* using log directory ‘/srv/hornik/tmp/CRAN/calibmsm.Rcheck’ * using R Under development (unstable) (2023-11-28 r85645) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 17.0.5 (1) Debian flang-new version 17.0.5 (1) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘calibmsm/DESCRIPTION’ ... OK * this is package ‘calibmsm’ version ‘1.0.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/5s] NOTE Maintainer: ‘Alexander Pate ’ New submission Possibly misspelled words in DESCRIPTION: Aalen (21:7) Johansen (21:13) Multistate (3:9) landmarking (22:8) multistate (13:24, 22:76) * 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 serialization versions ... OK * checking whether package ‘calibmsm’ can be installed ... [3s/3s] OK * checking package directory ... OK * checking for future file timestamps ... 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 R 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 use of S3 registration ... 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 ... [4s/4s] OK * checking Rd files ... [0s/0s] OK * checking Rd metadata ... OK * checking Rd line widths ... 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 ... [0s/0s] 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 ... [12s/12s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [0m/30m] ERROR Running ‘testthat.R’ [0m/30m] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > library(calibmsm) > > test_check("calibmsm") There were non-zero predicted transition probabilities into states 1,2,3,4,5,6 Calibration curves have been estimated for transitions into states 1,2,3,4,5,6 Calibration was assessed at time 1826 and calibration was assessed in a landmarked cohort of individuals in state j = 1 at time s = 0 A confidence interval was not estimated The estimated calibration curves are stored in list element `plotdata`: $state1 id pred obs 2 2 0.11401890 0.1095897 4 4 0.13838778 0.1036308 5 5 0.12332255 0.1051035 7 7 0.09737975 0.1236322 10 10 0.11371889 0.1097779 13 13 0.11385388 0.1096929 $state2 id pred obs 2 2 0.2316569 0.1698031 4 4 0.1836189 0.1855591 5 5 0.1609740 0.1759804 7 7 0.2121470 0.1785688 10 10 0.2315632 0.1698443 13 13 0.2316571 0.1698030 $state3 id pred obs 2 2 0.08442692 0.12485834 4 4 0.07579429 0.11666056 5 5 0.05508100 0.09189341 7 7 0.06154308 0.10011560 10 10 0.08440940 0.12484341 13 13 0.08257284 0.12323792 $state4 id pred obs 2 2 0.2328398 0.2427580 4 4 0.2179331 0.2243106 5 5 0.1828176 0.1851051 7 7 0.2206335 0.2275985 10 10 0.2326989 0.2425807 13 13 0.2326047 0.2424622 $state5 id pred obs 2 2 0.1481977 0.1909795 4 4 0.1538475 0.1654523 5 5 0.1425950 0.2215190 7 7 0.1441960 0.2123460 10 10 0.1488068 0.1879278 13 13 0.1505092 0.1797461 $state6 id pred obs 2 2 0.1888598 0.2069354 4 4 0.2304185 0.2542212 5 5 0.3352099 0.3163102 7 7 0.2641006 0.2800368 10 10 0.1888028 0.2068586 13 13 0.1888022 0.2068578 There were non-zero predicted transition probabilities into states 1,2,3,4,5,6 Calibration curves have been estimated for transitions into states 1,2,3,4,5,6 Calibration was assessed at time 1826 and calibration was assessed in a landmarked cohort of individuals in state j = 1 at time s = 0 A confidence interval was not estimated The estimated calibration curves are stored in list element `plotdata`: $state1 id pred obs 2 2 0.11401890 0.1245082 4 4 0.13838778 0.1143276 5 5 0.12332255 0.1280757 7 7 0.09737975 