_COMPACT_DATA_</code>
<a name="index-_005fR_005fCHECK_005fCOMPACT_005fDATA_005f"></a>
</dt>
<dd><p>If true, check data for ascii and uncompressed saves, and also check if
using <code>bzip2</code> or <code>xz</code> compression would be significantly
better.
Default: true.
</p></dd>
<dt><code>_R_CHECK_SKIP_ARCH_</code>
<a name="index-_005fR_005fCHECK_005fSKIP_005fARCH_005f"></a>
</dt>
<dd><p>Comma-separated list of architectures that will be omitted from
checking in a multi-arch setup.
Default: none.
</p></dd>
<dt><code>_R_CHECK_SKIP_TESTS_ARCH_</code>
<a name="index-_005fR_005fCHECK_005fSKIP_005fTESTS_005fARCH_005f"></a>
</dt>
<dd><p>Comma-separated list of architectures that will be omitted from
running tests in a multi-arch setup.
Default: none.
</p></dd>
<dt><code>_R_CHECK_SKIP_EXAMPLES_ARCH_</code>
<a name="index-_005fR_005fCHECK_005fSKIP_005fEXAMPLES_005fARCH_005f"></a>
</dt>
<dd><p>Comma-separated list of architectures that will be omitted from
running examples in a multi-arch setup.
Default: none.
</p></dd>
<dt><code>_R_CHECK_VC_DIRS_</code>
<a name="index-_005fR_005fCHECK_005fVC_005fDIRS_005f"></a>
</dt>
<dd><p>Should the unpacked package directory be checked for version-control
directories (<samp>CVS</samp>, <samp>.svn</samp> &hellip;)?
Default: true for tarballs.
</p></dd>
<dt><code>_R_CHECK_PKG_SIZES_</code>
<a name="index-_005fR_005fCHECK_005fPKG_005fSIZES_005f"></a>
</dt>
<dd><p>Should <code>du</code> be used to find the installed sizes of packages?
<code>R CMD check</code> does check for the availability of <code>du</code>.
but this option allows the check to be overruled if an unsuitable
command is found (including one that does not respect the <samp>-k</samp>
flag to report in units of 1Kb, or reports in a different format &ndash; the
GNU, OS X and Solaris <code>du</code> commands have been tested).
Default: true if <code>du</code> is found.
</p></dd>
<dt><code>_R_CHECK_DOC_SIZES_</code>
<a name="index-_005fR_005fCHECK_005fDOC_005fSIZES_005f"></a>
</dt>
<dd><p>Should <code>qpdf</code> be used to check the installed sizes of PDFs?
Default: true if <code>qpdf</code> is found.
</p></dd>
<dt><code>_R_CHECK_DOC_SIZES2_</code>
<a name="index-_005fR_005fCHECK_005fDOC_005fSIZES2_005f"></a>
</dt>
<dd><p>Should <code>gs</code> be used to check the installed sizes of PDFs?  This
is slower than (and in addition to) the previous check, but does detect
figures with excessive detail (often hidden by over-plotting) or bitmap
figures with too high a resolution.  Requires that <code>R_GSCMD</code> is set
to a valid program, or <code>gs</code> (or on Windows,
<code>gswin32.exe</code> or <code>gswin64c.exe</code>) is on the path.
Default: false (but true for CRAN submission checks).
</p></dd>
<dt><code>_R_CHECK_ALWAYS_LOG_VIGNETTE_OUTPUT_</code>
<a name="index-_005fR_005fCHECK_005fALWAYS_005fLOG_005fVIGNETTE_005fOUTPUT_005f"></a>
</dt>
<dd><p>By default the output from running the R code in the vignettes is
kept only if there is an error.
Default: false.
</p></dd>
<dt><code>_R_CHECK_CLEAN_VIGN_TEST_</code>
<a name="index-_005fR_005fCHECK_005fCLEAN_005fVIGN_005fTEST_005f"></a>
</dt>
<dd><p>Should the <samp>vign_test</samp> directory be removed if the test is successful?
Default: true.
</p></dd>
<dt><code>_R_CHECK_REPLACING_IMPORTS_</code>
<a name="index-_005fR_005fCHECK_005fREPLACING_005fIMPORTS_005f"></a>
</dt>
<dd><p>Should warnings about replacing imports be reported?  These sometimes come
from auto-generated <samp>NAMESPACE</samp> files in other packages, but most
often from importing the whole of a namespace rather than using
<code>importFrom</code>.
Default: false (but true for CRAN submission checks).
</p></dd>
<dt><code>_R_CHECK_UNSAFE_CALLS_</code>
<a name="index-_005fR_005fCHECK_005fUNSAFE_005fCALLS_005f"></a>
</dt>
<dd><p>Check for calls that appear to tamper with (or allow tampering with)
already loaded code not from the current package: such calls may well
contravene CRAN policies.
Default: true.
</p></dd>
<dt><code>_R_CHECK_TIMINGS_</code>
<a name="index-_005fR_005fCHECK_005fTIMINGS_005f"></a>
</dt>
<dd><p>Optionally report timings for installation, examples, tests and
running/re-building vignettes as part of the check log.  The format is
&lsquo;<samp>[as/bs]</samp>&rsquo; for the total CPU time (including child processes)
&lsquo;<samp>a</samp>&rsquo; and elapsed time &lsquo;<samp>b</samp>&rsquo;, except on Windows, when it is
&lsquo;<samp>[bs]</samp>&rsquo;.  In most cases timings are only given for &lsquo;<samp>OK</samp>&rsquo; checks.
Times with an elapsed component over 10 mins are reported in minutes
(with abbreviation &lsquo;<samp>m</samp>&rsquo;).  The value is the smallest numerical value
in elapsed seconds that should be reported: non-numerical values
indicate that no report is required, a value of &lsquo;<samp>0</samp>&rsquo; that a report
is always required.
Default: <code>&quot;&quot;</code>. (<code>10</code> for CRAN checks.)
</p>
</dd>
<dt><code>_R_CHECK_INSTALL_DEPENDS_</code>
<a name="index-_005fR_005fCHECK_005fINSTALL_005fDEPENDS_005f"></a>
</dt>
<dd><p>If set to a true value and a test installation is to be done, this is
done with <code>.libPaths()</code> containing just a temporary library
directory and <code>.Library</code>.  The temporary library is populated by
symbolic links<a name="DOCF22" href="#FOOT22"><sup>22</sup></a>
to the installed copies of all the Depends/Imports/LinkingTo packages
which are not in <code>.Library</code>.  Default: false (but true for CRAN
submission checks).
</p>
<p>Note that this is actually implemented in <code>R CMD INSTALL</code>, so it
is available to those who first install recording to a log, then call
<code>R CMD check</code>.
</p>
</dd>
<dt><code>_R_CHECK_DEPENDS_ONLY_</code>
<a name="index-_005fR_005fCHECK_005fDEPENDS_005fONLY_005f"></a>
</dt>
<dt><code>_R_CHECK_SUGGESTS_ONLY_</code>
<a name="index-_005fR_005fCHECK_005fSUGGESTS_005fONLY_005f"></a>
</dt>
<dd><p>If set to a true value, running examples, tests and vignettes is done
with <code>.libPaths()</code> containing just a temporary library directory
and <code>.Library</code>.  The temporary library is populated by symbolic
links<a name="DOCF23" href="#FOOT23"><sup>23</sup></a> to the installed copies of
all the Depends/Imports and (for the second only) Suggests packages
which are not in <code>.Library</code>.  (As an exception, packages in a
&lsquo;<samp>VignetteBuilder</samp>&rsquo; field are always made available.)
Default: false (but <code>_R_CHECK_SUGGESTS_ONLY_</code> is true for CRAN checks).
</p>
</dd>
<dt><code>_R_CHECK_NO_RECOMMENDED_</code>
<a name="index-_005fR_005fCHECK_005fNO_005fRECOMMENDED_005f"></a>
</dt>
<dd><p>If set to a true value, augment the previous checks to make recommended
packages unavailable unless declared.
Default: false (but true for CRAN submission checks).
</p>
<p>This may give false positives on code which uses
<code>grDevices::densCols</code> and <code>stats:::asSparse</code> as these invoke
<a href="https://CRAN.R-project.org/package=KernSmooth"><strong>KernSmooth</strong></a> and <a href="https://CRAN.R-project.org/package=Matrix"><strong>Matrix</strong></a> respectively.
</p>
</dd>
<dt><code>_R_CHECK_CODETOOLS_PROFILE_</code>
<a name="index-_005fR_005fCHECK_005fCODETOOLS_005fPROFILE_005f"></a>
</dt>
<dd><p>A string with comma-separated <code><var>name</var>=<var>value</var></code> pairs (with
<var>value</var> a logical constant) giving additional arguments for the
<a href="https://CRAN.R-project.org/package=codetools"><strong>codetools</strong></a> functions used for analyzing package code.  E.g.,
use <code>_R_CHECK_CODETOOLS_PROFILE_=&quot;suppressLocalUnused=FALSE&quot;</code> to
turn off suppressing warnings about unused local variables.  Default: no
additional arguments, corresponding to using <code>skipWith = TRUE</code>,
<code>suppressPartialMatchArgs = FALSE</code> and <code>suppressLocalUnused =
TRUE</code>.
</p>
</dd>
<dt><code>_R_CHECK_CRAN_INCOMING_</code>
<a name="index-_005fR_005fCHECK_005fCRAN_005fINCOMING_005f"></a>
</dt>
<dd><p>Check whether package is suitable for publication on CRAN.
Default: false, except for CRAN submission checks.
</p>
</dd>
<dt><code>_R_CHECK_XREFS_USE_ALIASES_FROM_CRAN_</code>
<a name="index-_005fR_005fCHECK_005fXREFS_005fUSE_005fALIASES_005fFROM_005fCRAN_005f"></a>
</dt>
<dd><p>When checking anchored Rd xrefs, use Rd aliases from the CRAN package
web areas in addition to those in the packages installed locally.
Default: false.
</p>
</dd>
<dt><code>_R_SHLIB_BUILD_OBJECTS_SYMBOL_TABLES_</code>
<a name="index-_005fR_005fSHLIB_005fBUILD_005fOBJECTS_005fSYMBOL_005fTABLES_005f"></a>
</dt>
<dd><p>Make the checks of compiled code more accurate by recording the symbol
tables for objects (<samp>.o</samp> files) at installation in a file
<samp>symbols.rds</samp>.  (Only currently supported on Linux, Solaris, OS X,
Windows and FreeBSD.)
Default: true.
</p>
</dd>
<dt><code>_R_CHECK_CODE_ASSIGN_TO_GLOBALENV_</code>
<a name="index-_005fR_005fCHECK_005fCODE_005fASSIGN_005fTO_005fGLOBALENV_005f"></a>
</dt>
<dd><p>Should the package code be checked for assignments to the global
environment?
Default: false (but true for CRAN submission checks).
</p>
</dd>
<dt><code>_R_CHECK_CODE_ATTACH_</code>
<a name="index-_005fR_005fCHECK_005fCODE_005fATTACH_005f"></a>
</dt>
<dd><p>Should the package code be checked for calls to <code>attach()</code>?
Default: false (but true for CRAN submission checks).
</p>
</dd>
<dt><code>_R_CHECK_CODE_DATA_INTO_GLOBALENV_</code>
<a name="index-_005fR_005fCHECK_005fCODE_005fDATA_005fINTO_005fGLOBALENV_005f"></a>
</dt>
<dd><p>Should the package code be checked for calls to <code>data()</code> which load
into the global environment?
Default: false (but true for CRAN submission checks).
</p>
</dd>
<dt><code>_R_CHECK_DOT_FIRSTLIB_</code>
<a name="index-_005fR_005fCHECK_005fDOT_005fFIRSTLIB_005f"></a>
</dt>
<dd><p>Should the package code be checked for the presence of the obsolete function
<code>.First.lib()</code>?
Default: false (but true for CRAN submission checks).
</p>
</dd>
<dt><code>_R_CHECK_DEPRECATED_DEFUNCT_</code>
<a name="index-_005fR_005fCHECK_005fDEPRECATED_005fDEFUNCT_005f"></a>
</dt>
<dd><p>Should the package code be checked for the presence of recently deprecated
or defunct functions (including completely removed functions).  Also for
platform-specific graphics devices.
Default: false (but true for CRAN submission checks).
</p>
</dd>
<dt><code>_R_CHECK_SCREEN_DEVICE_</code>
<a name="index-_005fR_005fCHECK_005fSCREEN_005fDEVICE_005f"></a>
</dt>
<dd><p>If set to &lsquo;<samp>warn</samp>&rsquo;, give a warning if examples etc open a screen
device.  If set to &lsquo;<samp>stop</samp>&rsquo;, give an error.
Default: empty (but &lsquo;<samp>stop</samp>&rsquo; for CRAN submission checks).
</p>
</dd>
<dt><code>_R_CHECK_WINDOWS_DEVICE_</code>
<a name="index-_005fR_005fCHECK_005fWINDOWS_005fDEVICE_005f"></a>
</dt>
<dd><p>If set to &lsquo;<samp>stop</samp>&rsquo;, give an error if a Windows-only device is used in
example etc.  This is only useful on Windows: the devices do not exist
elsewhere.
Default: empty (but &lsquo;<samp>stop</samp>&rsquo; for CRAN submission checks on Windows).
</p>
</dd>
<dt><code>_R_CHECK_TOPLEVEL_FILES_</code>
<a name="index-_005fR_005fCHECK_005fTOPLEVEL_005fFILES_005f"></a>
</dt>
<dd><p>Report on top-level files in the package sources that are not described
in &lsquo;Writing R Extensions&rsquo; nor are commonly understood (like
<samp>ChangeLog</samp>).  Variations on standard names (e.g.
<samp>COPYRIGHT</samp>) are also reported.
Default: false (but true for CRAN submission checks).
</p>
</dd>
<dt><code>_R_CHECK_GCT_N_</code>
<a name="index-_005fR_005fCHECK_005fGCT_005fN_005f"></a>
</dt>
<dd><p>Should the <samp>--use-gct</samp> use <code>gctorture2(<var>n</var>)</code> rather than
<code>gctorture(TRUE)</code>?  Use to a positive integer to enable this.
Default: <code>0</code>.
</p>
</dd>
<dt><code>_R_CHECK_LIMIT_CORES_</code>
<a name="index-_005fR_005fCHECK_005fLIMIT_005fCORES_005f"></a>
</dt>
<dd><p>If set, check the usage of too many cores in package <strong>parallel</strong>.  If
set to &lsquo;<samp>warn</samp>&rsquo; gives a warning, to &lsquo;<samp>false</samp>&rsquo; or &lsquo;<samp>FALSE</samp>&rsquo; the
check is skipped, and any other non-empty value gives an error when more
than 2 children are spawned.
Default: unset (but &lsquo;<samp>TRUE</samp>&rsquo; for CRAN submission checks).
</p>
</dd>
<dt><code>_R_CHECK_CODE_USAGE_VIA_NAMESPACES_</code>
<a name="index-_005fR_005fCHECK_005fCODE_005fUSAGE_005fVIA_005fNAMESPACES_005f"></a>
</dt>
<dd><p>If set, check code usage (via <a href="https://CRAN.R-project.org/package=codetools"><strong>codetools</strong></a>) directly on the
package namespace without loading and attaching the package and its
suggests and enhances.
Default: true (and true for CRAN submission checks).
</p>
</dd>
<dt><code>_R_CHECK_EXIT_ON_FIRST_ERROR_</code>
<a name="index-_005fR_005fCHECK_005fEXIT_005fON_005fFIRST_005fERROR_005f"></a>
</dt>
<dd><p>If set to a true value, the check will exit on the first error.
Default: false.
</p>
</dd>
<dt><code>_R_CHECK_S3_METHODS_NOT_REGISTERED_</code>
<a name="index-_005fR_005fCHECK_005fS3_005fMETHODS_005fNOT_005fREGISTERED_005f"></a>
</dt>
<dd><p>If set to a true value, report (apparent) S3 methods exported but not
registered.
Default: false (but true for CRAN submission checks).
</p>
</dd>
<dt><code>_R_CHECK_OVERWRITE_REGISTERED_S3_METHODS_</code>
<a name="index-_005fR_005fCHECK_005fOVERWRITE_005fREGISTERED_005fS3_005fMETHODS_005f"></a>
</dt>
<dd><p>If set to a true value, report already registered S3 methods in
base/recommended packages which are overwritten when this package&rsquo;s
namespace is loaded. 
Default: false (but true for CRAN submission checks).
</p></dd>
</dl>

