- using R version 4.5.2 Patched (2026-01-31 r89382)
- using platform: aarch64-apple-darwin20
- R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
- running under: macOS Ventura 13.7.8
- using session charset: UTF-8
- checking for file ‘Nestimate/DESCRIPTION’ ... OK
- this is package ‘Nestimate’ version ‘0.3.0’
- package encoding: UTF-8
- checking package namespace information ... OK
- checking package dependencies ... OK
- checking if this is a source package ... OK
- checking if there is a namespace ... OK
- checking for executable files ... OK
- checking for hidden files and directories ... OK
- checking for portable file names ... OK
- checking for sufficient/correct file permissions ... OK
- checking whether package ‘Nestimate’ can be installed ... [6s/6s] OK
See the install log for details.
- checking installed package size ... OK
- checking package directory ... OK
- checking ‘build’ directory ... OK
- checking DESCRIPTION meta-information ... OK
- checking top-level files ... OK
- checking for left-over files ... OK
- checking index information ... OK
- checking package subdirectories ... OK
- checking code files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... [0s/0s] OK
- checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
- checking whether the package can be unloaded cleanly ... [0s/0s] OK
- checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
- checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
- checking loading without being on the library search path ... [0s/0s] OK
- checking whether startup messages can be suppressed ... [0s/0s] OK
- checking dependencies in R code ... OK
- checking S3 generic/method consistency ... OK
- checking replacement functions ... OK
- checking foreign function calls ... OK
- checking R code for possible problems ... [6s/6s] OK
- checking Rd files ... [0s/0s] OK
- checking Rd metadata ... OK
- checking Rd cross-references ... OK
- checking for missing documentation entries ... OK
- checking for code/documentation mismatches ... OK
- checking Rd \usage sections ... OK
- checking Rd contents ... OK
- checking for unstated dependencies in examples ... OK
- checking contents of ‘data’ directory ... OK
- checking data for non-ASCII characters ... [1s/1s] OK
- checking LazyData ... OK
- checking data for ASCII and uncompressed saves ... OK
- checking installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... [2s/2s] OK
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [158s/163s] ERROR
Running ‘testthat.R’ [158s/163s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(Nestimate)
>
> test_check("Nestimate")
antecedent consequent support confidence lift conviction count
butter,milk eggs 0.4 1.0000 1.6667 Inf 2
eggs butter,milk 0.4 0.6667 1.6667 1.8 2
eggs milk 0.6 1.0000 1.2500 Inf 3
milk eggs 0.6 0.7500 1.2500 1.6 3
bread,eggs milk 0.4 1.0000 1.2500 Inf 2
butter,eggs milk 0.4 1.0000 1.2500 Inf 2
milk bread,eggs 0.4 0.5000 1.2500 1.2 2
milk butter,eggs 0.4 0.5000 1.2500 1.2 2
butter eggs 0.4 0.6667 1.1111 1.2 2
eggs butter 0.4 0.6667 1.1111 1.2 2
eggs bread,milk 0.4 0.6667 1.1111 1.2 2
bread,milk eggs 0.4 0.6667 1.1111 1.2 2
butter eggs,milk 0.4 0.6667 1.1111 1.2 2
eggs,milk butter 0.4 0.6667 1.1111 1.2 2
bread milk 0.6 0.7500 0.9375 0.8 3
milk bread 0.6 0.7500 0.9375 0.8 3
butter bread 0.4 0.6667 0.8333 0.6 2
eggs bread 0.4 0.6667 0.8333 0.6 2
butter milk 0.4 0.6667 0.8333 0.6 2
eggs,milk bread 0.4 0.6667 0.8333 0.6 2
bread butter 0.4 0.5000 0.8333 0.8 2
bread eggs 0.4 0.5000 0.8333 0.8 2
milk butter 0.4 0.5000 0.8333 0.8 2
bread eggs,milk 0.4 0.5000 0.8333 0.8 2
Metadata aggregated per session: ties resolved by first occurrence in 'code' (628 sessions), 'superclass' (158 sessions)
Multilevel Network (method: glasso)
-- Between-person --
Nodes: 3 | Edges: 0
Sample size: 20 (unique persons)
-- Within-person --
Nodes: 3 | Edges: 1
Sample size: 100 (observations)
Dropping non-syntactic columns: -0.0386419585834719, -0.0493752388182795, -0.143883408448767, -0.145077995956477, -0.222731942460929, -0.267762662765084, -0.376290756562357, -0.4563032693248, -0.475954635098868, -0.559970597875912, -0.644301463842431, -0.64562667761188, -0.688165944958397, -0.852405668800981, -0.892351954877378, -0.894775408854386, -0.917059466430073, -0.94773529068477, -0.998483923239605, -1.04042150945666, -1.09622406181774, -1.13070669385375, -1.20698680795195, -1.21434372820731, -1.40329484443177, -1.5468497009493, -1.61523891387173, -1.89440229591065, -2.10724139764119, 0.0429042307597339, 0.126909754004865, 0.201435319313383, 0.233476373591858, 0.314984939268516, 0.384985274109401, 0.468157951289336, 0.616796373421824, 0.666208635425536, 0.735664089599338, 0.758168827559491, 0.770061049420852, 0.786147216190763, 0.817544036941218, 0.904860838377467, 0.917327777548806, 0.989354069117418, 1.09221080842836, 1.24111623986206, 1.59568403496008, 1.76797780755595
Dropping non-syntactic columns: 0, 1, 10, 100, 1000, 1001, 1002, 1003, 1004, 1005, 1006, 1007, 1008, 1009, 101, 1010, 1011, 1012, 1013, 1014, 1015, 1016, 1017, 1018, 1019, 102, 1020, 1021, 1022, 1023, 1024, 1025, 1026, 1027, 1028, 1029, 103, 1030, 1031, 1032, 1033, 1034, 1035, 1036, 1037, 1038, 1039, 104, 1040, 1041, 1042, 1043, 1044, 1045, 1046, 1047, 1048, 1049, 105, 1050, 1051, 1052, 1053, 1054, 1055, 1056, 1057, 1058, 1059, 106, 1060, 1061, 1062, 1063, 1064, 1065, 1066, 1067, 1068, 1069, 107, 1070, 1071, 1072, 1073, 1074, 1075, 1076, 1077, 1078, 1079, 108, 1080, 1081, 1082, 1083, 1084, 1085, 1086, 1087, 1088, 1089, 109, 1090, 1091, 1092, 1093, 1094, 1095, 1096, 1097, 1098, 1099, 11, 110, 1100, 1101, 1102, 1103, 1104, 1105, 1106, 1107, 1108, 1109, 111, 1110, 1111, 1112, 1113, 1114, 1115, 1116, 1117, 1118, 1119, 112, 1120, 1121, 1122, 1123, 1124, 1125, 1126, 1127, 1128, 1129, 113, 1130, 1131, 1132, 1133, 1134, 1135, 1136, 1137, 1138, 1139, 114, 1140, 1141, 1142, 1143, 1144, 1145, 1146, 1147, 1148, 1149, 115, 1150, 1151, 1152, 1153, 1154, 1155, 1156, 1157, 1158, 1159, 116, 1160, 1161, 1162, 1163, 1164, 1165, 1166, 1167, 1168, 1169, 117, 1170, 1171, 1172, 1173, 1174, 1175, 1176, 1177, 1178, 1179, 118, 1180, 1181, 1182, 1183, 1184, 1185, 1186, 1187, 1188, 1189, 119, 1190, 1191, 1192, 1193, 1194, 1195, 1196, 1197, 1198, 1199, 12, 120, 1200, 1201, 1202, 1203, 1204, 1205, 1206, 1207, 1208, 1209, 121, 1210, 1211, 1212, 1213, 1214, 1215, 1216, 1217, 1218, 1219, 122, 1220, 1221, 1222, 1223, 1224, 1225, 1226, 1227, 1228, 1229, 123, 1230, 1231, 1232, 1233, 1234, 1235, 1236, 1237, 1238, 1239, 124, 1240, 1241, 1242, 1243, 1244, 1245, 1246, 1247, 1248, 1249, 125, 1250, 1251, 1252, 1253, 1254, 1255, 1256, 1257, 1258, 1259, 126, 1260, 1261, 1262, 1263, 1264, 1265, 1266, 1267, 1268, 1269, 127, 1270, 1271, 1272, 1273, 1274, 1275, 1276, 1277, 1278, 1279, 128, 1280, 1281, 1282, 1283, 1284, 1285, 1286, 1287, 1288, 1289, 129, 1290, 1291, 1292, 1293, 1294, 1295, 1296, 1297, 1298, 1299, 13, 130, 1300, 1301, 1302, 1303, 1304, 1305, 1306, 1307, 1308, 1309, 131, 1310, 1311, 1312, 1313, 1314, 1315, 1316, 1317, 1318, 1319, 132, 1320, 1321, 1322, 1323, 1324, 1325, 1326, 1327, 1328, 1329, 133, 1330, 1331, 1332, 1333, 1334, 1335, 1336, 1337, 1338, 1339, 134, 1340, 1341, 1342, 1343, 1344, 1345, 1346, 1347, 1348, 1349, 135, 1350, 1351, 1352, 1353, 1354, 1355, 1356, 1357, 1358, 1359, 136, 1360, 1361, 1362, 1363, 1364, 1365, 1366, 1367, 1368, 1369, 137, 1370, 1371, 1372, 1373, 1374, 1375, 1376, 1377, 1378, 1379, 138, 1380, 1381, 1382, 1383, 1384, 1385, 1386, 1387, 1388, 1389, 139, 1390, 1391, 1392, 1393, 1394, 1395, 1396, 1397, 1398, 1399, 14, 140, 1400, 1401, 1402, 1403, 1404, 1405, 1406, 1407, 1408, 1409, 141, 1410, 1411, 1412, 1413, 1414, 1415, 1416, 1417, 1418, 1419, 142, 1420, 1421, 1422, 1423, 1424, 1425, 1426, 1427, 1428, 1429, 143, 1430, 1431, 1432, 1433, 1434, 1435, 1436, 1437, 1438, 1439, 144, 1440, 1441, 1442, 1443, 1444, 1445, 1446, 1447, 1448, 1449, 145, 1450, 1451, 1452, 1453, 1454, 1455, 1456, 1457, 1458, 1459, 146, 1460, 1461, 1462, 1463, 1464, 1465, 