0.1115851 10 10 0.11371889 0.1243613 13 13 0.11385388 0.1244272 $state2 id pred obs 2 2 0.2316569 0.1693576 4 4 0.1836189 0.2008740 5 5 0.1609740 0.1509011 7 7 0.2121470 0.1854787 10 10 0.2315632 0.1694279 13 13 0.2316571 0.1693574 $state3 id pred obs 2 2 0.08442692 0.13900497 4 4 0.07579429 0.12943777 5 5 0.05508100 0.09293168 7 7 0.06154308 0.10449984 10 10 0.08440940 0.13899418 13 13 0.08257284 0.13763859 $state4 id pred obs 2 2 0.2328398 0.2097518 4 4 0.2179331 0.1871859 5 5 0.1828176 0.1985304 7 7 0.2206335 0.1902407 10 10 0.2326989 0.2094773 13 13 0.2326047 0.2092942 $state5 id pred obs 2 2 0.1481977 0.1838697 4 4 0.1538475 0.1451690 5 5 0.1425950 0.2266787 7 7 0.1441960 0.2145598 10 10 0.1488068 0.1792457 13 13 0.1505092 0.1692817 $state6 id pred obs 2 2 0.1888598 0.2048238 4 4 0.2304185 0.2302551 5 5 0.3352099 0.3267404 7 7 0.2641006 0.2926103 10 10 0.1888028 0.2047569 13 13 0.1888022 0.2047562 There were non-zero predicted transition probabilities into states 1,2,3,4,5,6 Calibration curves have been estimated for transitions into states 1,2,3,4,5,6 Calibration was assessed at time 1826 and calibration was assessed in a landmarked cohort of individuals in state j = 1 at time s = 0 A 95% confidence interval was estimated withb5 bootstrap replicates The estimated calibration curves are stored in list element `plotdata`: $state1 id pred obs obs.lower obs.upper 2 2 0.11401890 0.1095897 0.09762353 0.1233532 4 4 0.13838778 0.1036308 0.08457963 0.1085730 5 5 0.12332255 0.1051035 0.09141741 0.1147427 7 7 0.09737975 0.1236322 0.11290012 0.1460309 10 10 0.11371889 0.1097779 0.09786506 0.1236861 13 13 0.11385388 0.1096929 0.09775606 0.1235359 $state2 id pred obs obs.lower obs.upper 2 2 0.2316569 0.1698031 0.1455451 0.1930184 4 4 0.1836189 0.1855591 0.1578750 0.1956162 5 5 0.1609740 0.1759804 0.1423590 0.1908416 7 7 0.2121470 0.1785688 0.1625286 0.1849169 10 10 0.2315632 0.1698443 0.1456280 0.1929751 13 13 0.2316571 0.1698030 0.1455449 0.1930186 $state3 id pred obs obs.lower obs.upper 2 2 0.08442692 0.12485834 0.11253376 0.1389218 4 4 0.07579429 0.11666056 0.10448267 0.1275719 5 5 0.05508100 0.09189341 0.06869706 0.1088113 7 7 0.06154308 0.10011560 0.08010497 0.1137623 10 10 0.08440940 0.12484341 0.11252315 0.1389010 13 13 0.08257284 0.12323792 0.11134593 0.1366699 $state4 id pred obs obs.lower obs.upper 2 2 0.2328398 0.2427580 0.2218528 0.2906467 4 4 0.2179331 0.2243106 0.2184450 0.2584499 5 5 0.1828176 0.1851051 0.1785168 0.2052258 7 7 0.2206335 0.2275985 0.2191257 0.2639557 10 10 0.2326989 0.2425807 0.2218238 0.2903307 13 13 0.2326047 0.2424622 0.2218043 0.2901193 $state5 id pred obs obs.lower obs.upper 2 2 0.1481977 0.1909795 0.1793372 0.1914055 4 4 0.1538475 0.1654523 0.1588507 0.1694898 5 5 0.1425950 0.2215190 0.1981465 0.2313112 7 7 0.1441960 0.2123460 0.1925851 0.2188793 10 10 0.1488068 0.1879278 0.1772969 0.1888558 13 13 0.1505092 0.1797461 0.1718182 0.1819547 $state6 id pred obs obs.lower obs.upper 2 2 0.1888598 0.2069354 0.1963373 0.2111023 4 4 0.2304185 0.2542212 0.2432165 0.2602726 5 5 0.3352099 0.3163102 0.2751474 0.3450958 7 7 0.2641006 0.2800368 0.2671718 0.2907481 10 10 0.1888028 0.2068586 0.1962596 0.2110214 13 13 0.1888022 0.2068578 0.1962589 0.2110206 There were non-zero predicted transition probabilities into states 1,2,3,5,6 Calibration was assessed at time 1826 and calibration was assessed in a landmarked cohort of individuals