<p>CRAN&rsquo;s submission checks use something like
</p>
<div class="example">
<pre class="example">_R_CHECK_CRAN_INCOMING_=TRUE
_R_CHECK_VC_DIRS_=TRUE
_R_CHECK_TIMINGS_=10
_R_CHECK_INSTALL_DEPENDS_=TRUE
_R_CHECK_SUGGESTS_ONLY_=TRUE
_R_CHECK_NO_RECOMMENDED_=TRUE
_R_CHECK_EXECUTABLES_EXCLUSIONS_=FALSE
_R_CHECK_DOC_SIZES2_=TRUE
_R_CHECK_CODE_ASSIGN_TO_GLOBALENV_=TRUE
_R_CHECK_CODE_ATTACH_=TRUE
_R_CHECK_CODE_DATA_INTO_GLOBALENV_=TRUE
_R_CHECK_CODE_USAGE_VIA_NAMESPACES_=TRUE
_R_CHECK_DOT_FIRSTLIB_=TRUE
_R_CHECK_DEPRECATED_DEFUNCT_=TRUE
_R_CHECK_REPLACING_IMPORTS_=TRUE
_R_CHECK_SCREEN_DEVICE_=stop
_R_CHECK_TOPLEVEL_FILES_=TRUE
_R_CHECK_S3_METHODS_NOT_REGISTERED_=TRUE
_R_CHECK_OVERWRITE_REGISTERED_S3_METHODS_=TRUE
</pre></div>