1466, 1467, 1468, 1469, 147, 1470, 1471, 1472, 1473, 1474, 1475, 1476, 1477, 1478, 1479, 148, 1480, 1481, 1482, 1483, 1484, 1485, 1486, 1487, 1488, 1489, 149, 1490, 1491, 1492, 1493, 1494, 1495, 1496, 1497, 1498, 1499, 15, 150, 1500, 1501, 1502, 1503, 1504, 1505, 1506, 1507, 1508, 1509, 151, 1510, 1511, 1512, 1513, 1514, 1515, 1516, 1517, 1518, 1519, 152, 1520, 1521, 1522, 1523, 1524, 1525, 1526, 1527, 1528, 1529, 153, 1530, 1531, 1532, 1533, 1534, 1535, 1536, 1537, 1538, 1539, 154, 1540, 1541, 1542, 1543, 1544, 1545, 1546, 1547, 1548, 1549, 155, 1550, 1551, 1552, 1553, 1554, 1555, 1556, 1557, 1558, 1559, 156, 1560, 1561, 1562, 1563, 1564, 1565, 1566, 1567, 1568, 1569, 157, 1570, 1571, 1572, 1573, 1574, 1575, 1576, 1577, 1578, 1579, 158, 1580, 1581, 1582, 1583, 1584, 1585, 1586, 1587, 1588, 1589, 159, 1590, 1591, 1592, 1593, 1594, 1595, 1596, 1597, 1598, 1599, 16, 160, 1600, 1601, 1602, 1603, 1604, 1605, 1606, 1607, 1608, 1609, 161, 1610, 1611, 1612, 1613, 1614, 1615, 1616, 1617, 1618, 1619, 162, 1620, 1621, 1622, 1623, 1624, 1625, 1626, 1627, 1628, 1629, 163, 1630, 1631, 1632, 1633, 1634, 1635, 1636, 1637, 1638, 1639, 164, 1640, 1641, 1642, 1643, 1644, 1645, 1646, 1647, 1648, 1649, 165, 1650, 1651, 1652, 1653, 1654, 1655, 1656, 1657, 1658, 1659, 166, 1660, 1661, 1662, 1663, 1664, 1665, 1666, 1667, 1668, 1669, 167, 1670, 1671, 1672, 1673, 1674, 1675, 1676, 1677, 1678, 1679, 168, 1680, 1681, 1682, 1683, 1684, 1685, 1686, 1687, 1688, 1689, 169, 1690, 1691, 1692, 1693, 1694, 1695, 1696, 1697, 1698, 1699, 17, 170, 1700, 1701, 1702, 1703, 1704, 1705, 1706, 1707, 1708, 1709, 171, 1710, 1711, 1712, 1713, 1714, 1715, 1716, 1717, 1718, 1719, 172, 1720, 1721, 1722, 1723, 1724, 1725, 1726, 1727, 1728, 1729, 173, 1730, 1731, 1732, 1733, 1734, 1735, 1736, 1737, 1738, 1739, 174, 1740, 1741, 1742, 1743, 1744, 1745, 1746, 1747, 1748, 1749, 175, 1750, 1751, 1752, 1753, 1754, 1755, 1756, 1757, 1758, 1759, 176, 1760, 1761, 1762, 1763, 1764, 1765, 1766, 1767, 1768, 1769, 177, 1770, 1771, 1772, 1773, 1774, 1775, 1776, 1777, 1778, 1779, 178, 1780, 1781, 1782, 1783, 1784, 1785, 1786, 1787, 1788, 1789, 179, 1790, 1791, 1792, 1793, 1794, 1795, 1796, 1797, 1798, 1799, 18, 180, 1800, 1801, 1802, 1803, 1804, 1805, 1806, 1807, 1808, 1809, 181, 1810, 1811, 1812, 1813, 1814, 1815, 1816, 1817, 1818, 1819, 182, 1820, 1821, 1822, 1823, 1824, 1825, 1826, 1827, 1828, 1829, 183, 1830, 1831, 1832, 1833, 1834, 1835, 1836, 1837, 1838, 1839, 184, 1840, 1841, 1842, 1843, 1844, 1845, 1846, 1847, 1848, 1849, 185, 1850, 1851, 1852, 1853, 1854, 1855, 1856, 1857, 1858, 1859, 186, 1860, 1861, 1862, 1863, 1864, 1865, 1866, 1867, 1868, 1869, 187, 1870, 1871, 1872, 1873, 1874, 1875, 1876, 1877, 1878, 1879, 188, 1880, 1881, 1882, 1883, 1884, 1885, 1886, 1887, 1888, 1889, 189, 1890, 1891, 1892, 1893, 1894, 1895, 1896, 1897, 1898, 1899, 19, 190, 1900, 1901, 1902, 1903, 1904, 1905, 1906, 1907, 1908, 1909, 191, 1910, 1911, 1912, 1913, 1914, 1915, 1916, 1917, 1918, 1919, 192, 1920, 1921, 1922, 1923, 1924, 1925, 1926, 1927, 1928, 1929, 193, 1930, 1931, 1932, 1933, 1934, 1935, 1936, 1937, 1938, 1939, 194, 1940, 1941, 1942, 1943, 1944, 1945, 1946, 1947, 1948, 1949, 195, 1950, 1951, 1952, 1953, 1954, 1955, 1956, 1957, 1958, 1959, 196, 1960, 1961, 1962, 1963, 1964, 1965, 1966, 1967, 1968, 1969, 197, 1970, 1971, 1972, 1973, 1974, 1975, 1976, 1977, 1978, 1979, 198, 1980, 1981, 1982, 1983, 1984, 1985, 1986, 1987, 1988, 1989, 199, 1990, 1991, 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2, 20, 200, 2000, 201, 202, 203, 204, 205, 206, 207, 208, 209, 21, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 22, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 23, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 24, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 25, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 26, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 27, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 28, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 29, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 3, 30, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 31, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 32, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 33, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 34, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 35, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 36, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 37, 370, 371, 372, 373, 374, 375, 376, 377, 378, 379, 38, 380, 381, 382, 383, 384, 385, 386, 387, 388, 389, 39, 390, 391, 392, 393, 394, 395, 396, 397, 398, 399, 4, 40, 400, 401, 402, 403, 404, 405, 406, 407, 408, 409, 41, 410, 411, 412, 413, 414, 415, 416, 417, 418, 419, 42, 420, 421, 422, 423, 424, 425, 426, 427, 428, 429, 43, 430, 431, 432, 433, 434, 435, 436, 437, 438, 439, 44, 440, 441, 442, 443, 444, 445, 446, 447, 448, 449, 45, 450, 451, 452, 453, 454, 455, 456, 457, 458, 459, 46, 460, 461, 462, 463, 464, 465, 466, 467, 468, 469, 47, 470, 471, 472, 473, 474, 475, 476, 477, 478, 479, 48, 480, 481, 482, 483, 484, 485, 486, 487, 488, 489, 49, 490, 491, 492, 493, 494, 495, 496, 497, 498, 499, 5, 50, 500, 501, 502, 503, 504, 505, 506, 507, 508, 509, 51, 510, 511, 512, 513, 514, 515, 516, 517, 518, 519, 52, 520, 521, 522, 523, 524, 525, 526, 527, 528, 529, 53, 530, 531, 532, 533, 534, 535, 536, 537, 538, 539, 54, 540, 541, 542, 543, 544, 545, 546, 547, 548, 549, 55, 550, 551, 552, 553, 554, 555, 556, 557, 558, 559, 56, 560, 561, 562, 563, 564, 565, 566, 567, 568, 569, 57, 570, 571, 572, 573, 574, 575, 576, 577, 578, 579, 58, 580, 581, 582, 583, 584, 585, 586, 587, 588, 589, 59, 590, 591, 592, 593, 594, 595, 596, 597, 598, 599, 6, 60, 600, 601, 602, 603, 604, 605, 606, 607, 608, 609, 61, 610, 611, 612, 613, 614, 615, 616, 617, 618, 619, 62, 620, 621, 622, 623, 624, 625, 626, 627, 628, 629, 63, 630, 631, 632, 633, 634, 635, 636, 637, 638, 639, 64, 640, 641, 642, 643, 644, 645, 646, 647, 648, 649, 65, 650, 651, 652, 653, 654, 655, 656, 657, 658, 659, 66, 660, 661, 662, 663, 664, 665, 666, 667, 668, 669, 67, 670, 671, 672, 673, 674, 675, 676, 677, 678, 679, 68, 680, 681, 682, 683, 684, 685, 686, 687, 688, 689, 69, 690, 691, 692, 693, 694, 695, 696, 697, 698, 699, 7, 70, 700, 701, 702, 703, 704, 705, 706, 707, 708, 709, 71, 710, 711, 712, 713, 714, 715, 716, 717, 718, 719, 72, 720, 721, 722, 723, 724, 725, 726, 727, 728, 729, 73, 730, 731, 732, 733, 734, 735, 736, 737, 738, 739, 74, 740, 741, 742, 743, 744, 745, 746, 747, 748, 749, 75, 750, 751, 752, 753, 754, 755, 756, 757, 758, 759, 76, 760, 761, 762, 763, 764, 765, 766, 767, 768, 769, 77, 770, 771, 772, 773, 774, 775, 776, 777, 778, 779, 78, 780, 781, 782, 783, 784, 785, 786, 787, 788, 789, 79, 790, 791, 792, 793, 794, 795, 796, 797, 798, 799, 8, 80, 800, 801, 802, 803, 804, 805, 806, 807, 808, 809, 81, 810, 811, 812, 813, 814, 815, 816, 817, 818, 819, 82, 820, 821, 822, 823, 824, 825, 826, 827, 828, 829, 83, 830, 831, 832, 833, 834, 835, 836, 837, 838, 839, 84, 840, 841, 842, 843, 844, 845, 846, 847, 848, 849, 85, 850, 851, 852, 853, 854, 855, 856, 857, 858, 859, 86, 860, 861, 862, 863, 864, 865, 866, 867, 868, 869, 87, 870, 871, 872, 873, 874, 875, 876, 877, 878, 879, 88, 880, 881, 882, 883, 884, 885, 886, 887, 888, 889, 89, 890, 891, 892, 893, 894, 895, 896, 897, 898, 899, 9, 90, 900, 901, 902, 903, 904, 905, 906, 907, 908, 909, 91, 910, 911, 912, 913, 914, 915, 916, 917, 918, 919, 92, 920, 921, 922, 923, 924, 925, 926, 927, 928, 929, 93, 930, 931, 932, 933, 934, 935, 936, 937, 938, 939, 94, 940, 941, 942, 943, 944, 945, 946, 947, 948, 949, 95, 950, 951, 952, 953, 954, 955, 956, 957, 958, 959, 96, 960, 961, 962, 963, 964, 965, 966, 967, 968, 969, 97, 970, 971, 972, 973, 974, 975, 976, 977, 978, 979, 98, 980, 981, 982, 983, 984, 985, 986, 987, 988, 989, 99, 990, 991, 992, 993, 994, 995, 996, 997, 998, 999
Dropping 2 single-observation rows (within-person centering).
Dropping 3 rows with NA values.