in state j = 1 at time s = 0 The estimated calibration scatter plots are stored in list element `plotdata`: $state1 id pred obs 1 1 0.1135057 0.04329969 2 2 0.1135518 0.04274070 3 3 0.1131989 0.04261329 4 4 0.1376981 0.06999043 5 5 0.1227877 0.04333992 6 6 0.1131989 0.04261329 $state2 id pred obs 1 1 0.4093590 0.6169702 2 2 0.4114981 0.6186696 3 3 0.4117482 0.6191576 4 4 0.3870386 0.5377577 5 5 0.4277392 0.6008873 6 6 0.4117482 0.6191576 $state3 id pred obs 1 1 0.3964498 0.2501361 2 2 0.3942408 0.2495026 3 3 0.3944988 0.2490786 4 4 0.3728509 0.2949261 5 5 0.3496972 0.2731841 6 6 0.3944988 0.2490786 $state5 id pred obs 1 1 0.02688596 0.04742072 2 2 0.02689840 0.04751176 3 3 0.02681945 0.04720194 4 4 0.04027730 0.07167132 5 5 0.03130458 0.05498636 6 6 0.02681945 0.04720194 $state6 id pred obs 1 1 0.05379955 0.04217332 2 2 0.05381085 0.04157532 3 3 0.05373457 0.04194858 4 4 0.06213511 0.02565452 5 5 0.06847131 0.02760235 6 6 0.05373457 0.04194858 There were non-zero predicted transition probabilities into states 1,2,3,4,5,6 Calibration curves have been estimated for transitions into states 1,2,3,4,5,6 Calibration was assessed at time 1826 and calibration was assessed in a landmarked cohort of individuals in state j = 1 at time s = 0 A confidence interval was not estimated The estimated calibration curves are stored in list element `plotdata`: $state1 id pred obs 1 1 0.1139726 0.0007884881 2 2 0.1140189 0.0008356659 3 3 0.1136646 0.0005012250 4 4 0.1383878 0.0554854582 5 5 0.1233226 0.0239533161 6 6 0.1136646 0.0005012250 $state2 id pred obs 1 1 0.2295006 0.2472482 2 2 0.2316569 0.2648225 3 3 0.2317636 0.2654082 4 4 0.1836189 0.2354074 5 5 0.1609740 0.2600439 6 6 0.2317636 0.2654082 $state3 id pred obs 1 1 0.08450376 0.342589994 2 2 0.08442692 0.341419893 3 3 0.08274331 0.305981896 4 4 0.07579429 0.104422676 5 5 0.05508100 -0.008604324 6 6 0.08462424 0.344353242 $state4 id pred obs 1 1 0.2326861 0.2251249 2 2 0.2328398 0.2232169 3 3 0.2325663 0.2265976 4 4 0.2179331 0.3951682 5 5 0.1828176 0.2681653 6 6 0.2305854 0.2525980 $state5 id pred obs 1 1 0.1504855 0.3384060 2 2 0.1481977 0.3174861 3 3 0.1504787 0.3383704 4 4 0.1538475 0.3330829 5 5 0.1425950 0.2392080 6 6 0.1505534 0.3387299 $state6 id pred obs 1 1 0.1888514 0.1074200 2 2 0.1888598 0.1074443 3 3 0.1887834 0.1072239 4 4 0.2304185 0.2161003 5 5 0.3352099 0.1435163 6 6 0.1888087 0.1072971 [1] "Beginning bootstrapping for state = 1 2023-11-29 09:20:19.653423" [1] "WARNING, SOME BOOTSTRAPPED OBSERVED RISKS WERE NA FOR STATE 1" [1] "THERE ARE 2 ITERATIONS WITH NA's FOR OBSERVED RISKS" [1] "THE MEAN NUMBER OF NA's IN EACH ITERATION IS 0.666666666666667" [1] "Beginning bootstrapping for state = 2 2023-11-29 09:20:37.805877" [1] "WARNING, SOME BOOTSTRAPPED OBSERVED RISKS WERE NA FOR STATE 2" [1] "THERE ARE 2 ITERATIONS WITH NA's FOR OBSERVED RISKS" [1] "THE MEAN NUMBER OF NA's IN EACH ITERATION IS 1.66666666666667" There were non-zero predicted transition probabilities into states 1,2,3,4,5,6 Calibration curves have been estimated for transitions into states 1,2 Calibration was assessed at time 1826 and calibration was assessed in a landmarked cohort of individuals in state j = 1 at time s = 0 A 95% confidence interval was estimated with3 bootstrap replicates The estimated calibration curves are stored in list element `plotdata`: [[1]] id pred obs obs.lower obs.upper 1 1 0.1139726 