<p>These are turned on by <code>R CMD check --as-cran</code>: the incoming
checks also use
</p><div class="example">
<pre class="example">_R_CHECK_FORCE_SUGGESTS_=FALSE
</pre></div>

<p>since some packages do suggest other packages not available on CRAN or
other commonly-used repositories.
</p>

<hr>
<a name="R-coding-standards"></a>
<div class="header">
<p>
Next: <a href="#Testing-R-code" accesskey="n" rel="next">Testing R code</a>, Previous: <a href="#Tools" accesskey="p" rel="prev">Tools</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> &nbsp; [<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-coding-standards-1"></a>
<h2 class="chapter">9 R coding standards</h2>

<a name="index-coding-standards"></a>
<p>R is meant to run on a wide variety of platforms, including Linux and
most variants of Unix as well as Windows and OS X.
Therefore, when extending R by either adding to the R base
distribution or by providing an add-on package, one should not rely on
features specific to only a few supported platforms, if this can be
avoided.  In particular, although most R developers use <acronym>GNU</acronym>
tools, they should not employ the <acronym>GNU</acronym> extensions to standard
tools.  Whereas some other software packages explicitly rely on e.g.
<acronym>GNU</acronym> make or the <acronym>GNU</acronym> C++ compiler, R does not.
Nevertheless, R is a <acronym>GNU</acronym> project, and the spirit of the
<cite><acronym>GNU</acronym> Coding Standards</cite> should be followed if possible.
</p>
<p>The following tools can &ldquo;safely be assumed&rdquo; for R extensions.
</p>
<ul>
<li> An ISO C99 C compiler.  Note that extensions such as <acronym>POSIX</acronym>
1003.1 must be tested for, typically using Autoconf unless you are sure
they are supported on all mainstream R platforms (including Windows
and OS X).

</li><li> A FORTRAN 77 compiler (but not Fortran 9x, although it is nowadays
widely available).

</li><li> A simple <code>make</code>, considering the features of <code>make</code> in
4.2 <acronym>BSD</acronym> systems as a baseline.
<a name="index-make"></a>

<p><acronym>GNU</acronym> or other extensions, including pattern rules using
&lsquo;<samp>%</samp>&rsquo;, the automatic variable &lsquo;<samp>$^</samp>&rsquo;, the &lsquo;<samp>+=</samp>&rsquo; syntax to
append to the value of a variable, the (&ldquo;safe&rdquo;) inclusion of makefiles
with no error, conditional execution, and many more, must not be used
(see Chapter &ldquo;Features&rdquo; in the <cite><acronym>GNU</acronym> Make Manual</cite> for
more information).  On the other hand, building R in a separate
directory (not containing the sources) should work provided that
<code>make</code> supports the <code>VPATH</code> mechanism.
</p>
<p>Windows-specific makefiles can assume <acronym>GNU</acronym> <code>make</code> 3.79
or later, as no other <code>make</code> is viable on that platform.
</p>
</li><li> A Bourne shell and the &ldquo;traditional&rdquo; Unix programming tools, including
<code>grep</code>, <code>sed</code>, and <code>awk</code>.

<p>There are <acronym>POSIX</acronym> standards for these tools, but these may not
be fully supported.  Baseline features could be determined from a book
such as <cite>The UNIX Programming Environment</cite> by Brian W. Kernighan &amp;
Rob Pike.  Note in particular that &lsquo;<samp>|</samp>&rsquo; in a regexp is an extended
regexp, and is not supported by all versions of <code>grep</code> or
<code>sed</code>.  The Open Group Base Specifications, Issue 7, which are
technically identical to  IEEE Std 1003.1 (POSIX), 2008,
are available at
<a href="http://pubs.opengroup.org/onlinepubs/9699919799/mindex.html">http://pubs.opengroup.org/onlinepubs/9699919799/mindex.html</a>.
</p></li></ul>

<p>Under Windows, most users will not have these tools installed, and you
should not require their presence for the operation of your package.
However, users who install your package from source will have them, as
they can be assumed to have followed the instructions in &ldquo;the Windows
toolset&rdquo; appendix of the &ldquo;R Installation and Administration&rdquo; manual
to obtain them.  Redirection cannot be assumed to be available via
<code>system</code> as this does not use a standard shell (let alone a
Bourne shell).
</p>
<p>In addition, the following tools are needed for certain tasks.
</p>
<ul>
<li> Perl version 5 is only needed for a few uncommonly-used tools: <code>make
install-info</code> needs Perl installed if there is no command
<code>install-info</code> on the system, and for the maintainer-only script
<samp>tools/help2man.pl</samp>.
<a name="index-Perl"></a>

</li><li> Makeinfo version 4.7 or later is needed to build the Info files for the
R manuals written in the <acronym>GNU</acronym> Texinfo system.
<a name="index-makeinfo"></a>
</li></ul>

<p>It is also important that code is written in a way that allows others to
understand it.  This is particularly helpful for fixing problems, and
includes using self-descriptive variable names, commenting the code, and
also formatting it properly.  The R Core Team recommends to use a
basic indentation of 4 for R and C (and most likely also Perl) code,
and 2 for documentation in Rd format.  Emacs (21 or later) users can
implement this indentation style by putting the following in one of
their startup files, and using customization to set the
<code>c-default-style</code> to <code>&quot;bsd&quot;</code> and <code>c-basic-offset</code> to
<code>4</code>.)
<a name="index-emacs"></a>
</p>
<div class="smallexample">
<pre class="smallexample">;;; ESS
(add-hook 'ess-mode-hook
          (lambda ()
            (ess-set-style 'C++ 'quiet)
            ;; Because
            ;;                                 DEF GNU BSD K&amp;R C++
            ;; ess-indent-level                  2   2   8   5   4
            ;; ess-continued-statement-offset    2   2   8   5   4
            ;; ess-brace-offset                  0   0  -8  -5  -4
            ;; ess-arg-function-offset           2   4   0   0   0
            ;; ess-expression-offset             4   2   8   5   4
            ;; ess-else-offset                   0   0   0   0   0
            ;; ess-close-brace-offset            0   0   0   0   0
            (add-hook 'local-write-file-hooks
                      (lambda ()
                        (ess-nuke-trailing-whitespace)))))
(setq ess-nuke-trailing-whitespace-p 'ask)
;; or even
;; (setq ess-nuke-trailing-whitespace-p t)
</pre><pre class="smallexample">;;; Perl
(add-hook 'perl-mode-hook
          (lambda () (setq perl-indent-level 4)))
</pre></div>

<p>(The &lsquo;GNU&rsquo; styles for Emacs&rsquo; C and R modes use a basic indentation of 2,
which has been determined not to display the structure clearly enough
when using narrow fonts.)
</p>
<hr>
<a name="Testing-R-code"></a>
<div class="header">
<p>
Next: <a href="#Use-of-TeX-dialects" accesskey="n" rel="next">Use of TeX dialects</a>, Previous: <a href="#R-coding-standards" accesskey="p" rel="prev">R coding standards</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> &nbsp; [<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-R-code-1"></a>
<h2 class="chapter">10 Testing R code</h2>

<p>When you (as R developer) add new functions to the R base (all the
packages distributed with R), be careful to check if <kbd>make
test-Specific</kbd> or particularly, <kbd>cd tests; make no-segfault.Rout</kbd>
still works (without interactive user intervention, and on a standalone
computer).  If the new function, for example, accesses the Internet, or
requires <acronym>GUI</acronym> interaction, please add its name to the &ldquo;stop
list&rdquo; in <samp>tests/no-segfault.Rin</samp>.
</p>
<p>[To be revised: use <code>make check-devel</code>, check the write barrier
if you change internal structures.]
</p>
<hr>
<a name="Use-of-TeX-dialects"></a>
<div class="header">
<p>
Next: <a href="#Current-and-future-directions" accesskey="n" rel="next">Current and future directions</a>, Previous: <a href="#Testing-R-code" accesskey="p" rel="prev">Testing R code</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> &nbsp; [<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="Use-of-TeX-dialects-1"></a>
<h2 class="chapter">11 Use of TeX dialects</h2>