NOTICE: One A matrix provided. No subgroups generated.
group-level search
individual-level search, subject 1 (sub_01)
individual-level search, subject 2 (sub_02)
individual-level search, subject 3 (sub_03)
individual-level search, subject 4 (sub_04)
individual-level search, subject 5 (sub_05)
individual-level search, subject 6 (sub_06)
individual-level search, subject 7 (sub_07)
individual-level search, subject 8 (sub_08)
individual-level search, subject 9 (sub_09)
individual-level search, subject 10 (sub_10)
individual-level search, subject 11 (sub_11)
individual-level search, subject 12 (sub_12)
gimme finished running normally
output is stored in /Volumes/Temp/tmp/RtmpJo8avU/gimme_equiv_out
NOTICE: One A matrix provided. No subgroups generated.
group-level search
individual-level search, subject 1 (sub_01)
individual-level search, subject 2 (sub_02)
individual-level search, subject 3 (sub_03)
individual-level search, subject 4 (sub_04)
individual-level search, subject 5 (sub_05)
individual-level search, subject 6 (sub_06)
individual-level search, subject 7 (sub_07)
individual-level search, subject 8 (sub_08)
individual-level search, subject 9 (sub_09)
individual-level search, subject 10 (sub_10)
individual-level search, subject 11 (sub_11)
individual-level search, subject 12 (sub_12)
gimme finished running normally
output is stored in /Volumes/Temp/tmp/RtmpJo8avU/gimme_equiv_out2
NOTICE: One A matrix provided. No subgroups generated.
group-level search
individual-level search, subject 1 (sub_01)
individual-level search, subject 2 (sub_02)
individual-level search, subject 3 (sub_03)
individual-level search, subject 4 (sub_04)
individual-level search, subject 5 (sub_05)
individual-level search, subject 6 (sub_06)
individual-level search, subject 7 (sub_07)
individual-level search, subject 8 (sub_08)
gimme finished running normally
output is stored in /Volumes/Temp/tmp/RtmpJo8avU/gimme_equiv_out3
method n_predictions score_mean score_sd score_max
common_neighbors 5 0.24554091 0.025361007 0.28752003
resource_allocation 5 0.01952464 0.003175748 0.02494878
adamic_adar 5 0.09671932 0.012386162 0.11741831
jaccard 5 0.03775938 0.002096290 0.04141314
preferential_attachment 5 35.60000000 4.277849927 42.00000000
katz 5 0.98604784 0.100755707 1.12595954
score_min
0.21843750
0.01668069
0.08406102
0.03624546
30.00000000
0.84853836
Metadata aggregated per session: ties resolved by first occurrence in 'code' (628 sessions), 'superclass' (158 sessions)
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: .mmm_em(counts, init_state, k, screen_iter, tol, smooth, n_states, init_posterior = init, from_ind = from_ind, cov_df = NULL)
2: FUN(X[[i]], ...)
3: lapply(X = S, FUN = FUN, ...)
Traceback:
1: .mmm_em(counts, init_state, k, screen_iter, tol, smooth, n_states, init_posterior = init, from_ind = from_ind, cov_df = NULL)
2: FUN(X[[i]], ...)
3: lapply(X = S, FUN = FUN, ...)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") 4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]]) .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
8: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
9: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
6: tryCatchList(expr, classes, parentenv, handlers)
7: 10: FUN(X[[i]], ...)
11: lapply(seq_len(cores), inner.do)
tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L)12: parallel::mclapply(inits, .run_screen, mc.cores = n_cores)
13: build_mmm(model, k = 2, n_starts = 3, seed = 1) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : "
14: eval(code, test_env)
15: msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
8: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
9: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
10: eval(code, test_env)
16: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) {FUN(X[[i]], ...)
11: lapply(seq_len(cores), inner.do)
12: parallel::mclapply(inits, .run_screen, mc.cores = n_cores)
13: skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) {build_mmm(model, k = 2, n_starts = 3, seed = 1)
14: eval(code, test_env)
15: eval(code, test_env) snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
17:
16: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectationsdoTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)
if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty()20: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) } skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed."))}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")
17: doTryCatch(return(expr), name, parentenv, handler)
18: }, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
21: doWithOneRestart(return(expr), restart)
22: withOneRestart(expr, restarts[[1L]])tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)
23: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty()20: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) } skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
24: test_code(code, parent.frame())
25: }, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
21: doWithOneRestart(return(expr), restart)
22: withOneRestart(expr, restarts[[1L]])
23: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") }test_that("build_mmm works with tna input", { skip_if_not_installed("tna") model <- tna::tna(tna::group_regulation) mmm <- build_mmm(model, k = 2, n_starts = 3, seed = 1) expect_s3_class(mmm, "net_mmm") expect_equal(mmm$k, 2) expect_true(length(mmm$states) > 2)}) else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) {
26: eval(code, test_env)
27: eval(code, test_env)
28: withCallingHandlers({ eval(code, test_env) skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { end_test = function() { })
24: test_code(code, parent.frame()) skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message,
25: test_that("build_mmm works with tna input", { skip_if_not_installed("tna") model <- tna::tna(tna::group_regulation) mmm <- build_mmm(model, k = 2, n_starts = 3, seed = 1) expect_s3_class(mmm, "net_mmm") expect_equal(mmm$k, 2) expect_true(length(mmm$states) > 2)}) error = handle_error, interrupt = handle_interrupt)
29: doTryCatch(return(expr), name, parentenv, handler)
30: tryCatchOne(expr, names, parentenv, handlers[[1L]])
31:
26: eval(code, test_env)
27: eval(code, test_env)
tryCatchList(expr, classes, parentenv, handlers)
32: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations28: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) } if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty()}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt) }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE
29: doTryCatch(return(expr), name, parentenv, handler)
30: invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
tryCatchOne(expr, names, parentenv, handlers[[1L]])
31: tryCatchList(expr, classes, parentenv, handlers)
32: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }33: doWithOneRestart(return(expr), restart)
34: withOneRestart(expr, restarts[[1L]])
35: withRestarts(tryCatch(withCallingHandlers({}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
33: doWithOneRestart(return(expr), restart) eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) {
34: withOneRestart(expr, restarts[[1L]])
35: skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed."))withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) {}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { }) snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
36:
36: test_code(code = exprs, env = env, reporter = get_reporter() %||% test_code(code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new())
37: source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call)
38: FUN(X[[i]], ...)
StopReporter$new())
37: source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call)
38: FUN(X[[i]], ...)39: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)
40:
39: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)
doTryCatch(return(expr), name, parentenv, handler)
41: tryCatchOne(expr, names, parentenv, handlers[[1L]])
40: doTryCatch(return(expr), name, parentenv, handler)
41: tryCatchOne(expr, names, parentenv, handlers[[1L]])42: tryCatchList(expr, classes, parentenv, handlers)
43: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
42: tryCatchList(expr, classes, parentenv, handlers)
43: tryCatch(code, testthat_abort_reporter = function(cnd) {
44: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call))
cat(conditionMessage(cnd), "\n") NULL})
44: 45: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, shuffle = shuffle, with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call))
45: test_files_serial(test_dir = test_dir, test_package = test_package, error_call = error_call)
46: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel, shuffle = shuffle)
47: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
48: test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, shuffle = shuffle, error_call = error_call)
46: test_check("Nestimate")
An irrecoverable exception occurred. R is aborting now ...
test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel, shuffle = shuffle)
47: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
48: test_check("Nestimate")
An irrecoverable exception occurred. R is aborting now ...
Traceback:
1: .mmm_em(counts, init_state, k, screen_iter, tol, smooth, n_states, init_posterior = init, from_ind = from_ind, cov_df = NULL)
2: FUN(X[[i]], ...)
3: lapply(X = S, FUN = FUN, ...)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
8: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
9: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
10: FUN(X[[i]], ...)
11: lapply(seq_len(cores), inner.do)
12: parallel::mclapply(inits, .run_screen, mc.cores = n_cores)
13: build_mmm(model, k = 2, n_starts = 3, seed = 1)
14: eval(code, test_env)
15: eval(code, test_env)
16: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
17: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)
20: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
21: doWithOneRestart(return(expr), restart)
22: withOneRestart(expr, restarts[[1L]])
23: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
24: test_code(code, parent.frame())
25: test_that("build_mmm works with tna input", { skip_if_not_installed("tna") model <- tna::tna(tna::group_regulation) mmm <- build_mmm(model, k = 2, n_starts = 3, seed = 1) expect_s3_class(mmm, "net_mmm") expect_equal(mmm$k, 2) expect_true(length(mmm$states) > 2)})
26: eval(code, test_env)
27: eval(code, test_env)
28: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
29: doTryCatch(return(expr), name, parentenv, handler)
30: tryCatchOne(expr, names, parentenv, handlers[[1L]])
31: tryCatchList(expr, classes, parentenv, handlers)
32: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
33: doWithOneRestart(return(expr), restart)
34: withOneRestart(expr, restarts[[1L]])
35: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
36: test_code(code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new())
37: source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call)
38: FUN(X[[i]], ...)
39: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)
40: doTryCatch(return(expr), name, parentenv, handler)
41: tryCatchOne(expr, names, parentenv, handlers[[1L]])
42: tryCatchList(expr, classes, parentenv, handlers)
43: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
44: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call))
45: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, shuffle = shuffle, error_call = error_call)
46: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel, shuffle = shuffle)
47: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
48: test_check("Nestimate")
An irrecoverable exception occurred. R is aborting now ...
Saving _problems/test-mmm-173.R
Metadata aggregated per session: ties resolved by first occurrence in 'timestamp' (2 sessions)
Metadata aggregated per session: ties resolved by first occurrence in 'timestamp' (2 sessions)
[ FAIL 1 | WARN 1 | SKIP 17 | PASS 2937 ]
══ Skipped tests (17) ══════════════════════════════════════════════════════════
• No metadata column detected in this data (1): 'test-build_network.R:851:5'
• Python not available (9): 'test-hon.R:421:3', 'test-hon.R:453:3',
'test-hon.R:487:3', 'test-hon.R:516:3', 'test-hon.R:544:3',
'test-hon.R:1022:3', 'test-hon.R:1048:3', 'test-hon.R:1073:3',
'test-hon.R:1101:3'
• empty test (1): 'test-link_prediction.R:432:1'
• ggplot2 installed; skipping test (2): 'test-mmm.R:497:3', 'test-mmm.R:509:3'
• gridExtra is installed; can't test missing (3): 'test-simplicial.R:634:3',
'test-simplicial.R:642:3', 'test-simplicial.R:650:3'
• lavaan is installed; skipping no-lavaan test (1): 'test-gimme.R:441:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-mmm.R:173:3'): build_mmm works with tna input ──────────────────
Error in `matrix(P_vec, nrow = n_states, ncol = n_states)`: 'data' must be of a vector type, was 'NULL'
Backtrace:
▆
1. └─Nestimate::build_mmm(model, k = 2, n_starts = 3, seed = 1) at test-mmm.R:173:3
2. └─base::lapply(...)