0.0007884881 -0.0170110656 0.1344807 2 2 0.1140189 0.0008356659 -0.0169373160 0.1346741 3 3 0.1136646 0.0005012250 -0.0175025139 0.1332428 4 4 0.1383878 0.0554854582 0.0003658572 0.1321414 5 5 0.1233226 0.0239533161 0.0015515649 0.1142898 6 6 0.1136646 0.0005012250 -0.0175025139 0.1332428 [[2]] id pred obs obs.lower obs.upper 1 1 0.2295006 0.2472482 0.1821089 0.3679923 2 2 0.2316569 0.2648225 0.1962351 0.3790783 3 3 0.2317636 0.2654082 0.1968696 0.3793399 4 4 0.1836189 0.2354074 0.1287354 0.3891982 5 5 0.1609740 0.2600439 0.1038494 0.5418796 6 6 0.2317636 0.2654082 0.1968696 0.3793399 There were non-zero predicted transition probabilities into states 1,2,3,4,5,6 Calibration curves have been estimated for transitions into states 1,2 Calibration was assessed at time 1826 and calibration was assessed in a landmarked cohort of individuals in state j = 1 at time s = 0 A 95% confidence interval was estimated with bootstrap replicates The estimated calibration curves are stored in list element `plotdata`: $state1 id pred obs obs.lower obs.upper 1 1 0.1139726 0.0007884881 -0.10292450 0.1045015 2 2 0.1140189 0.0008356659 -0.10300552 0.1046769 3 3 0.1136646 0.0005012250 -0.10234645 0.1033489 4 4 0.1383878 0.0554854582 -0.04332935 0.1543003 5 5 0.1233226 0.0239533161 -0.12234560 0.1702522 6 6 0.1136646 0.0005012250 -0.10234645 0.1033489 $state2 id pred obs obs.lower obs.upper 1 1 0.2295006 0.2472482 0.01381089 0.4806856 2 2 0.2316569 0.2648225 0.03932820 0.4903169 3 3 0.2317636 0.2654082 0.04043786 0.4903786 4 4 0.1836189 0.2354074 0.04208295 0.4287318 5 5 0.1609740 0.2600439 0.02470363 0.4953843 6 6 0.2317636 0.2654082 0.04043786 0.4903786 There were non-zero predicted transition probabilities into states 1,2,3,4,5,6 Calibration curves have been estimated for transitions into states 1,2,3,4,5,6 Calibration was assessed at time 1826 and calibration was assessed in a landmarked cohort of individuals in state j = 1 at time s = 0 A confidence interval was not estimated The estimated calibration curves are stored in list element `plotdata`: $state1 pred obs 1 0.1139726 0.0007884881 2 0.1140189 0.0008356659 3 0.1136646 0.0005012250 4 0.1383878 0.0554854582 5 0.1233226 0.0239533161 6 0.1136646 0.0005012250 $state2 pred obs 1 0.2295006 0.2472482 2 0.2316569 0.2648225 3 0.2317636 0.2654082 4 0.1836189 0.2354074 5 0.1609740 0.2600439 6 0.2317636 0.2654082 $state3 pred obs 1 0.08450376 0.342589994 2 0.08442692 0.341419893 3 0.08274331 0.305981896 4 0.07579429 0.104422676 5 0.05508100 -0.008604324 6 0.08462424 0.344353242 $state4 pred obs 1 0.2326861 0.2251249 2 0.2328398 0.2232169 3 0.2325663 0.2265976 4 0.2179331 0.3951682 5 0.1828176 0.2681653 6 0.2305854 0.2525980 $state5 pred obs 1 0.1504855 0.3384060 2 0.1481977 0.3174861 3 0.1504787 0.3383704 4 0.1538475 0.3330829 5 0.1425950 0.2392080 6 0.1505534 0.3387299 $state6 pred obs 1 0.1888514 0.1074200 2 0.1888598 0.1074443 3 0.1887834 0.1072239 4 0.2304185 0.2161003 5 0.3352099 0.1435163 6 0.1888087 0.1072971 [1] "Beginning bootstrapping for state = 1 2023-11-29 09:21:07.515495" [1] "WARNING, SOME BOOTSTRAPPED OBSERVED RISKS WERE NA FOR STATE 1" [1] "THERE ARE 2 ITERATIONS WITH NA's FOR OBSERVED RISKS" [1] "THE MEAN NUMBER OF NA's IN EACH ITERATION IS 1.33333333333333" [1] "Beginning bootstrapping for state = 2 2023-11-29 09:21:25.090392" [1] "WARNING, SOME BOOTSTRAPPED OBSERVED RISKS WERE NA FOR STATE 2" [1] "THERE