<p>Various dialects of TeX and used for different purposes in R.  The
policy is that manuals be written in &lsquo;<samp>texinfo</samp>&rsquo;, and for convenience
the main and Windows FAQs are also.  This has the advantage that is is
easy to produce <acronym>HTML</acronym> and plain text versions as well as typeset manuals.
</p>
<p>LaTeX is not used directly, but rather as an intermediate format for
typeset help documents and for vignettes.
</p>
<p>Care needs to be taken about the assumptions made about the R user&rsquo;s
system: it may not have either &lsquo;<samp>texinfo</samp>&rsquo; or a TeX system
installed.  We have attempted to abstract out the cross-platform
differences, and almost all the setting of typeset documents is done by
<code>tools::texi2dvi</code>.  This is used for offline printing of help
documents, preparing vignettes and for package manuals via <code>R
CMD Rd2pdf</code>.  It is not currently used for the R manuals created in
directory <samp>doc/manual</samp>.
</p>
<p><code>tools::texi2dvi</code> makes use of a system command <code>texi2dvi</code>
where available.  On a Unix-alike this is usually part of
&lsquo;<samp>texinfo</samp>&rsquo;, whereas on Windows if it exists at all it would be an
executable, part of MiKTeX.  If none is available, the R code runs
a sequence of <code>(pdf)latex</code>, <code>bibtex</code> and
<code>makeindex</code> commands.
</p>
<p>This process has been rather vulnerable to the versions of the external
software used: particular issues have been <code>texi2dvi</code> and
<samp>texinfo.tex</samp> updates, mismatches between the two<a name="DOCF24" href="#FOOT24"><sup>24</sup></a>,
versions of the LaTeX package &lsquo;<samp>hyperref</samp>&rsquo; and quirks in index
production.  The licenses used for LaTeX and latterly &lsquo;<samp>texinfo</samp>&rsquo;
prohibit us from including &lsquo;known good&rsquo; versions in the R
distribution.
</p>
<p>On a Unix-alike <code>configure</code> looks for the executables for TeX and
friends and if found records the absolute paths in the system
<samp>Renviron</samp> file.  This used to record &lsquo;<samp>false</samp>&rsquo; if no command
was found, but it nowadays records the name for looking up on the path
at run time.  The latter can be important for binary distributions: one
does not want to be tied to, for example, TeX Live 2007.
</p>

<hr>
<a name="Current-and-future-directions"></a>
<div class="header">
<p>
Next: <a href="#Function-and-variable-index" accesskey="n" rel="next">Function and variable index</a>, Previous: <a href="#Use-of-TeX-dialects" accesskey="p" rel="prev">Use of TeX dialects</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> &nbsp; [<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="Current-and-future-directions-1"></a>
<h2 class="chapter">12 Current and future directions</h2>

<p>This chapter is for notes about possible in-progress and future changes
to R: there is no commitment to release such changes, let alone to a
timescale.
</p>
<table summary="" class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">&bull; <a href="#Long-vectors" accesskey="1">Long vectors</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">&bull; <a href="#g_t64_002dbit-types" accesskey="2">64-bit types</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
<tr><td align="left" valign="top">&bull; <a href="#Large-matrices" accesskey="3">Large matrices</a>:</td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
</td></tr>
</table>

<hr>
<a name="Long-vectors"></a>
<div class="header">
<p>
Next: <a href="#g_t64_002dbit-types" accesskey="n" rel="next">64-bit types</a>, Previous: <a href="#Current-and-future-directions" accesskey="p" rel="prev">Current and future directions</a>, Up: <a href="#Current-and-future-directions" accesskey="u" rel="up">Current and future directions</a> &nbsp; [<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="Long-vectors-1"></a>
<h3 class="section">12.1 Long vectors</h3>

<p>Vectors in R 2.x.y were limited to a length of 2^31 - 1 elements
(about 2 billion), as the length is stored in the <code>SEXPREC</code> as a C
<code>int</code>, and that type is used extensively to record lengths and
element numbers, including in packages.
</p>
<p>Note that longer vectors are effectively impossible under 32-bit
platforms because of their address limit, so this section applies only
on 64-bit platforms.  The internals are unchanged on a 32-bit build of
R.
</p>
<p>A single object with 2^31 or more elements will take up at least 8GB of
memory if integer or logical and 16GB if numeric or character, so
routine use of such objects is still some way off.
</p>
<p>There is now some support for long vectors.  This applies to raw,
logical, integer, numeric and character vectors, and lists and
expression vectors.  (Elements of character vectors (<code>CHARSXP</code>s)
remain limited to 2^31 - 1 bytes.)  Some considerations:
</p>

<ul>
<li> This has been implemented by recording the length (and true length) as
<code>-1</code> and recording the actual length as a 64-bit field at the
beginning of the header.  Because a fair amount of code in R uses a
signed type for the length, the &lsquo;long length&rsquo; is recorded using the
signed C99 type <code>ptrdiff_t</code>, which is typedef-ed to
<code>R_xlen_t</code>.

</li><li> These can in theory have 63-bit lengths, but note that current 64-bit
OSes do not even theoretically offer 64-bit address spaces and there is
currently a 52-bit limit (which exceeds the theoretical limit of current
OSes and ensures that such lengths can be stored exactly in doubles).

</li><li> The serialization format has been changed to accommodate longer lengths,
but vectors of lengths up to 2^31-1 are stored in the same way as
before.  Longer vectors have their length field set to <code>-1</code> and
followed by two 32-bit fields giving the upper and lower 32-bits of the
actual length.  There is currently a sanity check which limits lengths
to 2^48 on unserialization.

</li><li> The type <code>R_xlen_t</code> is made available to packages in C header
<samp>Rinternals.h</samp>: this should be fine in C code since C99 is
required.  People do try to use R internals in C++, but C++98
compilers are not required to support these types.

</li><li> Indexing can be done via the use of doubles.  The internal indexing code
used to work with positive integer indices (and negative, logical and
matrix indices were all converted to positive integers): it now works
with either <code>INTSXP</code> or <code>REALSXP</code> indices.

</li><li> R function <code>length</code> was documented to currently return an
integer, possibly <code>NA</code>.  A lot of code has been written that
assumes that, and even code which calls <code>as.integer(length(x))</code>
before passing to <code>.C</code>/<code>.Fortran</code> rarely checks for an
<code>NA</code> result.

<p>There is a new function <code>xlength</code> which works for long vectors and
returns a double value if the length exceeds 2^31-1. At present
<code>length</code> returns <code>NA</code> for long vectors, but it may be safer to
make that an error.
</p>
</li></ul>

<hr>
<a name="g_t64_002dbit-types"></a>
<div class="header">
<p>
Next: <a href="#Large-matrices" accesskey="n" rel="next">Large matrices</a>, Previous: <a href="#Long-vectors" accesskey="p" rel="prev">Long vectors</a>, Up: <a href="#Current-and-future-directions" accesskey="u" rel="up">Current and future directions</a> &nbsp; [<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-types-1"></a>
<h3 class="section">12.2 64-bit types</h3>

<p>There is also some desire to be able to store larger integers in R,
although the possibility of storing these as <code>double</code> is often
overlooked (and e.g. file pointers as returned by <code>seek</code> are
already stored as <code>double</code>).
</p>
<p>Different routes have been proposed:
</p>
<ul>
<li> Add a new type to R and use that for lengths and indices&mdash;most likely
this would be a 64-bit signed type, say <code>longint</code>.  R&rsquo;s usual
implicit coercion rules would ensure that supplying an <code>integer</code>
vector for indexing or <code>length&lt;-</code> would work.

</li><li> A more radical alternative is to change the existing <code>integer</code> type
to be 64-bit on 64-bit platforms (which was the approach taken by S-PLUS
for DEC/Compaq Alpha systems).  Or even on all platforms.

</li><li> Allow either <code>integer</code> or <code>double</code> values for lengths and
indices, and return <code>double</code> only when necessary.

</li></ul>

<p>The third has the advantages of minimal disruption to existing code and
not increasing memory requirements. In the first and third scenarios
both R&rsquo;s own code and user code would have to be adapted for lengths
that were not of type <code>integer</code>, and in the third code branches for
long vectors would be tested rarely.
</p>
<p>Most users of the <code>.C</code> and <code>.Fortran</code> interfaces use
<code>as.integer</code> for lengths and element numbers, but a few omit these
in the knowledge that these were of type <code>integer</code>.  It may be
reasonable to assume that these are never intended to be used with long
vectors.
</p>
<p>The remaining interfaces will need to cope with the changed
<code>VECTOR_SEXPREC</code> types.  It seems likely that in most cases lengths
are accessed by the <code>length</code> and <code>LENGTH</code>
functions<a name="DOCF25" href="#FOOT25"><sup>25</sup></a>  The current approach is to keep these returning 32-bit lengths and
introduce &lsquo;long&rsquo; versions <code>xlength</code> and <code>XLENGTH</code> which return
<code>R_xlen_t</code> values.
</p>

<p>See also <a href="http://homepage.cs.uiowa.edu/~luke/talks/useR10.pdf">http://homepage.cs.uiowa.edu/~luke/talks/useR10.pdf</a>.
</p>
<hr>
<a name="Large-matrices"></a>
<div class="header">
<p>
Previous: <a href="#g_t64_002dbit-types" accesskey="p" rel="prev">64-bit types</a>, Up: <a href="#Current-and-future-directions" accesskey="u" rel="up">Current and future directions</a> &nbsp; [<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="Large-matrices-1"></a>
<h3 class="section">12.3 Large matrices</h3>