3. └─Nestimate (local) FUN(X[[i]], ...)
4. ├─base::t(matrix(P_vec, nrow = n_states, ncol = n_states))
5. └─base::matrix(P_vec, nrow = n_states, ncol = n_states)
[ FAIL 1 | WARN 1 | SKIP 17 | PASS 2937 ]
Error:
! Test failures.
Execution halted
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [18s/17s] ERROR
Error(s) in re-building vignettes:
--- re-building ‘clustering.Rmd’ using rmarkdown
2026-04-09 20:25:33.684 R[72612:403595] XType: Using static font registry.
--- finished re-building ‘clustering.Rmd’
--- re-building ‘co-occurrence-networks.Rmd’ using rmarkdown
--- finished re-building ‘co-occurrence-networks.Rmd’
--- re-building ‘link-prediction-association-rules.Rmd’ using rmarkdown
2026-04-09 20:25:39.540 R[72656:403727] XType: Using static font registry.
--- finished re-building ‘link-prediction-association-rules.Rmd’
--- re-building ‘psychological-networks.Rmd’ using rmarkdown
--- finished re-building ‘psychological-networks.Rmd’
--- re-building ‘transition-networks.Rmd’ using rmarkdown
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: .mmm_em(counts, init_state, k, screen_iter, tol, smooth, n_states, init_posterior = init, from_ind = from_ind, cov_df = NULL)
2: FUN(X[[i]], ...)
3: lapply(X = S, FUN = FUN, ...)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
8: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
9: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
10: FUN(X[[i]], ...)
11: lapply(seq_len(cores), inner.do)
12: parallel::mclapply(inits, .run_screen, mc.cores = n_cores)
13: build_mmm(net_GR, k = 2, covariates = c("Group"))
14: eval(expr, envir)
15: eval(expr, envir)
16: withVisible(eval(expr, envir))
17: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
18: eval(call)
19: eval(call)
20: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
21: doWithOneRestart(return(expr), restart)
22: withOneRestart(expr, restarts[[1L]])
23: withRestartList(expr, restarts[-nr])
24: doWithOneRestart(return(expr), restart)
25: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
26: withRestartList(expr, restarts)
27: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
28: evaluate::evaluate(...)
29: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))
30: in_dir(input_dir(), expr)
31: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)))
32: eng_r(options)
33: block_exec(params)
34: call_block(x)
35: process_group(group)
36: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) })
37: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global()))
38: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
39: process_file(text, output)
40: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
41: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
42: vweave_rmarkdown(...)
43: engine$weave(file, quiet = quiet, encoding = enc)
44: doTryCatch(return(expr), name, parentenv, handler)
45: tryCatchOne(expr, names, parentenv, handlers[[1L]])
46: tryCatchList(expr, classes, parentenv, handlers)
47: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) }}, error = function(e) { OK <<- FALSE message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
48: tools:::.buildOneVignette("transition-networks.Rmd", "/Volumes/Builds/packages/big-sur-arm64/results/4.5/Nestimate.Rcheck/vign_test/Nestimate", TRUE, FALSE, "transition-networks", "UTF-8", "/Volumes/Temp/tmp/RtmpxaL00L/file11a94792e0301.rds")
An irrecoverable exception occurred. R is aborting now ...
Traceback:
1: .mmm_em(counts, init_state, k, screen_iter, tol, smooth, n_states, init_posterior = init, from_ind = from_ind, cov_df = NULL)
2: FUN(X[[i]], ...)
3: lapply(X = S, FUN = FUN, ...)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
8: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
9: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
10: FUN(X[[i]], ...)
11: lapply(seq_len(cores), inner.do)
12: parallel::mclapply(inits, .run_screen, mc.cores = n_cores)
13: build_mmm(net_GR, k = 2, covariates = c("Group"))
14: eval(expr, envir)
15: eval(expr, envir)
16: withVisible(eval(expr, envir))
17: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
18: eval(call)
19: eval(call)
Traceback:
1: 20: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir))
Traceback:
watcher$capture_plot_and_output() 1: .mmm_em(counts, init_state, k, screen_iter, tol, smooth, n_states, init_posterior = init, from_ind = from_ind, cov_df = NULL)
2: FUN(X[[i]], ...).mmm_em(counts, init_state, k, screen_iter, tol, smooth, n_states, init_posterior = init, from_ind = from_ind, cov_df = NULL)
2: FUN(X[[i]], ...)
3:
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
21: doWithOneRestart(return(expr), restart)
22: withOneRestart(expr, restarts[[1L]])
23: withRestartList(expr, restarts[-nr])
24: doWithOneRestart(return(expr), restart)
25: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
26: withRestartList(expr, restarts)
27: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
28: evaluate::evaluate(...)
29: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))
30: in_dir(input_dir(), expr)
31: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)))
32: eng_r(options)
*** caught segfault ***
address 0x110, cause 'invalid permissions'
33: block_exec(params)
34: call_block(x)
35: process_group(group)
36: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) })
37: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global()))
38: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
39:
Traceback:
1:
3: lapply(X = S, FUN = FUN, ...)
4: doTryCatch(return(expr), name, parentenv, handler).mmm_em(counts, init_state, k, screen_iter, tol, smooth, n_states, lapply(X = S, FUN = FUN, ...)
4: doTryCatch(return(expr), name, parentenv, handler)
5:
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: process_file(text, output)tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
8: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
9: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
10: FUN(X[[i]], ...)
11: lapply(seq_len(cores), inner.do)
12: parallel::mclapply(inits, .run_screen, mc.cores = n_cores)
13: build_mmm(net_GR, k = 2, covariates = c("Group"))
14: eval(expr, envir)
15: eval(expr, envir)
16: withVisible(eval(expr, envir))
17: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
18: eval(call)
19: eval(call)
20: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
21: doWithOneRestart(return(expr), restart)
22: withOneRestart(expr, restarts[[1L]])
23: withRestartList(expr, restarts[-nr])
24: doWithOneRestart(return(expr), restart)
25: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
26: withRestartList(expr, restarts)
27: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
28: evaluate::evaluate(...)
29: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))
30: in_dir(input_dir(), expr)
31: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)))
32: eng_r(options)
33: block_exec(params)
34: call_block(x)
35: process_group(group)
36: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) })
37: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global()))
38: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
39: process_file(text, output)
40: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
41: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
42: vweave_rmarkdown(...)
43: engine$weave(file, quiet = quiet, encoding = enc)
44: doTryCatch(return(expr), name, parentenv, handler)
45: tryCatchOne(expr, names, parentenv, handlers[[1L]])
46: tryCatchList(expr, classes, parentenv, handlers)
47: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) }}, error = function(e) { OK <<- FALSE message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
48: tools:::.buildOneVignette("transition-networks.Rmd", "/Volumes/Builds/packages/big-sur-arm64/results/4.5/Nestimate.Rcheck/vign_test/Nestimate", TRUE, FALSE, "transition-networks", "UTF-8", "/Volumes/Temp/tmp/RtmpxaL00L/file11a94792e0301.rds")
An irrecoverable exception occurred. R is aborting now ...
Traceback:
1: .mmm_em(counts, init_state, k, screen_iter, tol, smooth, n_states, init_posterior = init, from_ind = from_ind, cov_df = NULL)
2: FUN(X[[i]], ...)
3: lapply(X = S, FUN = FUN, ...)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
8: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
9: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
10: FUN(X[[i]], ...)
11: lapply(seq_len(cores), inner.do)
12: parallel::mclapply(inits, .run_screen, mc.cores = n_cores)
13: build_mmm(net_GR, k = 2, covariates = c("Group"))
14: eval(expr, envir)
15: eval(expr, envir)
16: withVisible(eval(expr, envir))
17: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
18: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
40: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
41: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
42: vweave_rmarkdown(...)
43: engine$weave(file, quiet = quiet, encoding = enc)
44: doTryCatch(return(expr), name, parentenv, handler)
45: tryCatchOne(expr, names, parentenv, handlers[[1L]])
46: tryCatchList(expr, classes, parentenv, handlers)
47: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) }}, error = function(e) { OK <<- FALSE message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
48: tools:::.buildOneVignette("transition-networks.Rmd", "/Volumes/Builds/packages/big-sur-arm64/results/4.5/Nestimate.Rcheck/vign_test/Nestimate", TRUE, FALSE, "transition-networks", "UTF-8", "/Volumes/Temp/tmp/RtmpxaL00L/file11a94792e0301.rds")
An irrecoverable exception occurred. R is aborting now ...
8: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
9: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
10: FUN(X[[i]], ...)
11: lapply(seq_len(cores), inner.do)
12: parallel::mclapply(inits, .run_screen, mc.cores = n_cores)
13: build_mmm(net_GR, k = 2, covariates = c("Group"))
14: eval(expr, envir)
15: eval(expr, envir)
16: withVisible(eval(expr, envir))
17: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) {eval(call)
19: eval(call)
20: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
21: doWithOneRestart(return(expr), restart)
22: withOneRestart(expr, restarts[[1L]])
23: withRestartList(expr, restarts[-nr])
24: doWithOneRestart(return(expr), restart)
25: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
26: withRestartList(expr, restarts)
27: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
28: evaluate::evaluate(...)
29: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))
30: in_dir(input_dir(), expr)
31: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)))
32: eng_r(options)
33: block_exec(params)
34: call_block(x)
35: process_group(group)
36: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) })
37: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global()))
38: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
39: process_file(text, output)
40: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
41: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
42: vweave_rmarkdown(...)
43: engine$weave(file, quiet = quiet, encoding = enc)
44: doTryCatch(return(expr), name, parentenv, handler)
45: tryCatchOne(expr, names, parentenv, handlers[[1L]])
46: tryCatchList(expr, classes, parentenv, handlers)
47: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) }}, error = function(e) { OK <<- FALSE message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
48: tools:::.buildOneVignette("transition-networks.Rmd", "/Volumes/Builds/packages/big-sur-arm64/results/4.5/Nestimate.Rcheck/vign_test/Nestimate", TRUE, FALSE, "transition-networks", "UTF-8", "/Volumes/Temp/tmp/RtmpxaL00L/file11a94792e0301.rds")
An irrecoverable exception occurred. R is aborting now ...
Traceback:
1: .mmm_em(counts, init_state, k, screen_iter, tol, smooth, n_states, init_posterior = init, from_ind = from_ind, cov_df = NULL)
2: FUN(X[[i]], ...)
3: lapply(X = S, FUN = FUN, ...)