ARE 3 ITERATIONS WITH NA's FOR OBSERVED RISKS" [1] "THE MEAN NUMBER OF NA's IN EACH ITERATION IS 2" [1] "Beginning bootstrapping for state = 3 2023-11-29 09:21:42.168102" [1] "WARNING, SOME BOOTSTRAPPED OBSERVED RISKS WERE NA FOR STATE 3" [1] "THERE ARE 1 ITERATIONS WITH NA's FOR OBSERVED RISKS" [1] "THE MEAN NUMBER OF NA's IN EACH ITERATION IS 0.333333333333333" [1] "Beginning bootstrapping for state = 4 2023-11-29 09:21:59.978514" [1] "WARNING, SOME BOOTSTRAPPED OBSERVED RISKS WERE NA FOR STATE 4" [1] "THERE ARE 1 ITERATIONS WITH NA's FOR OBSERVED RISKS" [1] "THE MEAN NUMBER OF NA's IN EACH ITERATION IS 2" [1] "Beginning bootstrapping for state = 5 2023-11-29 09:22:18.48068" [1] "WARNING, SOME BOOTSTRAPPED OBSERVED RISKS WERE NA FOR STATE 5" [1] "THERE ARE 2 ITERATIONS WITH NA's FOR OBSERVED RISKS" [1] "THE MEAN NUMBER OF NA's IN EACH ITERATION IS 0.666666666666667" [1] "Beginning bootstrapping for state = 6 2023-11-29 09:22:37.062557" [1] "WARNING, SOME BOOTSTRAPPED OBSERVED RISKS WERE NA FOR STATE 6" [1] "THERE ARE 2 ITERATIONS WITH NA's FOR OBSERVED RISKS" [1] "THE MEAN NUMBER OF NA's IN EACH ITERATION IS 2.33333333333333" There were non-zero predicted transition probabilities into states 1,2,3,4,5,6 Calibration curves have been estimated for transitions into states 1,2,3,4,5,6 Calibration was assessed at time 1826 and calibration was assessed in a landmarked cohort of individuals in state j = 1 at time s = 0 A 95% confidence interval was estimated with3 bootstrap replicates The estimated calibration curves are stored in list element `plotdata`: [[1]] pred obs obs.lower obs.upper 1 0.1139726 0.0007884881 -0.02926604 0.02187037 2 0.1140189 0.0008356659 -0.02923222 0.02192965 3 0.1136646 0.0005012250 -0.02943169 0.02145311 4 0.1383878 0.0554854582 0.04136289 0.11929470 5 0.1233226 0.0239533161 0.01212070 0.04887519 6 0.1136646 0.0005012250 -0.02943169 0.02145311 [[2]] pred obs obs.lower obs.upper 1 0.2295006 0.2472482 0.22308207 0.2682812 2 0.2316569 0.2648225 0.24709254 0.3399264 3 0.2317636 0.2654082 0.24810259 0.3422260 4 0.1836189 0.2354074 -0.05495939 0.3822846 5 0.1609740 0.2600439 -0.04955216 0.6736235 6 0.2317636 0.2654082 0.24810259 0.3422260 [[3]] pred obs obs.lower obs.upper 1 0.08450376 0.342589994 0.190404238 0.739157393 2 0.08442692 0.341419893 0.189531323 0.735160150 3 0.08274331 0.305981896 0.162634353 0.629504906 4 0.07579429 0.104422676 -0.019250843 0.258569646 5 0.05508100 -0.008604324 -0.008827794 -0.002501862 6 0.08462424 0.344353242 0.191802409 0.745257831 [[4]] pred obs obs.lower obs.upper 1 0.2326861 0.2251249 0.05876376 0.1476903 2 0.2328398 0.2232169 0.05760816 0.1462650 3 0.2325663 0.2265976 0.05967635 0.1487943 4 0.2179331 0.3951682 0.18192889 0.3029824 5 0.1828176 0.2681653 0.11253665 0.3360440 6 0.2305854 0.2525980 0.07727933 0.1692262 [[5]] pred obs obs.lower obs.upper 1 0.1504855 0.3384060 0.1412983 0.5659074 2 0.1481977 0.3174861 0.1727881 0.5121030 3 0.1504787 0.3383704 0.1413304 0.5658706 4 0.1538475 0.3330829 0.1788977 0.5162644 5 0.1425950 0.2392080 0.1236260 0.3876119 6 0.1505534 0.3387299 0.1411505 0.5662366 [[6]] pred obs obs.lower obs.upper 1 0.1888514 0.1074200 0.180656264 0.37838642 2 0.1888598 0.1074443 0.180683250 0.37842078 3 0.1887834 0.1072239 0.180438699 0.37810907 4 0.2304185 0.2161003 0.234988126 0.43702320 5 0.3352099 0.1435163 -0.006566974 0.08871346 6 0.1888087 0.1072971 