<p>Matrices are stored as vectors and so were also limited to 2^31-1
elements.  Now longer vectors are allowed on 64-bit platforms, matrices
with more elements are supported provided that each of the dimensions is
no more than 2^31-1.  However, not all applications can be supported.
</p>
<p>The main problem is linear algebra done by FORTRAN code compiled
with 32-bit <code>INTEGER</code>.  Although not guaranteed, it seems that all
the compilers currently used with R on a 64-bit platform allow
matrices each of whose dimensions is less than 2^31 but with more than
2^31 elements, and index them correctly, and a substantial part of the
support software (such as <acronym>BLAS</acronym> and <acronym>LAPACK</acronym>) also
work.
</p>
<p>There are exceptions: for example some complex <acronym>LAPACK</acronym>
auxiliary routines do use a single <code>INTEGER</code> index and hence
overflow silently and segfault or give incorrect results.  One example
is <code>svd()</code> on a complex matrix.
</p>
<p>Since this is implementation-dependent, it is possible that optimized
<acronym>BLAS</acronym> and <acronym>LAPACK</acronym> may have further restrictions,
although none have yet been encountered.  For matrix algebra on large
matrices one almost certainly wants a machine with a lot of RAM (100s of
gigabytes), many cores and a multi-threaded <acronym>BLAS</acronym>.
</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="#Current-and-future-directions" accesskey="p" rel="prev">Current and future directions</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> &nbsp; [<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 summary=""><tr><th valign="top">Jump to: &nbsp; </th><td><a class="summary-letter" href="#Function-and-variable-index_vr_symbol-1"><b>.</b></a>
 &nbsp; 
<a class="summary-letter" href="#Function-and-variable-index_vr_symbol-2"><b>_</b></a>
 &nbsp; 
<br>
<a class="summary-letter" href="#Function-and-variable-index_vr_letter-A"><b>A</b></a>
 &nbsp; 
<a class="summary-letter" href="#Function-and-variable-index_vr_letter-C"><b>C</b></a>
 &nbsp; 
<a class="summary-letter" href="#Function-and-variable-index_vr_letter-D"><b>D</b></a>
 &nbsp; 
<a class="summary-letter" href="#Function-and-variable-index_vr_letter-E"><b>E</b></a>
 &nbsp; 
<a class="summary-letter" href="#Function-and-variable-index_vr_letter-F"><b>F</b></a>
 &nbsp; 
<a class="summary-letter" href="#Function-and-variable-index_vr_letter-G"><b>G</b></a>
 &nbsp; 
<a class="summary-letter" href="#Function-and-variable-index_vr_letter-I"><b>I</b></a>
 &nbsp; 
<a class="summary-letter" href="#Function-and-variable-index_vr_letter-L"><b>L</b></a>
 &nbsp; 
<a class="summary-letter" href="#Function-and-variable-index_vr_letter-M"><b>M</b></a>
 &nbsp; 
<a class="summary-letter" href="#Function-and-variable-index_vr_letter-N"><b>N</b></a>
 &nbsp; 
<a class="summary-letter" href="#Function-and-variable-index_vr_letter-P"><b>P</b></a>
 &nbsp; 
<a class="summary-letter" href="#Function-and-variable-index_vr_letter-R"><b>R</b></a>
 &nbsp; 
<a class="summary-letter" href="#Function-and-variable-index_vr_letter-S"><b>S</b></a>
 &nbsp; 
<a class="summary-letter" href="#Function-and-variable-index_vr_letter-T"><b>T</b></a>
 &nbsp; 
<a class="summary-letter" href="#Function-and-variable-index_vr_letter-U"><b>U</b></a>
 &nbsp; 
<a class="summary-letter" href="#Function-and-variable-index_vr_letter-V"><b>V</b></a>
 &nbsp; 
<a class="summary-letter" href="#Function-and-variable-index_vr_letter-W"><b>W</b></a>
 &nbsp; 
</td></tr></table>
<table summary="" class="index-vr" border="0">
<tr><td></td><th align="left">Index Entry</th><td>&nbsp;</td><th align="left"> Section</th></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Function-and-variable-index_vr_symbol-1">.</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-_002eDevice"><code>.Device</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Base-environment">Base environment</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_002eDevices"><code>.Devices</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Base-environment">Base environment</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_002eInternal"><code>.Internal</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#g_t_002eInternal-vs-_002ePrimitive">.Internal vs .Primitive</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_002eLast_002evalue"><code>.Last.value</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Base-environment">Base environment</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_002eOptions"><code>.Options</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Base-environment">Base environment</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_002ePrimitive"><code>.Primitive</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#g_t_002eInternal-vs-_002ePrimitive">.Internal vs .Primitive</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_002eRandom_002eseed"><code>.Random.seed</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Global-environment">Global environment</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_002eSavedPlots"><code>.SavedPlots</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Global-environment">Global environment</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_002eTraceback"><code>.Traceback</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Base-environment">Base environment</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Function-and-variable-index_vr_symbol-2">_</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fALL_005fNON_005fISO_005fC_005f"><code>_R_CHECK_ALL_NON_ISO_C_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fALWAYS_005fLOG_005fVIGNETTE_005fOUTPUT_005f"><code>_R_CHECK_ALWAYS_LOG_VIGNETTE_OUTPUT_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fASCII_005fCODE_005f"><code>_R_CHECK_ASCII_CODE_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fASCII_005fDATA_005f"><code>_R_CHECK_ASCII_DATA_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fCLEAN_005fVIGN_005fTEST_005f"><code>_R_CHECK_CLEAN_VIGN_TEST_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fCODETOOLS_005fPROFILE_005f"><code>_R_CHECK_CODETOOLS_PROFILE_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fCODE_005fASSIGN_005fTO_005fGLOBALENV_005f"><code>_R_CHECK_CODE_ASSIGN_TO_GLOBALENV_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fCODE_005fATTACH_005f"><code>_R_CHECK_CODE_ATTACH_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fCODE_005fDATA_005fINTO_005fGLOBALENV_005f"><code>_R_CHECK_CODE_DATA_INTO_GLOBALENV_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fCODE_005fUSAGE_005fVIA_005fNAMESPACES_005f"><code>_R_CHECK_CODE_USAGE_VIA_NAMESPACES_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fCODOC_005fS4_005fMETHODS_005f"><code>_R_CHECK_CODOC_S4_METHODS_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fCOMPACT_005fDATA_005f"><code>_R_CHECK_COMPACT_DATA_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fCRAN_005fINCOMING_005f"><code>_R_CHECK_CRAN_INCOMING_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fDEPENDS_005fONLY_005f"><code>_R_CHECK_DEPENDS_ONLY_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fDEPRECATED_005fDEFUNCT_005f"><code>_R_CHECK_DEPRECATED_DEFUNCT_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fDOC_005fSIZES2_005f"><code>_R_CHECK_DOC_SIZES2_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fDOC_005fSIZES_005f"><code>_R_CHECK_DOC_SIZES_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fDOT_005fFIRSTLIB_005f"><code>_R_CHECK_DOT_FIRSTLIB_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fDOT_005fINTERNAL_005f"><code>_R_CHECK_DOT_INTERNAL_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fEXECUTABLES_005f"><code>_R_CHECK_EXECUTABLES_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fEXECUTABLES_005fEXCLUSIONS_005f"><code>_R_CHECK_EXECUTABLES_EXCLUSIONS_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fEXIT_005fON_005fFIRST_005fERROR_005f"><code>_R_CHECK_EXIT_ON_FIRST_ERROR_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fFF_005fCALLS_005f"><code>_R_CHECK_FF_CALLS_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fFF_005fDUP_005f"><code>_R_CHECK_FF_DUP_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fFORCE_005fSUGGESTS_005f"><code>_R_CHECK_FORCE_SUGGESTS_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fGCT_005fN_005f"><code>_R_CHECK_GCT_N_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fINSTALL_005fDEPENDS_005f"><code>_R_CHECK_INSTALL_DEPENDS_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fLICENSE_005f"><code>_R_CHECK_LICENSE_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fLIMIT_005fCORES_005f"><code>_R_CHECK_LIMIT_CORES_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fNO_005fRECOMMENDED_005f"><code>_R_CHECK_NO_RECOMMENDED_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fOVERWRITE_005fREGISTERED_005fS3_005fMETHODS_005f"><code>_R_CHECK_OVERWRITE_REGISTERED_S3_METHODS_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fPERMISSIONS_005f"><code>_R_CHECK_PERMISSIONS_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fPKG_005fSIZES_005f"><code>_R_CHECK_PKG_SIZES_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fRD_005fCHECKRD_005fMINLEVEL_005f"><code>_R_CHECK_RD_CHECKRD_MINLEVEL_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fRD_005fCONTENTS_005f"><code>_R_CHECK_RD_CONTENTS_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fRD_005fEXAMPLES_005fT_005fAND_005fF_005f"><code>_R_CHECK_RD_EXAMPLES_T_AND_F_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fRD_005fLINE_005fWIDTHS_005f"><code>_R_CHECK_RD_LINE_WIDTHS_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fRD_005fSTYLE_005f"><code>_R_CHECK_RD_STYLE_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fRD_005fXREFS_005f"><code>_R_CHECK_RD_XREFS_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fREPLACING_005fIMPORTS_005f"><code>_R_CHECK_REPLACING_IMPORTS_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fS3_005fMETHODS_005fNOT_005fREGISTERED_005f"><code>_R_CHECK_S3_METHODS_NOT_REGISTERED_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fSCREEN_005fDEVICE_005f"><code>_R_CHECK_SCREEN_DEVICE_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fSKIP_005fARCH_005f"><code>_R_CHECK_SKIP_ARCH_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fSKIP_005fEXAMPLES_005fARCH_005f"><code>_R_CHECK_SKIP_EXAMPLES_ARCH_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fSKIP_005fTESTS_005fARCH_005f"><code>_R_CHECK_SKIP_TESTS_ARCH_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fSRC_005fMINUS_005fW_005fIMPLICIT_005f"><code>_R_CHECK_SRC_MINUS_W_IMPLICIT_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fSRC_005fMINUS_005fW_005fUNUSED_005f"><code>_R_CHECK_SRC_MINUS_W_UNUSED_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fSUBDIRS_005fNOCASE_005f"><code>_R_CHECK_SUBDIRS_NOCASE_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fSUBDIRS_005fSTRICT_005f"><code>_R_CHECK_SUBDIRS_STRICT_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fSUGGESTS_005fONLY_005f"><code>_R_CHECK_SUGGESTS_ONLY_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fTIMINGS_005f"><code>_R_CHECK_TIMINGS_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fTOPLEVEL_005fFILES_005f"><code>_R_CHECK_TOPLEVEL_FILES_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fUNSAFE_005fCALLS_005f"><code>_R_CHECK_UNSAFE_CALLS_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fUSE_005fCODETOOLS_005f"><code>_R_CHECK_USE_CODETOOLS_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fUSE_005fINSTALL_005fLOG_005f"><code>_R_CHECK_USE_INSTALL_LOG_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fVC_005fDIRS_005f"><code>_R_CHECK_VC_DIRS_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fVIGNETTES_005fNLINES_005f"><code>_R_CHECK_VIGNETTES_NLINES_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fWALL_005fFORTRAN_005f"><code>_R_CHECK_WALL_FORTRAN_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fWINDOWS_005fDEVICE_005f"><code>_R_CHECK_WINDOWS_DEVICE_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fXREFS_005fREPOSITORIES_005f"><code>_R_CHECK_XREFS_REPOSITORIES_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fCHECK_005fXREFS_005fUSE_005fALIASES_005fFROM_005fCRAN_005f"><code>_R_CHECK_XREFS_USE_ALIASES_FROM_CRAN_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005fR_005fSHLIB_005fBUILD_005fOBJECTS_005fSYMBOL_005fTABLES_005f"><code>_R_SHLIB_BUILD_OBJECTS_SYMBOL_TABLES_</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Tools">Tools</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Function-and-variable-index_vr_letter-A">A</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-alloca"><code>alloca</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Memory-allocators">Memory