4: doTryCatch(return(expr), name, parentenv, handler)
5:
Traceback:
watcher$capture_plot_and_output() init_posterior = init, from_ind = from_ind, cov_df = NULL)tryCatchOne(expr, names, parentenv, handlers[[1L]])
1: .mmm_em(counts, init_state, k, screen_iter, tol, smooth, n_states, init_posterior = init, from_ind = from_ind, cov_df = NULL)
2: FUN(X[[i]], ...)
3: lapply(X = S, FUN = FUN, ...)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
8: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
9: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
10: FUN(X[[i]], ...)
11: if (on_message$capture) {lapply(seq_len(cores), inner.do) watcher$push(cnd)
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
}
*** caught segfault ***
12: 1: .mmm_em(counts, init_state, k, screen_iter, tol, smooth, n_states, init_posterior = init, from_ind = from_ind, cov_df = NULL)
2: FUN(X[[i]], ...)
3: lapply(X = S, FUN = FUN, ...)
parallel::mclapply(inits, .run_screen, mc.cores = n_cores)address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
6: tryCatchList(expr, classes, parentenv, handlers)
7: 2: FUN(X[[i]], ...)
3: lapply(X = S, FUN = FUN, ...)
4: tryCatch(expr, error = function(e) {doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) 4: doTryCatch(return(expr), name, parentenv, handler)
5: prefix <- paste("Error in", dcall, ": ")
13: build_mmm(net_GR, k = 2, covariates = c("Group")) LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L]))
*** caught segfault ***
if (!silent && isTRUE(getOption("show.error.messages"))) {
14: eval(expr, envir) cat(msg, file = outFile) if (on_message$silence) { .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
address 0x110, cause 'invalid permissions'
invokeRestart("muffleMessage") 8: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
9: call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]]tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
}}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) {
7: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n")15: eval(expr, envir)
16: call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") return() } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) .Internal(seterrmessage(msg[1L]))withVisible(eval(expr, envir))
17: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) 10: FUN(X[[i]], ...)
if (!silent && isTRUE(getOption("show.error.messages"))) {11: watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL){
*** caught segfault ***
watcher$capture_plot_and_output() }lapply(seq_len(cores), inner.do) cat(msg, file = outFile) if (on_message$capture) { watcher$push(cnd) } .Internal(printDeferredWarnings())
if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) }{ invisible(structure(msg, class = "try-error", condition = e))12: if (getOption("warn") >= 2 || getOption("warn") < 0) { return() }parallel::mclapply(inits, .run_screen, mc.cores = n_cores)
13: build_mmm(net_GR, k = 2, covariates = c("Group"))
14: else prefix <- "Error : "eval(expr, envir)
*** caught segfault ***
msg <- paste0(prefix, conditionMessage(e), "\n")address 0x110, cause 'invalid permissions'
watcher$capture_plot_and_output() if (on_warning$capture) { .Internal(seterrmessage(msg[1L])) cnd <- sanitize_call(cnd)
address 0x110, cause 'invalid permissions'
})
18: eval(call)
19: eval(call)
20: watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd) {with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } TRUE}, handlers)
21: invisible(structure(msg, class = "try-error", condition = e))
*** caught segfault ***
doWithOneRestart(return(expr), restart)
22: withOneRestart(expr, restarts[[1L]])})
8: address 0x110, cause 'invalid permissions'
15: eval(expr, envir)23: })
8: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
9: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
9: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
10: switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)FUN(X[[i]], ...)})
18: eval(call)
19: eval(call)
20: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir)withRestartList(expr, restarts[-nr])
16:
11: }24:
doWithOneRestart(return(expr), restart)withVisible(eval(expr, envir))
25: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
26: withRestartList(expr, restarts) TRUE10: FUN(X[[i]], ...)
11: lapply(seq_len(cores), inner.do)
12: parallel::mclapply(inits, .run_screen, mc.cores = n_cores)}, handlers)lapply(seq_len(cores), inner.do)
Traceback:
1: .mmm_em(counts, init_state, k, screen_iter, tol, smooth, n_states, init_posterior = init, from_ind = from_ind, cov_df = NULL)
27:
2: 21: FUN(X[[i]], ...)doWithOneRestart(return(expr), restart)13: withRestarts(with_handlers({
Traceback:
3: 17: for (expr in tle$exprs) {
Traceback:
lapply(X = S, FUN = FUN, ...) ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() 1:
build_mmm(net_GR, k = 2, covariates = c("Group"))
4: doTryCatch(return(expr), name, parentenv, handler)
5: watcher$print_value(ev$value, ev$visible, envir).mmm_em(counts, init_state, k, screen_iter, tol, smooth, n_states, withCallingHandlers(code, error = function (e)
Traceback:
1: 12: rlang::entrace(e), message = function (cnd) tryCatchOne(expr, names, parentenv, handlers[[1L]])
init_posterior = init, from_ind = from_ind, cov_df = NULL)
parallel::mclapply(inits, .run_screen, mc.cores = n_cores)22: }
14: 2: 6: { 1: tryCatchList(expr, classes, parentenv, handlers) TRUE.mmm_em(counts, init_state, k, screen_iter, tol, smooth, n_states, }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
28: evaluate::evaluate(...)
.mmm_em(counts, init_state, k, screen_iter, tol, smooth, n_states, eval(expr, envir)
15: eval(expr, envir)FUN(X[[i]], ...) watcher$capture_plot_and_output()withOneRestart(expr, restarts[[1L]]) 7:
3: lapply(X = S, FUN = FUN, ...)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
tryCatch(expr, error = function(e) {
16: withVisible(eval(expr, envir))
17: init_posterior = init, from_ind = from_ind, cov_df = NULL)29:
init_posterior = init, from_ind = from_ind, cov_df = NULL)13: build_mmm(net_GR, k = 2, covariates = c("Group"))
14: eval(expr, envir)
15: eval(expr, envir)
16: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) } if (on_message$silence) {23: 6: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, tryCatchList(expr, classes, parentenv, handlers)
withVisible(eval(expr, envir)) call <- conditionCall(e) invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") } keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L
if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L)
if (on_message$capture) { watcher$push(cnd)}, error = function (cnd) withRestartList(expr, restarts[-nr]) else 2L
Traceback:
2: 7: {
2: }
Traceback:
FUN(X[[i]], ...) }, output_handler = knit_handlers(options$render, options)) 1: prefix <- paste("Error in", dcall, ": ")FUN(X[[i]], ...) if (on_message$silence) {
invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { 1: .mmm_em(counts, init_state, k, screen_iter, tol, smooth, n_states, init_posterior = init, from_ind = from_ind, cov_df = NULL) return() }
2: FUN(X[[i]], ...)
3: lapply(X = S, FUN = FUN, ...)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]]) LONG <- 75LtryCatch(expr, error = function(e) {.mmm_em(counts, init_state, k, screen_iter, tol, smooth, n_states, watcher$capture_plot_and_output()30:
Traceback:
in_dir(input_dir(), expr)
31: in_input_dir(evaluate(code, envir = env, new_device = FALSE, 3: 17:
call <- conditionCall(e) watcher$capture_plot_and_output() 1:
sm <- strsplit(conditionMessage(e), "\n")[[1L]] init_posterior = init, from_ind = from_ind, cov_df = NULL) if (on_warning$capture) { 3: lapply(X = S, FUN = FUN, ...) keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, cnd <- sanitize_call(cnd)24:
lapply(X = S, FUN = FUN, ...) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")withCallingHandlers(code, error = function (e) .mmm_em(counts, init_state, k, screen_iter, tol, smooth, n_states, cnd <- sanitize_call(cnd)doWithOneRestart(return(expr), restart) keep_message = if (is.numeric(options$message)) TRUE else options$message, watcher$push(cnd)rlang::entrace(e), message = function (cnd) 2: init_posterior = init, from_ind = from_ind, cov_df = NULL) watcher$push(cnd) 6: stop_on_error = if (is.numeric(options$error)) options$error else {
if (is.na(w))
}{
if (!is.null(call)) { w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], 4: tryCatchList(expr, classes, parentenv, handlers)
4: 25: switch(on_error, continue = invokeRestart("eval_continue"), withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
stop = invokeRestart("eval_stop"), error = NULL)})
18: eval(call)
19: eval(call)
20: with_handlers({ 2: FUN(X[[i]], ...)doTryCatch(return(expr), name, parentenv, handler)
26: for (expr in tle$exprs) {FUN(X[[i]], ...)
7: withRestartList(expr, restarts) if (identical(call[[1L]], quote(doTryCatch))) watcher$capture_plot_and_output()
if (on_warning$silence) {tryCatch(expr, error = function(e) { ev <- withVisible(eval(expr, envir)) 3: call <- sys.call(-4L) 3:
invokeRestart("muffleWarning") 5: type = "b") if (options$error && options$include) call <- conditionCall(e)lapply(X = S, FUN = FUN, ...)lapply(X = S, FUN = FUN, ...) }doTryCatch(return(expr), name, parentenv, handler) if (on_message$capture) { watcher$capture_plot_and_output() if (!is.null(call)) {
}, error = function (cnd) 0L dcall <- deparse(call, nlines = 1L) if (w > LONG) watcher$print_value(ev$value, ev$visible, envir)
watcher$push(cnd)27: withRestarts(with_handlers({ if (identical(call[[1L]], quote(doTryCatch))) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 4: prefix <- paste0(prefix, "\n "){ } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL) }
doTryCatch(return(expr), name, parentenv, handler) prefix <- paste("Error in", dcall, ": ") } else 2L}) call <- sys.call(-4L)
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
.Internal(seterrmessage(msg[1L])) 5: if (on_message$silence) { LONG <- 75L invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
18: eval(call)
19: eval(call)
20: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) }
type = "b") if (!silent && isTRUE(getOption("show.error.messages"))) { dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") cat(msg, file = outFile) for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) 5: TRUE 4: if (w > LONG) }, output_handler = knit_handlers(options$render, options)))tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))}, handlers)
21: doWithOneRestart(return(expr), restart)
22: withOneRestart(expr, restarts[[1L]])
23: withRestartList(expr, restarts[-nr])
24: doWithOneRestart(return(expr), restart)
25: tryCatchOne(expr, names, parentenv, handlers[[1L]]) watcher$capture_plot_and_output() prefix <- paste0(prefix, "\n ") TRUE}, handlers) .Internal(printDeferredWarnings()) }18: }) watcher$print_value(ev$value, ev$visible, envir)withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) }doTryCatch(return(expr), name, parentenv, handler) sm <- strsplit(conditionMessage(e), "\n")[[1L]]
else prefix <- "Error : "eval(call) if (w > LONG)
invisible(structure(msg, class = "try-error", condition = e))
} 8: w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
26: 32: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)21: 5: 19: withRestartList(expr, restarts) if (is.na(w))
})tryCatchOne(expr, names, parentenv, handlers[[1L]])eval(call)doWithOneRestart(return(expr), restart) 6: eng_r(options)
msg <- paste0(prefix, conditionMessage(e), "\n") w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], 9: TRUE
prefix <- paste0(prefix, "\n ") .Internal(seterrmessage(msg[1L]))
sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) 8: 6: tryCatchList(expr, classes, parentenv, handlers) if (!silent && isTRUE(getOption("show.error.messages"))) {
try(lapply(X = S, FUN = FUN, ...), silent = TRUE)20: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
21: doWithOneRestart(return(expr), restart)
22: withOneRestart(expr, restarts[[1L]])
23: withRestartList(expr, restarts[-nr])
24: doWithOneRestart(return(expr), restart)
27:
withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
8: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)10: FUN(X[[i]], ...)