0.180519789 0.37821250 There were non-zero predicted transition probabilities into states 1,2,3,4,5,6 Calibration curves have been estimated for transitions into states 1 Calibration was assessed at time 1826 and calibration was assessed in a landmarked cohort of individuals in state j = 1 at time s = 0 A confidence interval was not estimated The estimated calibration curves are stored in list element `plotdata`: $state1 id pred obs 1 1 0.1139726 0.06224459 2 2 0.1140189 0.06224677 3 3 0.1136646 0.06223052 4 4 0.1383878 0.06737669 5 5 0.1233226 0.06313142 6 6 0.1136646 0.06223052 [1] "Beginning bootstrapping for state = 1 2023-11-29 09:23:37.392827" There were non-zero predicted transition probabilities into states 1,2,3,4,5,6 Calibration curves have been estimated for transitions into states 1 Calibration was assessed at time 1826 and calibration was assessed in a landmarked cohort of individuals in state j = 1 at time s = 0 A 95% confidence interval was estimated with3 bootstrap replicates The estimated calibration curves are stored in list element `plotdata`: [[1]] id pred obs obs.lower obs.upper 1 1 0.1139726 0.06224459 0.06287824 0.06521343 2 2 0.1140189 0.06224677 0.06287035 0.06520027 3 3 0.1136646 0.06223052 0.06293114 0.06530161 4 4 0.1383878 0.06737669 0.04602105 0.06400183 5 5 0.1233226 0.06313142 0.05442572 0.06355284 6 6 0.1136646 0.06223052 0.06293114 0.06530161 There were non-zero predicted transition probabilities into states 1,2,3,4,5,6 Calibration curves have been estimated for transitions into states 1 Calibration was assessed at time 1826 and calibration was assessed in a landmarked cohort of individuals in state j = 1 at time s = 0 A 95% confidence interval was estimated with bootstrap replicates The estimated calibration curves are stored in list element `plotdata`: $state1 id pred obs obs.lower obs.upper 1 1 0.1139726 0.06224459 0.02033303 0.1751051 2 2 0.1140189 0.06224677 0.02036087 0.1749143 3 3 0.1136646 0.06223052 0.02014802 0.1763868 4 4 0.1383878 0.06737669 0.03205659 0.1361392 5 5 0.1233226 0.06313142 0.02583614 0.1461847 6 6 0.1136646 0.06223052 0.02014802 0.1763868 [ FAIL 0 | WARN 0 | SKIP 0 | PASS 289 ] > > proc.time() user system elapsed 627.046 1.314 628.453 Assertion failure at kmp_runtime.cpp(6891): temp_reg_status_file_name. OMP: Error #13: Assertion failure at kmp_runtime.cpp(6891). OMP: Hint Please submit a bug report with this message, compile and run commands used, and machine configuration info including native compiler and operating system versions. Faster response will be obtained by including all program sources. For information on submitting this issue, please see https://github.com/llvm/llvm-project/issues/. Assertion failure at kmp_runtime.cpp(6891): temp_reg_status_file_name. OMP: Error #13: Assertion failure at kmp_runtime.cpp(6891). OMP: Hint Please submit a bug report with this message, compile and run commands used, and machine configuration info including native compiler and operating system versions. Faster response will be obtained by including all program sources. For information on submitting this issue, please see https://github.com/llvm/llvm-project/issues/. * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking re-building of vignette outputs ... [1s/1s] OK * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [0s/0s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 1 NOTE