allocators</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ARGSUSED"><code>ARGSUSED</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Rest-of-header">Rest of header</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ATTRIB"><code>ATTRIB</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Attributes">Attributes</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-attribute_005fhidden"><code>attribute_hidden</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Hiding-C-entry-points">Hiding C entry points</a></td></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-Calloc"><code>Calloc</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Memory-allocators">Memory allocators</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-copyMostAttributes"><code>copyMostAttributes</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Attributes">Attributes</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Function-and-variable-index_vr_letter-D">D</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-DDVAL"><code>DDVAL</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Rest-of-header">Rest of header</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-debug-bit"><code>debug bit</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Rest-of-header">Rest of header</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-DispatchGeneric"><code>DispatchGeneric</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Argument-evaluation">Argument evaluation</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-DispatchOrEval"><code>DispatchOrEval</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Argument-evaluation">Argument evaluation</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-dump_002eframes"><code>dump.frames</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Global-environment">Global environment</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-DUPLICATE_005fATTRIB"><code>DUPLICATE_ATTRIB</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Attributes">Attributes</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Function-and-variable-index_vr_letter-E">E</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-emacs"><code>emacs</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#R-coding-standards">R coding standards</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-error"><code>error</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Warnings-and-errors">Warnings and errors</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-errorcall"><code>errorcall</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Warnings-and-errors">Warnings and errors</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Function-and-variable-index_vr_letter-F">F</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-Free"><code>Free</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Memory-allocators">Memory allocators</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Function-and-variable-index_vr_letter-G">G</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-gp-bits"><code>gp bits</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Rest-of-header">Rest of header</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-invisible"><code>invisible</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Autoprinting">Autoprinting</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Function-and-variable-index_vr_letter-L">L</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-last_002ewarning"><code>last.warning</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Base-environment">Base environment</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-LEVELS"><code>LEVELS</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Rest-of-header">Rest of header</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>&nbsp;</td><td valign="top"><a href="#R-coding-standards">R coding standards</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-makeinfo"><code>makeinfo</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#R-coding-standards">R coding standards</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-MISSING"><code>MISSING</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Rest-of-header">Rest of header</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-MISSING-1"><code>MISSING</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Missingness">Missingness</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-mkChar"><code>mkChar</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#The-CHARSXP-cache">The CHARSXP cache</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-mkCharLenCE"><code>mkCharLenCE</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#The-CHARSXP-cache">The CHARSXP cache</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Function-and-variable-index_vr_letter-N">N</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-NAMED"><code>NAMED</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Rest-of-header">Rest of header</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-NAMED-1"><code>NAMED</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Argument-evaluation">Argument evaluation</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-NAMED-2"><code>NAMED</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#g_t_002eInternal-vs-_002ePrimitive">.Internal vs .Primitive</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-named-bit"><code>named bit</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Rest-of-header">Rest of header</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Function-and-variable-index_vr_letter-P">P</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-Perl"><code>Perl</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#R-coding-standards">R coding standards</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-PRIMPRINT"><code>PRIMPRINT</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Autoprinting">Autoprinting</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-PRSEEN"><code>PRSEEN</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Rest-of-header">Rest of header</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-Rdll_002ehide"><code>Rdll.hide</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Hiding-C-entry-points">Hiding C entry points</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-Realloc"><code>Realloc</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Memory-allocators">Memory allocators</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-R_005falloc"><code>R_alloc</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Memory-allocators">Memory allocators</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-R_005fAllocStringBuffer"><code>R_AllocStringBuffer</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Memory-allocators">Memory allocators</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-R_005fBaseNamespace"><code>R_BaseNamespace</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Namespaces">Namespaces</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-R_005fCheckStack"><code>R_CheckStack</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Memory-allocators">Memory allocators</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-R_005fCheckStack2"><code>R_CheckStack2</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Memory-allocators">Memory allocators</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-R_005fFreeStringBuffer"><code>R_FreeStringBuffer</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Memory-allocators">Memory allocators</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-R_005fFreeStringBufferL"><code>R_FreeStringBufferL</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Memory-allocators">Memory allocators</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-R_005fMissingArg"><code>R_MissingArg</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Missingness">Missingness</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-R_005fVisible"><code>R_Visible</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Autoprinting">Autoprinting</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Function-and-variable-index_vr_letter-S">S</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-SETLEVELS"><code>SETLEVELS</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Rest-of-header">Rest of header</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-SET_005fARGUSED"><code>SET_ARGUSED</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Rest-of-header">Rest of header</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-SET_005fATTRIB"><code>SET_ATTRIB</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Attributes">Attributes</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-SET_005fDDVAL"><code>SET_DDVAL</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Rest-of-header">Rest of header</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-SET_005fMISSING"><code>SET_MISSING</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Rest-of-header">Rest of header</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-SET_005fNAMED"><code>SET_NAMED</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Rest-of-header">Rest of header</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-spare-bit"><code>spare bit</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Rest-of-header">Rest of header</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Function-and-variable-index_vr_letter-T">T</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-trace-bit"><code>trace bit</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Rest-of-header">Rest of header</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-UseMethod"><code>UseMethod</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Contexts">Contexts</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Function-and-variable-index_vr_letter-V">V</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-vmaxget"><code>vmaxget</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Memory-allocators">Memory allocators</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-vmaxset"><code>vmaxset</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Memory-allocators">Memory allocators</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Function-and-variable-index_vr_letter-W">W</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-warning"><code>warning</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Warnings-and-errors">Warnings and errors</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-warningcall"><code>warningcall</code></a>:</td><td>&nbsp;</td><td valign="top"><a href="#Warnings-and-errors">Warnings and errors</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
</table>
<table summary=""><tr><th valign="top">Jump to: &nbsp; </th><td><a class="summary-letter" href="#Function-and-variable-index_vr_symbol-1"><b>.</b></a>
 &nbsp; 
<a class="summary-letter" href="#Function-and-variable-index_vr_symbol-2"><b>_</b></a>
 &nbsp; 
<br>
<a class="summary-letter" href="#Function-and-variable-index_vr_letter-A"><b>A</b></a>
 &nbsp; 
<a class="summary-letter" href="#Function-and-variable-index_vr_letter-C"><b>C</b></a>
 &nbsp; 
<a class="summary-letter" href="#Function-and-variable-index_vr_letter-D"><b>D</b></a>
 &nbsp; 
<a class="summary-letter" href="#Function-and-variable-index_vr_letter-E"><b>E</b></a>
 &nbsp; 
<a class="summary-letter" href="#Function-and-variable-index_vr_letter-F"><b>F</b></a>
 &nbsp; 
<a class="summary-letter" href="#Function-and-variable-index_vr_letter-G"><b>G</b></a>
 &nbsp; 
<a class="summary-letter" href="#Function-and-variable-index_vr_letter-I"><b>I</b></a>
 &nbsp; 
<a class="summary-letter" href="#Function-and-variable-index_vr_letter-L"><b>L</b></a>
 &nbsp; 
<a class="summary-letter" href="#Function-and-variable-index_vr_letter-M"><b>M</b></a>
 &nbsp; 
<a class="summary-letter" href="#Function-and-variable-index_vr_letter-N"><b>N</b></a>
 &nbsp; 
<a class="summary-letter" href="#Function-and-variable-index_vr_letter-P"><b>P</b></a>
 &nbsp; 
<a class="summary-letter" href="#Function-and-variable-index_vr_letter-R"><b>R</b></a>
 &nbsp; 
<a class="summary-letter" href="#Function-and-variable-index_vr_letter-S"><b>S</b></a>
 &nbsp; 
<a class="summary-letter" href="#Function-and-variable-index_vr_letter-T"><b>T</b></a>
 &nbsp; 
<a class="summary-letter" href="#Function-and-variable-index_vr_letter-U"><b>U</b></a>
 &nbsp; 
<a class="summary-letter" href="#Function-and-variable-index_vr_letter-V"><b>V</b></a>
 &nbsp; 
<a class="summary-letter" href="#Function-and-variable-index_vr_letter-W"><b>W</b></a>
 &nbsp; 
</td></tr></table>