11: lapply(seq_len(cores), inner.do)
12: parallel::mclapply(inits, .run_screen, mc.cores = n_cores)
13: build_mmm(net_GR, k = 2, covariates = c("Group"))
14: eval(expr, envir)
15: eval(expr, envir)
16: withVisible(eval(expr, envir))
17: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) {tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ")22:
25: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
26: withRestartList(expr, restarts)
27: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output()withOneRestart(expr, restarts[[1L]])
return()33: watcher$print_value(ev$value, ev$visible, envir)}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)28:
7: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L)
} 9:
evaluate::evaluate(...) type = "b")sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) LONG <- 75L else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L]))block_exec(params) prefix <- paste("Error in", dcall, ": ") } } sm <- strsplit(conditionMessage(e), "\n")[[1L]] if (!silent && isTRUE(getOption("show.error.messages"))) {23:
watcher$capture_plot_and_output() LONG <- 75L 9: TRUE if (w > LONG)
cat(msg, file = outFile)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))29:
prefix <- paste0(prefix, "\n ") sm <- strsplit(conditionMessage(e), "\n")[[1L]]10: if (on_warning$capture) {evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 28:
}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)FUN(X[[i]], ...)34: .Internal(printDeferredWarnings()) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")10: withRestartList(expr, restarts[-nr])evaluate::evaluate(...)
24: doWithOneRestart(return(expr), restart)
25: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
26: withRestartList(expr, restarts)
27: call_block(x) } w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") keep_message = if (is.numeric(options$message)) TRUE else options$message, withRestarts(with_handlers({
invisible(structure(msg, class = "try-error", condition = e))35: process_group(group)
36: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) })
37: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global()))
38: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) stop_on_error = if (is.numeric(options$error)) options$error else {
29: if (is.na(w))
if (is.na(w)) if (options$error && options$include) 11: pb$interrupt() w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], 28: w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], }) }evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, type = "b") for (expr in tle$exprs) { type = "b")
else prefix <- "Error : " 0Llapply(seq_len(cores), inner.do) ev <- withVisible(eval(expr, envir)) if (w > LONG) evaluate::evaluate(...) if (is_R_CMD_build() || is_R_CMD_check()) else 2L
FUN(X[[i]], ...) if (w > LONG)
error <<- format(e) keep_message = if (is.numeric(options$message)) TRUE else options$message, msg <- paste0(prefix, conditionMessage(e), "\n")
cnd <- sanitize_call(cnd) 8: }), list(rlang_trace_top_env = knit_global())), function(loc) { stop_on_error = if (is.numeric(options$error)) options$error else { watcher$capture_plot_and_output() prefix <- paste0(prefix, "\n ")12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE) prefix <- paste0(prefix, "\n ") }, output_handler = knit_handlers(options$render, options)) watcher$push(cnd) } .Internal(seterrmessage(msg[1L]))parallel::mclapply(inits, .run_screen, mc.cores = n_cores) watcher$print_value(ev$value, ev$visible, envir)
29: else prefix <- "Error : " if (!silent && isTRUE(getOption("show.error.messages"))) { msg <- paste0(prefix, conditionMessage(e), "\n") }11: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, if (options$error && options$include) 30: .Internal(seterrmessage(msg[1L])) TRUElapply(seq_len(cores), inner.do) cat(msg, file = outFile) 0L
keep_message = if (is.numeric(options$message)) TRUE else options$message,
} .Internal(printDeferredWarnings()) }}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
9: else 2L13: in_dir(input_dir(), expr) setwd(wd) else prefix <- "Error : " }
if (!silent && isTRUE(getOption("show.error.messages"))) {12: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) stop_on_error = if (is.numeric(options$error)) options$error else {build_mmm(net_GR, k = 2, covariates = c("Group"))
write_utf8(res, output %n% stdout()) msg <- paste0(prefix, conditionMessage(e), "\n") invisible(structure(msg, class = "try-error", condition = e)) if (options$error && options$include) if (on_warning$silence) {parallel::mclapply(inits, .run_screen, mc.cores = n_cores)
.Internal(seterrmessage(msg[1L])) }, output_handler = knit_handlers(options$render, options)) 0L invokeRestart("muffleWarning")
})31: 28: cat(msg, file = outFile) } if (!silent && isTRUE(getOption("show.error.messages"))) {
evaluate::evaluate(...) paste0("\nQuitting from ", loc, if (!is.null(error)) 10: 13: 30: 14: in_input_dir(evaluate(code, envir = env, new_device = FALSE, cat(msg, file = outFile) paste0("\n", rule(), error, "\n", rule()))build_mmm(net_GR, k = 2, covariates = c("Group"))
keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, .Internal(printDeferredWarnings())
.Internal(printDeferredWarnings())FUN(X[[i]], ...)14: keep_message = if (is.numeric(options$message)) TRUE else options$message, }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) 8: }in_dir(input_dir(), expr)29: stop_on_error = if (is.numeric(options$error)) options$error else { else 2L
}, error = function (cnd)
evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, try(lapply(X = S, FUN = FUN, ...), silent = TRUE) }, output_handler = knit_handlers(options$render, options))11:
eval(expr, envir) invisible(structure(msg, class = "try-error", condition = e))eval(expr, envir) } if (options$error && options$include) keep_message = if (is.numeric(options$message)) TRUE else options$message,
{
39: 31: lapply(seq_len(cores), inner.do) 9:
})
in_input_dir(evaluate(code, envir = env, new_device = FALSE,
15: stop_on_error = if (is.numeric(options$error)) options$error else { 0L invisible(structure(msg, class = "try-error", condition = e))process_file(text, output)15:
keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))12: eval(expr, envir)eval(expr, envir) else 2L})
parallel::mclapply(inits, .run_screen, mc.cores = n_cores) 8: if (options$error && options$include) }, output_handler = knit_handlers(options$render, options))) watcher$capture_plot_and_output()
try(lapply(X = S, FUN = FUN, ...), silent = TRUE)30: 10:
cnd <- sanitize_call(cnd)13:
FUN(X[[i]], ...)16:
in_dir(input_dir(), expr)build_mmm(net_GR, k = 2, covariates = c("Group"))40: 0L
9: 16:
withVisible(eval(expr, envir)) else 2L
withVisible(eval(expr, envir))11: watcher$push(cnd)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))32: 8:
keep_message = if (is.numeric(options$message)) TRUE else options$message, 31:
in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)))
32: eng_r(options)
33: block_exec(params)lapply(seq_len(cores), inner.do) switch(on_error, continue = invokeRestart("eval_continue"), stop_on_error = if (is.numeric(options$error)) options$error else {try(lapply(X = S, FUN = FUN, ...), silent = TRUE)17: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
10: }, output_handler = knit_handlers(options$render, options))
34: 14: if (options$error && options$include) FUN(X[[i]], ...)eng_r(options)
eval(expr, envir)
15: eval(expr, envir)30: in_dir(input_dir(), expr)
31: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L12:
0L stop = invokeRestart("eval_stop"), error = NULL)call_block(x)
withCallingHandlers(code, error = function (e) 17:
})
}, output_handler = knit_handlers(options$render, options)))rlang::entrace(e), message = function (cnd) parallel::mclapply(inits, .run_screen, mc.cores = n_cores) 9: else 2LwithCallingHandlers(code, error = function (e)
16:
41:
{32: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 18: withVisible(eval(expr, envir))eng_r(options)rlang::entrace(e), message = function (cnd) 35: }, output_handler = knit_handlers(options$render, options)))13: process_group(group){ watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd) { output_dir = getwd(), ...)33:
watcher$capture_plot_and_output()
build_mmm(net_GR, k = 2, covariates = c("Group"))eval(call) watcher$capture_plot_and_output() cnd <- sanitize_call(cnd)block_exec(params)32:
10: watcher$push(cnd)
11: if (on_message$capture) {19: FUN(X[[i]], ...)eng_r(options)42: 33: watcher$push(cnd)eval(call)14:
vweave_rmarkdown(...)
lapply(seq_len(cores), inner.do)
eval(expr, envir)11:
block_exec(params)34:
36: 17: 20:
switch(on_error, continue = invokeRestart("eval_continue"), 43:
withCallingHandlers(code, error = function (e) lapply(seq_len(cores), inner.do)34: }
15: rlang::entrace(e), message = function (cnd) 33: engine$weave(file, quiet = quiet, encoding = enc) if (on_message$silence) { stop = invokeRestart("eval_stop"), error = NULL)withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), with_handlers({12:
invokeRestart("muffleMessage")44: doTryCatch(return(expr), name, parentenv, handler)
45: tryCatchOne(expr, names, parentenv, handlers[[1L]])
46: tryCatchList(expr, classes, parentenv, handlers)
}}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd)47: tryCatch({
error = function(e) { for (expr in tle$exprs) {{block_exec(params) engine$weave(file, quiet = quiet, encoding = enc)12: if (progress && is.function(pb$interrupt)) call_block(x) watcher$capture_plot_and_output()
eval(expr, envir)})
18: eval(call)
19: eval(call)
20: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
21: doWithOneRestart(return(expr), restart)
22: withOneRestart(expr, restarts[[1L]])
23: withRestartList(expr, restarts[-nr])
24: doWithOneRestart(return(expr), restart)
25: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
26: withRestartList(expr, restarts)
27: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
28: evaluate::evaluate(...)