<hr>
<a name="Concept-index"></a>
<div class="header">
<p>
Previous: <a href="#Function-and-variable-index" accesskey="p" rel="prev">Function and variable index</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> &nbsp; [<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 summary=""><tr><th valign="top">Jump to: &nbsp; </th><td><a class="summary-letter" href="#Concept-index_cp_symbol-1"><b>.</b></a>
 &nbsp; 
<br>
<a class="summary-letter" href="#Concept-index_cp_letter-A"><b>A</b></a>
 &nbsp; 
<a class="summary-letter" href="#Concept-index_cp_letter-B"><b>B</b></a>
 &nbsp; 
<a class="summary-letter" href="#Concept-index_cp_letter-C"><b>C</b></a>
 &nbsp; 
<a class="summary-letter" href="#Concept-index_cp_letter-E"><b>E</b></a>
 &nbsp; 
<a class="summary-letter" href="#Concept-index_cp_letter-F"><b>F</b></a>
 &nbsp; 
<a class="summary-letter" href="#Concept-index_cp_letter-G"><b>G</b></a>
 &nbsp; 
<a class="summary-letter" href="#Concept-index_cp_letter-L"><b>L</b></a>
 &nbsp; 
<a class="summary-letter" href="#Concept-index_cp_letter-M"><b>M</b></a>
 &nbsp; 
<a class="summary-letter" href="#Concept-index_cp_letter-N"><b>N</b></a>
 &nbsp; 
<a class="summary-letter" href="#Concept-index_cp_letter-P"><b>P</b></a>
 &nbsp; 
<a class="summary-letter" href="#Concept-index_cp_letter-S"><b>S</b></a>
 &nbsp; 
<a class="summary-letter" href="#Concept-index_cp_letter-U"><b>U</b></a>
 &nbsp; 
<a class="summary-letter" href="#Concept-index_cp_letter-V"><b>V</b></a>
 &nbsp; 
<a class="summary-letter" href="#Concept-index_cp_letter-W"><b>W</b></a>
 &nbsp; 
</td></tr></table>
<table summary="" class="index-cp" border="0">
<tr><td></td><th align="left">Index Entry</th><td>&nbsp;</td><th align="left"> Section</th></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Concept-index_cp_symbol-1">.</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-_002e_002e_002e-argument">... argument</a>:</td><td>&nbsp;</td><td valign="top"><a href="#Rest-of-header">Rest of header</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_002e_002e_002e-argument-1">... argument</a>:</td><td>&nbsp;</td><td valign="top"><a href="#Dot_002ddot_002ddot-arguments">Dot-dot-dot arguments</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_002eInternal-function">.Internal function</a>:</td><td>&nbsp;</td><td valign="top"><a href="#Argument-evaluation">Argument evaluation</a></td></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-allocation-classes">allocation classes</a>:</td><td>&nbsp;</td><td valign="top"><a href="#Allocation-classes">Allocation classes</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-argument-evaluation">argument evaluation</a>:</td><td>&nbsp;</td><td valign="top"><a href="#Argument-evaluation">Argument evaluation</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-argument-list">argument list</a>:</td><td>&nbsp;</td><td valign="top"><a href="#SEXPTYPEs">SEXPTYPEs</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-atomic-vector-type">atomic vector type</a>:</td><td>&nbsp;</td><td valign="top"><a href="#SEXPTYPEs">SEXPTYPEs</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-attributes">attributes</a>:</td><td>&nbsp;</td><td valign="top"><a href="#Attributes">Attributes</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-attributes_002c-preserving">attributes, preserving</a>:</td><td>&nbsp;</td><td valign="top"><a href="#Attributes">Attributes</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-autoprinting">autoprinting</a>:</td><td>&nbsp;</td><td valign="top"><a href="#Autoprinting">Autoprinting</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-base-environment">base environment</a>:</td><td>&nbsp;</td><td valign="top"><a href="#Environments-and-variable-lookup">Environments and variable lookup</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-base-environment-1">base environment</a>:</td><td>&nbsp;</td><td valign="top"><a href="#Base-environment">Base environment</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-base-namespace">base namespace</a>:</td><td>&nbsp;</td><td valign="top"><a href="#Namespaces">Namespaces</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-builtin-function">builtin function</a>:</td><td>&nbsp;</td><td valign="top"><a href="#Argument-evaluation">Argument evaluation</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Concept-index_cp_letter-C">C</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-coding-standards">coding standards</a>:</td><td>&nbsp;</td><td valign="top"><a href="#R-coding-standards">R coding standards</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-context">context</a>:</td><td>&nbsp;</td><td valign="top"><a href="#Contexts">Contexts</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-copying-semantics">copying semantics</a>:</td><td>&nbsp;</td><td valign="top"><a href="#Rest-of-header">Rest of header</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-copying-semantics-1">copying semantics</a>:</td><td>&nbsp;</td><td valign="top"><a href="#Attributes">Attributes</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Concept-index_cp_letter-E">E</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-environment">environment</a>:</td><td>&nbsp;</td><td valign="top"><a href="#Environments-and-variable-lookup">Environments and variable lookup</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-environment_002c-base">environment, base</a>:</td><td>&nbsp;</td><td valign="top"><a href="#Environments-and-variable-lookup">Environments and variable lookup</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-environment_002c-base-1">environment, base</a>:</td><td>&nbsp;</td><td valign="top"><a href="#Base-environment">Base environment</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-environment_002c-global">environment, global</a>:</td><td>&nbsp;</td><td valign="top"><a href="#Global-environment">Global environment</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-expression">expression</a>:</td><td>&nbsp;</td><td valign="top"><a href="#SEXPTYPEs">SEXPTYPEs</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-function">function</a>:</td><td>&nbsp;</td><td valign="top"><a href="#SEXPTYPEs">SEXPTYPEs</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Concept-index_cp_letter-G">G</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-garbage-collector">garbage collector</a>:</td><td>&nbsp;</td><td valign="top"><a href="#The-write-barrier">The write barrier</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-generic_002c-generic">generic, generic</a>:</td><td>&nbsp;</td><td valign="top"><a href="#Argument-evaluation">Argument evaluation</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-generic_002c-internal">generic, internal</a>:</td><td>&nbsp;</td><td valign="top"><a href="#Argument-evaluation">Argument evaluation</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-global-environment">global environment</a>:</td><td>&nbsp;</td><td valign="top"><a href="#Global-environment">Global environment</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-language-object">language object</a>:</td><td>&nbsp;</td><td valign="top"><a href="#SEXPTYPEs">SEXPTYPEs</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-method-dispatch">method dispatch</a>:</td><td>&nbsp;</td><td valign="top"><a href="#Contexts">Contexts</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-missingness">missingness</a>:</td><td>&nbsp;</td><td valign="top"><a href="#Missingness">Missingness</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-modules">modules</a>:</td><td>&nbsp;</td><td valign="top"><a href="#Modules">Modules</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="Concept-index_cp_letter-N">N</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-namespace">namespace</a>:</td><td>&nbsp;</td><td valign="top"><a href="#Namespaces">Namespaces</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-namespace_002c-base">namespace, base</a>:</td><td>&nbsp;</td><td valign="top"><a href="#Namespaces">Namespaces</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-node">node</a>:</td><td>&nbsp;</td><td valign="top"><a href="#SEXPs">SEXPs</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-preserving-attributes">preserving attributes</a>:</td><td>&nbsp;</td><td valign="top"><a href="#Attributes">Attributes</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-primitive-function">primitive function</a>:</td><td>&nbsp;</td><td valign="top"><a href="#Argument-evaluation">Argument evaluation</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-promise">promise</a>:</td><td>&nbsp;</td><td valign="top"><a href="#Rest-of-header">Rest of header</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-S4-type">S4 type</a>:</td><td>&nbsp;</td><td valign="top"><a href="#SEXPTYPEs">SEXPTYPEs</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-search-path">search path</a>:</td><td>&nbsp;</td><td valign="top"><a href="#Search-paths">Search paths</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-serialization">serialization</a>:</td><td>&nbsp;</td><td valign="top"><a href="#Serialization-Formats">Serialization Formats</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-SEXP">SEXP</a>:</td><td>&nbsp;</td><td valign="top"><a href="#SEXPs">SEXPs</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-SEXPRREC">SEXPRREC</a>:</td><td>&nbsp;</td><td valign="top"><a href="#SEXPs">SEXPs</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-SEXPTYPE">SEXPTYPE</a>:</td><td>&nbsp;</td><td valign="top"><a href="#SEXPTYPEs">SEXPTYPEs</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-SEXPTYPE-table">SEXPTYPE table</a>:</td><td>&nbsp;</td><td valign="top"><a href="#SEXPTYPEs">SEXPTYPEs</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-special-function">special function</a>:</td><td>&nbsp;</td><td valign="top"><a href="#Argument-evaluation">Argument evaluation</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-databases">user databases</a>:</td><td>&nbsp;</td><td valign="top"><a href="#Environments-and-variable-lookup">Environments and variable lookup</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-variable-lookup">variable lookup</a>:</td><td>&nbsp;</td><td valign="top"><a href="#Environments-and-variable-lookup">Environments and variable lookup</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-vector-type">vector type</a>:</td><td>&nbsp;</td><td valign="top"><a href="#The-_0027data_0027">The 'data'</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-visibility">visibility</a>:</td><td>&nbsp;</td><td valign="top"><a href="#Visibility">Visibility</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-write-barrier">write barrier</a>:</td><td>&nbsp;</td><td valign="top"><a href="#The-write-barrier">The write barrier</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
</table>
<table summary=""><tr><th valign="top">Jump to: &nbsp; </th><td><a class="summary-letter" href="#Concept-index_cp_symbol-1"><b>.</b></a>
 &nbsp; 
<br>
<a class="summary-letter" href="#Concept-index_cp_letter-A"><b>A</b></a>
 &nbsp; 
<a class="summary-letter" href="#Concept-index_cp_letter-B"><b>B</b></a>
 &nbsp; 
<a class="summary-letter" href="#Concept-index_cp_letter-C"><b>C</b></a>
 &nbsp; 
<a class="summary-letter" href="#Concept-index_cp_letter-E"><b>E</b></a>
 &nbsp; 
<a class="summary-letter" href="#Concept-index_cp_letter-F"><b>F</b></a>
 &nbsp; 
<a class="summary-letter" href="#Concept-index_cp_letter-G"><b>G</b></a>
 &nbsp; 
<a class="summary-letter" href="#Concept-index_cp_letter-L"><b>L</b></a>
 &nbsp; 
<a class="summary-letter" href="#Concept-index_cp_letter-M"><b>M</b></a>
 &nbsp; 
<a class="summary-letter" href="#Concept-index_cp_letter-N"><b>N</b></a>
 &nbsp; 
<a class="summary-letter" href="#Concept-index_cp_letter-P"><b>P</b></a>
 &nbsp; 
<a class="summary-letter" href="#Concept-index_cp_letter-S"><b>S</b></a>
 &nbsp; 
<a class="summary-letter" href="#Concept-index_cp_letter-U"><b>U</b></a>
 &nbsp; 
<a class="summary-letter" href="#Concept-index_cp_letter-V"><b>V</b></a>
 &nbsp; 
<a class="summary-letter" href="#Concept-index_cp_letter-W"><b>W</b></a>
 &nbsp; 
</td></tr></table>