29: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2Lparallel::mclapply(inits, .run_screen, mc.cores = n_cores) if (on_message$capture) { ev <- withVisible(eval(expr, envir)) watcher$push(cnd) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) }, output_handler = knit_handlers(options$render, options))
watcher$push(cnd)call_block(x)parallel::mclapply(inits, .run_screen, mc.cores = n_cores)
13: build_mmm(net_GR, k = 2, covariates = c("Group"))
14: eval(expr, envir)
15: eval(expr, envir)
16:
35: 34:
withVisible(eval(expr, envir))
pb$interrupt()16: 35: process_group(group)
36: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) })
37: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), }withVisible(eval(expr, envir)) if (is_R_CMD_build() || is_R_CMD_check()) 13: setwd(startdir) } if (on_message$silence) {
call_block(x)build_mmm(net_GR, k = 2, covariates = c("Group")) output <- find_vignette_product(name, by = "weave", engine = engine) if (on_warning$silence) { error = function(e) {17:
process_group(group) invokeRestart("muffleWarning") }withCallingHandlers(code, error = function (e) if (!have.makefile && vignette_is_tex(output)) {14:
} TRUE if (progress && is.function(pb$interrupt))
30: rlang::entrace(e), message = function (cnd) texi2pdf(file = output, clean = FALSE, quiet = quiet)35: pb$interrupt()}, error = function (cnd) }, handlers){36: process_group(group)in_dir(input_dir(), expr)eval(expr, envir) output <- find_vignette_product(name, by = "texi2pdf",
15: eval(expr, envir)
16: withVisible(eval(expr, envir))
17: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) } if (on_message$silence) { if (is_R_CMD_build() || is_R_CMD_check()) withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error <<- format(e) invokeRestart("muffleMessage")
engine = engine){ error = function(e) { invokeRestart("muffleMessage") if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) })
37: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global()))
38: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) watcher$capture_plot_and_output() }) }
31: paste0("\n", rule(), error, "\n", rule())) watcher$capture_plot_and_output() error <<- format(e)
} if (on_message$capture) {
cnd <- sanitize_call(cnd)36: in_input_dir(evaluate(code, envir = env, new_device = FALSE, 17: }37: 21: }, error = function(e) { watcher$push(cnd)}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) watcher$push(cnd)withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), }, warning = function (cnd) OK <<- FALSE}, warning = function (cnd) with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, }{
{ error = function(e) { keep_message = if (is.numeric(options$message)) TRUE else options$message, doWithOneRestart(return(expr), restart) error = function(e) {39: if (progress && is.function(pb$interrupt)) if (progress && is.function(pb$interrupt)) if (getOption("warn") >= 2 || getOption("warn") < 0) { if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)))
pb$interrupt() message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", withCallingHandlers(code, error = function (e) switch(on_error, continue = invokeRestart("eval_continue"), process_file(text, output)32:
40: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
41: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)eng_r(options) pb$interrupt() if (getOption("warn") >= 2 || getOption("warn") < 0) { file, conditionMessage(e)))
{ return() }), list(rlang_trace_top_env = knit_global())) return()rlang::entrace(e), message = function (cnd)
if (is_R_CMD_build() || is_R_CMD_check()) 33: block_exec(params)
34: call_block(x)
35: process_group(group)
36: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) })
37: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global()))
38: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e)}) }{
stop = invokeRestart("eval_stop"), error = NULL)38: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) 22: error <<- format(e) if (getOption("warn") >= 2 || getOption("warn") < 0) { }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
39: process_file(text, output)
40: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
41: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
42: vweave_rmarkdown(...)
43: engine$weave(file, quiet = quiet, encoding = enc)
})
if (is_R_CMD_build() || is_R_CMD_check()) 42: watcher$capture_plot_and_output() }withOneRestart(expr, restarts[[1L]]) paste0("\n", rule(), error, "\n", rule()))
23: withRestartList(expr, restarts[-nr])
24: vweave_rmarkdown(...)44: watcher$capture_plot_and_output() error <<- format(e) if (on_message$capture) {doWithOneRestart(return(expr), restart)
}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)48: tools:::.buildOneVignette("transition-networks.Rmd", "/Volumes/Builds/packages/big-sur-arm64/results/4.5/Nestimate.Rcheck/vign_test/Nestimate", TRUE, FALSE, "transition-networks", "UTF-8", "/Volumes/Temp/tmp/RtmpxaL00L/file11a94792e0301.rds")
An irrecoverable exception occurred. R is aborting now ...
}), list(rlang_trace_top_env = knit_global()))
38: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), watcher$capture_plot_and_output() return()
})
if (on_warning$capture) {doTryCatch(return(expr), name, parentenv, handler) }18: watcher$push(cnd)43: if (on_warning$capture) {
eval(call) cnd <- sanitize_call(cnd)25: engine$weave(file, quiet = quiet, encoding = enc)39: } error = function(e) { watcher$capture_plot_and_output()withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
if (on_message$silence) { if (progress && is.function(pb$interrupt)) 37: process_file(text, output)19: cnd <- sanitize_call(cnd)
pb$interrupt()with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 45: watcher$push(cnd) if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
error = function(e) { invokeRestart("muffleMessage") }}, warning = function (cnd) {
watcher$push(cnd)tryCatchOne(expr, names, parentenv, handlers[[1L]]) if (on_warning$capture) {26: eval(call)39: } if (progress && is.function(pb$interrupt)) if (getOption("warn") >= 2 || getOption("warn") < 0) {withRestartList(expr, restarts)
process_file(text, output) pb$interrupt()
40: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
41: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
42: vweave_rmarkdown(...)
43: engine$weave(file, quiet = quiet, encoding = enc)
44: doTryCatch(return(expr), name, parentenv, handler)
45: tryCatchOne(expr, names, parentenv, handlers[[1L]])
46: tryCatchList(expr, classes, parentenv, handlers)
47: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) }}, error = function(e) { OK <<- FALSE message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
48: tools:::.buildOneVignette("transition-networks.Rmd", "/Volumes/Builds/packages/big-sur-arm64/results/4.5/Nestimate.Rcheck/vign_test/Nestimate", TRUE, FALSE, "transition-networks", "UTF-8", "/Volumes/Temp/tmp/RtmpxaL00L/file11a94792e0301.rds")
An irrecoverable exception occurred. R is aborting now ...
if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global()))40:
44: return()
knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) if (on_warning$silence) {20: with_handlers({doTryCatch(return(expr), name, parentenv, handler) invokeRestart("muffleWarning") }}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
18: eval(call)
19: eval(call)
20: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output()
45: tryCatchOne(expr, names, parentenv, handlers[[1L]])
46:
for (expr in tle$exprs) { } cnd <- sanitize_call(cnd)tryCatchList(expr, classes, parentenv, handlers) watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning")38:
watcher$capture_plot_and_output() }27: }47: 41: if (on_warning$capture) {46: cnd <- sanitize_call(cnd)tryCatchList(expr, classes, parentenv, handlers)
47: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) }}, error = function(e) { OK <<- FALSE message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
48: tools:::.buildOneVignette("transition-networks.Rmd", "/Volumes/Builds/packages/big-sur-arm64/results/4.5/Nestimate.Rcheck/vign_test/Nestimate", TRUE, FALSE, "transition-networks", "UTF-8", "/Volumes/Temp/tmp/RtmpxaL00L/file11a94792e0301.rds")
An irrecoverable exception occurred. R is aborting now ...
watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
18: eval(call)
19: eval(call)
20: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
}, error = function (cnd) rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
42: vweave_rmarkdown(...)
43: engine$weave(file, quiet = quiet, encoding = enc)
44: doTryCatch(return(expr), name, parentenv, handler)
45: tryCatchOne(expr, names, parentenv, handlers[[1L]])
46: withRestarts(with_handlers({{xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), ev <- withVisible(eval(expr, envir)) error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
21: doWithOneRestart(return(expr), restart)
22: withOneRestart(expr, restarts[[1L]])
23: withRestartList(expr, restarts[-nr])
watcher$print_value(ev$value, ev$visible, envir)21: doWithOneRestart(return(expr), restart)
22: withOneRestart(expr, restarts[[1L]])
23: withRestartList(expr, restarts[-nr])
24: doWithOneRestart(return(expr), restart)
25: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
26: withRestartList(expr, restarts)
27: withRestarts(with_handlers({ watcher$capture_plot_and_output() paste0("\nQuitting from ", loc, if (!is.null(error)) tryCatch({ if (on_warning$silence) { cnd <- sanitize_call(cnd) invokeRestart("muffleWarning") } } paste0("\n", rule(), error, "\n", rule())) engine$weave(file, quiet = quiet, encoding = enc) for (expr in tle$exprs) {tryCatchList(expr, classes, parentenv, handlers) for (expr in tle$exprs) {
47: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) }}, error = function(e) { OK <<- FALSE message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) watcher$push(cnd)}, error = function (cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
18: eval(call)
19: eval(call)
20: ev <- withVisible(eval(expr, envir))24:
48: { TRUE watcher$capture_plot_and_output()doWithOneRestart(return(expr), restart)39: tools:::.buildOneVignette("transition-networks.Rmd", "/Volumes/Builds/packages/big-sur-arm64/results/4.5/Nestimate.Rcheck/vign_test/Nestimate", watcher$capture_plot_and_output()}, handlers) watcher$print_value(ev$value, ev$visible, envir)with_handlers({ setwd(startdir) ev <- withVisible(eval(expr, envir)) cnd <- sanitize_call(cnd)
} for (expr in tle$exprs) { output <- find_vignette_product(name, by = "weave", engine = engine) watcher$capture_plot_and_output() TRUE, FALSE, "transition-networks", "UTF-8", "/Volumes/Temp/tmp/RtmpxaL00L/file11a94792e0301.rds") watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
28: evaluate::evaluate(...)
29: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))
30: process_file(text, output) ev <- withVisible(eval(expr, envir)) if (!have.makefile && vignette_is_tex(output)) { watcher$capture_plot_and_output() watcher$push(cnd)in_dir(input_dir(), expr)
25: watcher$print_value(ev$value, ev$visible, envir)withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
26: withRestartList(expr, restarts)
27: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir))
21: switch(on_error, continue = invokeRestart("eval_continue"), doWithOneRestart(return(expr), restart)
22: withOneRestart(expr, restarts[[1L]])
23: withRestartList(expr, restarts[-nr])
} stop = invokeRestart("eval_stop"), error = NULL)})
18: eval(call)
19: eval(call)
20: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
21: doWithOneRestart(return(expr), restart)
22: withOneRestart(expr, restarts[[1L]]) TRUE watcher$capture_plot_and_output()An irrecoverable exception occurred. R is aborting now ...
24: 31: TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)}, handlers)
21: doWithOneRestart(return(expr), restart)
22: withOneRestart(expr, restarts[[1L]])
23: withRestartList(expr, restarts[-nr])
24: doWithOneRestart(return(expr), restart)
25: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
26: withRestartList(expr, restarts)
27: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
28: evaluate::evaluate(...)
29: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,
in_input_dir(evaluate(code, envir = env, new_device = FALSE, watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
28: evaluate::evaluate(...)
29: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 28: texi2pdf(file = output, clean = FALSE, quiet = quiet) keep_message = if (is.numeric(options$message)) TRUE else options$message, keep_message = if (is.numeric(options$message)) TRUE else options$message, output <- find_vignette_product(name, by = "texi2pdf", keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,
stop_on_error = if (is.numeric(options$error)) options$error else {evaluate::evaluate(...)40: keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else {doWithOneRestart(return(expr), restart)23: stop_on_error = if (is.numeric(options$error)) options$error else {
if (options$error && options$include) 0L29: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, if (options$error && options$include) withRestartList(expr, restarts[-nr])knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) 0L else 2L }, output_handler = knit_handlers(options$render, options)))
32: eng_r(options) engine = engine) if (options$error && options$include)
41: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
42: vweave_rmarkdown(...)
43: engine$weave(file, quiet = quiet, encoding = enc)
44: } else 2L
0L
33: block_exec(params)
34: call_block(x)
else 2L24: }, output_handler = knit_handlers(options$render, options))
25: doWithOneRestart(return(expr), restart)35: process_group(group)withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])30: keep_message = if (is.numeric(options$message)) TRUE else options$message,
stop_on_error = if (is.numeric(options$error)) options$error else {
36:
25: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) if (options$error && options$include) 26: 0L else 2LwithRestartList(expr, restarts)
27: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUEin_dir(input_dir(), expr)withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), }, output_handler = knit_handlers(options$render, options)) error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) })
}, output_handler = knit_handlers(options$render, options))}, error = function(e) {doTryCatch(return(expr), name, parentenv, handler)
37:
30: 30: 31: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
in_dir(input_dir(), expr)in_dir(input_dir(), expr) error = function(e) {
in_input_dir(evaluate(code, envir = env, new_device = FALSE, OK <<- FALSE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
48: tools:::.buildOneVignette("transition-networks.Rmd", "/Volumes/Builds/packages/big-sur-arm64/results/4.5/Nestimate.Rcheck/vign_test/Nestimate", TRUE, FALSE, "transition-networks", "UTF-8", "/Volumes/Temp/tmp/RtmpxaL00L/file11a94792e0301.rds") if (progress && is.function(pb$interrupt))
keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 26: withRestartList(expr, restarts)
27: withRestarts(with_handlers({
31:
pb$interrupt()28: evaluate::evaluate(...)
29: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))
30: in_dir(input_dir(), expr)
31: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)))
32: eng_r(options)
33: block_exec(params)
34: call_block(x)
keep_message = if (is.numeric(options$message)) TRUE else options$message, 31: 45: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0LAn irrecoverable exception occurred. R is aborting now ...
tryCatchOne(expr, names, parentenv, handlers[[1L]])
46: tryCatchList(expr, classes, parentenv, handlers)
47: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) }}, error = function(e) { OK <<- FALSE message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))}) for (expr in tle$exprs) { stop_on_error = if (is.numeric(options$error)) options$error else { if (is_R_CMD_build() || is_R_CMD_check()) in_input_dir(evaluate(code, envir = env, new_device = FALSE, error <<- format(e) }), list(rlang_trace_top_env = knit_global()))
ev <- withVisible(eval(expr, envir))
38: else 2L watcher$capture_plot_and_output() }, output_handler = knit_handlers(options$render, options)))
32: eng_r(options)
33: block_exec(params)
34: call_block(x)
35: process_group(group)
36: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) watcher$print_value(ev$value, ev$visible, envir) }xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 35: if (options$error && options$include) process_group(group)
36: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) })
37: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global()))
38: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
39: process_file(text, output) 0L else 2L }, output_handler = knit_handlers(options$render, options)))
32: eng_r(options)
33: block_exec(params)
34: TRUE error = function(e) {}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
28: evaluate::evaluate(...)
29: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))
30: in_dir(input_dir(), expr)
31: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)))
32: if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
39: process_file(text, output)
40: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
41: keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
42: vweave_rmarkdown(...)
43: engine$weave(file, quiet = quiet, encoding = enc)
44: doTryCatch(return(expr), name, parentenv, handler)
45: tryCatchOne(expr, names, parentenv, handlers[[1L]])
46: tryCatchList(expr, classes, parentenv, handlers)
47: tryCatch({ }) keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)))
32: eng_r(options)
33: block_exec(params)
34: call_block(x)
35: process_group(group)
36: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt))
eng_r(options)call_block(x)
40: 48: tools:::.buildOneVignette("transition-networks.Rmd", "/Volumes/Builds/packages/big-sur-arm64/results/4.5/Nestimate.Rcheck/vign_test/Nestimate", TRUE, FALSE, "transition-networks", "UTF-8", "/Volumes/Temp/tmp/RtmpxaL00L/file11a94792e0301.rds")
An irrecoverable exception occurred. R is aborting now ...
engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine)35: process_group(group)
36: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt()33: pb$interrupt()knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
41: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
42: vweave_rmarkdown(...)block_exec(params) }}, error = function(e) { if (is_R_CMD_build() || is_R_CMD_check()) 37: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global()))
38: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) OK <<- FALSE error <<- format(e) if (progress && is.function(pb$interrupt))
message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e))) }) }) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) {34:
37: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) })
48: tools:::.buildOneVignette("transition-networks.Rmd", "/Volumes/Builds/packages/big-sur-arm64/results/4.5/Nestimate.Rcheck/vign_test/Nestimate", TRUE, FALSE, "transition-networks", "UTF-8", "/Volumes/Temp/tmp/RtmpxaL00L/file11a94792e0301.rds")
An irrecoverable exception occurred. R is aborting now ...
error <<- format(e)call_block(x) }), list(rlang_trace_top_env = knit_global()))
35: 43: engine$weave(file, quiet = quiet, encoding = enc)
44: 38: process_group(group)
setwd(wd)xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) 36: doTryCatch(return(expr), name, parentenv, handler) paste0("\n", rule(), error, "\n", rule()))37:
paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt()}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
39: process_file(text, output)
40: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
if (is_R_CMD_build() || is_R_CMD_check()) 41: error = function(e) {45: tryCatchOne(expr, names, parentenv, handlers[[1L]])
46: tryCatchList(expr, classes, parentenv, handlers)
47: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 39: process_file(text, output)
40: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
41: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), if (progress && is.function(pb$interrupt)) error <<- format(e) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) })
37: output_dir = getwd(), ...) output_dir = getwd(), ...)with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global()))
38: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) {
42: vweave_rmarkdown(...)
43: engine$weave(file, quiet = quiet, encoding = enc)
44: doTryCatch(return(expr), name, parentenv, handler)
45: tryCatchOne(expr, names, parentenv, handlers[[1L]])
42: vweave_rmarkdown(...)
43: engine$weave(file, quiet = quiet, encoding = enc)
44: doTryCatch(return(expr), name, parentenv, handler)
45: tryCatchOne(expr, names, parentenv, handlers[[1L]])
46: tryCatchList(expr, classes, parentenv, handlers)
47: engine = engine) if (progress && is.function(pb$interrupt)) }}, error = function(e) { OK <<- FALSE message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
48: tools:::.buildOneVignette("transition-networks.Rmd", "/Volumes/Builds/packages/big-sur-arm64/results/4.5/Nestimate.Rcheck/vign_test/Nestimate", TRUE, FALSE, "transition-networks", "UTF-8", "/Volumes/Temp/tmp/RtmpxaL00L/file11a94792e0301.rds")
An irrecoverable exception occurred. R is aborting now ...
}), list(rlang_trace_top_env = knit_global()))
38: pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
39: process_file(text, output)
40: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
41: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
42: vweave_rmarkdown(...)
43: engine$weave(file, quiet = quiet, encoding = enc)
44: doTryCatch(return(expr), name, parentenv, handler)
45: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 46: tryCatch({tryCatchList(expr, classes, parentenv, handlers)tryCatchOne(expr, names, parentenv, handlers[[1L]])
error = function(e) { if (progress && is.function(pb$interrupt)) 46: engine$weave(file, quiet = quiet, encoding = enc)
setwd(startdir) pb$interrupt()tryCatchList(expr, classes, parentenv, handlers)
47: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) }}, error = function(e) { OK <<- FALSE message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
48: tools:::.buildOneVignette("transition-networks.Rmd", "/Volumes/Builds/packages/big-sur-arm64/results/4.5/Nestimate.Rcheck/vign_test/Nestimate", TRUE, FALSE, "transition-networks", "UTF-8", "/Volumes/Temp/tmp/RtmpxaL00L/file11a94792e0301.rds")
An irrecoverable exception occurred. R is aborting now ...
output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", 47: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) }}, error = function(e) { OK <<- FALSE message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
48: tools:::.buildOneVignette("transition-networks.Rmd", "/Volumes/Builds/packages/big-sur-arm64/results/4.5/Nestimate.Rcheck/vign_test/Nestimate", TRUE, FALSE, "transition-networks", "UTF-8", "/Volumes/Temp/tmp/RtmpxaL00L/file11a94792e0301.rds")
An irrecoverable exception occurred. R is aborting now ...
engine = engine) }}, error = function(e) { OK <<- FALSE message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
48: tools:::.buildOneVignette("transition-networks.Rmd", "/Volumes/Builds/packages/big-sur-arm64/results/4.5/Nestimate.Rcheck/vign_test/Nestimate", TRUE, FALSE, "transition-networks", "UTF-8", "/Volumes/Temp/tmp/RtmpxaL00L/file11a94792e0301.rds")
An irrecoverable exception occurred. R is aborting now ...
if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
39: process_file(text, output)
40: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
41: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
42: vweave_rmarkdown(...)
43: engine$weave(file, quiet = quiet, encoding = enc)
44: doTryCatch(return(expr), name, parentenv, handler)
45: tryCatchOne(expr, names, parentenv, handlers[[1L]])
46: tryCatchList(expr, classes, parentenv, handlers)
47: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) }}, error = function(e) { OK <<- FALSE message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
48: tools:::.buildOneVignette("transition-networks.Rmd", "/Volumes/Builds/packages/big-sur-arm64/results/4.5/Nestimate.Rcheck/vign_test/Nestimate", TRUE, FALSE, "transition-networks", "UTF-8", "/Volumes/Temp/tmp/RtmpxaL00L/file11a94792e0301.rds")
An irrecoverable exception occurred. R is aborting now ...
Quitting from transition-networks.Rmd:208-217 [mmm]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `matrix()`:
! 'data' must be of a vector type, was 'NULL'
---
Backtrace:
▆
1. └─Nestimate::build_mmm(net_GR, k = 2, covariates = c("Group"))
2. └─base::lapply(...)
3. └─Nestimate (local) FUN(X[[i]], ...)
4. ├─base::t(matrix(P_vec, nrow = n_states, ncol = n_states))
5. └─base::matrix(P_vec, nrow = n_states, ncol = n_states)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'transition-networks.Rmd' failed with diagnostics:
'data' must be of a vector type, was 'NULL'
--- failed re-building ‘transition-networks.Rmd’
SUMMARY: processing the following file failed:
‘transition-networks.Rmd’
Error: Vignette re-building failed.
Execution halted
- checking PDF version of manual ... [4s/4s] OK
- DONE
Status: 2 ERRORs
- using check arguments '--no-clean-on-error '