<div class="footnote">
<hr>
<h4 class="footnotes-heading">Footnotes</h4>

<h3><a name="FOOT1" href="#DOCF1">(1)</a></h3>
<p>strictly, a <code>SEXPREC</code>
node; <code>VECTOR_SEXPREC</code> nodes are slightly smaller but followed by
data in the node.</p>
<h3><a name="FOOT2" href="#DOCF2">(2)</a></h3>
<p>a pointer to a function or a symbol to look up the
function by name, or a language object to be evaluated to give a
function.</p>
<h3><a name="FOOT3" href="#DOCF3">(3)</a></h3>
<p>This is almost unused.  The only
current use is for hash tables of environments (<code>VECSXP</code>s), where
<code>length</code> is the size of the table and <code>truelength</code> is the
number of primary slots in use, and for the reference hash tables in
serialization (<code>VECSXP</code>s), where <code>truelength</code> is the number of
slots in use.</p>
<h3><a name="FOOT4" href="#DOCF4">(4)</a></h3>
<p>Remember that attaching a list or
a saved image actually creates and populates an environment and attaches
that.</p>
<h3><a name="FOOT5" href="#DOCF5">(5)</a></h3>
<p>There is currently one other
difference: when profiling builtin functions are counted as function
calls but specials are not.</p>
<h3><a name="FOOT6" href="#DOCF6">(6)</a></h3>
<p>the other current example
is left brace, which is implemented as a primitive.</p>
<h3><a name="FOOT7" href="#DOCF7">(7)</a></h3>
<p>only bits 0:4 are currently used
for <code>SEXPTYPE</code>s but values 241:255 are used for
pseudo-<code>SEXPTYPE</code>s.</p>
<h3><a name="FOOT8" href="#DOCF8">(8)</a></h3>
<p>Currently the only relevant bits are 0:1, 4, 14:15.</p>
<h3><a name="FOOT9" href="#DOCF9">(9)</a></h3>
<p>See define
<code>USE_UTF8_IF_POSSIBLE</code> in file <samp>src/main/gram.c</samp>.</p>
<h3><a name="FOOT10" href="#DOCF10">(10)</a></h3>
<p>or UTF-16 if support for surrogates is enabled in the OS,
which it is not normally so at least for Western versions of Windows,
despite some claims to the contrary on the Microsoft website.</p>
<h3><a name="FOOT11" href="#DOCF11">(11)</a></h3>
<p>but not the
GraphApp toolkit.</p>
<h3><a name="FOOT12" href="#DOCF12">(12)</a></h3>
<p>This can also create
non-S4 objects, as in <code>new(&quot;integer&quot;)</code>.</p>
<h3><a name="FOOT13" href="#DOCF13">(13)</a></h3>
<p>although this is
not recommended as it is less future-proof.</p>
<h3><a name="FOOT14" href="#DOCF14">(14)</a></h3>
<p>but apparently not on Windows.</p>
<h3><a name="FOOT15" href="#DOCF15">(15)</a></h3>
<p>The C code is in files
<code>base.c</code>, <code>graphics.c</code>, <code>par.c</code>, <code>plot.c</code> and
<code>plot3d.c</code> in directory <samp>src/main</samp>.</p>
<h3><a name="FOOT16" href="#DOCF16">(16)</a></h3>
<p>although that needs to be
handled carefully, as for example the <code>circle</code> callback is given a
radius (and that should be interpreted as in the x units).</p>
<h3><a name="FOOT17" href="#DOCF17">(17)</a></h3>
<p>It is
possible for the device to find the <code>GEDevDesc</code> which points to its
<code>DevDesc</code>, and this is done often enough that there is a
convenience function <code>desc2GEDesc</code> to do so.</p>
<h3><a name="FOOT18" href="#DOCF18">(18)</a></h3>
<p>Calling
<code>R_CheckDeviceAvailable()</code> ensures there is a free slot or throws
an error.</p>
<h3><a name="FOOT19" href="#DOCF19">(19)</a></h3>
<p>in device coordinates</p>
<h3><a name="FOOT20" href="#DOCF20">(20)</a></h3>
<p>It is technically possible to use alpha-blending on
metafile devices such as printers, but it seems few drivers have support
for this.</p>
<h3><a name="FOOT21" href="#DOCF21">(21)</a></h3>
<p>an Xcode project, in SVN at
<a href="https://svn.r-project.org/R-packages/trunk/Mac-GUI">https://svn.r-project.org/R-packages/trunk/Mac-GUI</a>.</p>
<h3><a name="FOOT22" href="#DOCF22">(22)</a></h3>
<p>under Windows, junction points, or copies if
environment variable <code>R_WIN_NO_JUNCTIONS</code> has a non-empty value.</p>
<h3><a name="FOOT23" href="#DOCF23">(23)</a></h3>
<p>see the previous footnote.</p>
<h3><a name="FOOT24" href="#DOCF24">(24)</a></h3>
<p>Linux
distributions tend to unbundle <samp>texinfo.tex</samp> from &lsquo;<samp>texinfo</samp>&rsquo;.</p>
<h3><a name="FOOT25" href="#DOCF25">(25)</a></h3>
<p>but <code>LENGTH</code> is a macro under some internal
uses.</p>
</div>
<hr>



</body>
</html>