CRAN Package Check Results for Maintainer ‘Bart-Jan van Rossum <bart-jan.vanrossum at wur.nl>’

Last updated on 2025-03-12 08:53:19 CET.

Package ERROR NOTE OK
douconca 15
factReg 15
isatabr 2 13
LMMsolver 15
statgenGWAS 10 5
statgenGxE 2 8 5
statgenHTP 8 7
statgenIBD 6 9
statgenMPP 15
statgenQTLxT 7 8
statgenSTA 2 8 5

Package douconca

Current CRAN status: OK: 15

Package factReg

Current CRAN status: OK: 15

Package isatabr

Current CRAN status: NOTE: 2, OK: 13

Version: 1.0.1
Check: package dependencies
Result: NOTE Package suggested but not available for checking: ‘xcms’ Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64

Package LMMsolver

Current CRAN status: OK: 15

Package statgenGWAS

Current CRAN status: NOTE: 10, OK: 5

Version: 1.0.10
Check: top-level files
Result: NOTE possible bashism in configure.ac line 31 (should be 'b = a'): if test x"${RSysinfoName}" == x"Darwin"; then possible bashism in configure.ac line 42 (should be 'b = a'): if test x"${hasOpenMP}" == x""; then Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 1.0.10
Check: installed package size
Result: NOTE installed size is 8.9Mb sub-directories of 1Mb or more: data 2.7Mb libs 5.1Mb Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64

Version: 1.0.10
Check: package dependencies
Result: NOTE Package suggested but not available for checking: ‘snpStats’ Flavor: r-oldrel-macos-arm64

Version: 1.0.10
Check: Rd cross-references
Result: NOTE Package unavailable to check Rd xrefs: ‘snpStats’ Flavor: r-oldrel-macos-arm64

Package statgenGxE

Current CRAN status: ERROR: 2, NOTE: 8, OK: 5

Version: 1.0.9
Check: tests
Result: ERROR Running ‘testthat.R’ [62s/147s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(statgenGxE) > > test_check("statgenGxE") [ FAIL 14 | WARN 47 | SKIP 17 | PASS 434 ] ══ Skipped tests (17) ══════════════════════════════════════════════════════════ • On CRAN (17): 'test-gxeMegaEnv.R:72:3', 'test-gxeMegaEnv.R:103:3', 'test-gxeVarComp.R:52:3', 'test-gxeVarComp.R:116:3', 'test-gxeVarComp.R:151:3', 'test-gxeVarComp.R:187:3', 'test-gxeVarComp.R:216:3', 'test-gxeVarCov.R:24:3', 'test-gxeVarCov.R:37:3', 'test-gxeVarCov.R:78:3', 'test-gxeVarCov.R:90:3', 'test-gxeVarCov.R:100:3', 'test-report.R:7:3', 'test-report.R:21:3', 'test-report.R:31:3', 'test-report.R:41:3', 'test-summaries.R:75:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-gxeMegaEnv.R:68:3'): predict.megaEnv functions correctly ───── geTabLm$predictedValue[1, ] not equivalent to c(79.2407761061078, 79.4858110738655). Component 1: Mean relative difference: 0.01361819 Component 2: Mean relative difference: 0.02727539 ── Failure ('test-gxeMegaEnv.R:70:3'): predict.megaEnv functions correctly ───── geTabLm$standardError[1, ] not equivalent to c(6.83087991095342, 6.38912904851271). Component 1: Mean relative difference: 0.2039639 Component 2: Mean relative difference: 0.392072 ── Failure ('test-gxeMegaEnv.R:96:3'): option year in gxeTable functions properly ── megaEnvPred$predictedValue[1, ] not equivalent to c(75.7340426279225, 72.8307799806527). Component 1: Mean relative difference: 0.02866731 Component 2: Mean relative difference: 0.04765296 ── Failure ('test-gxeMegaEnv.R:98:3'): option year in gxeTable functions properly ── megaEnvPred$standardError[1, ] not equivalent to c(5.69948967193805, 7.83055991157765). Component 1: Mean relative difference: 0.3108429 Component 2: Mean relative difference: 0.1233996 ── Failure ('test-gxeVarComp.R:35:3'): lme4 model gives the correct output ───── geVCLm$fullRandVC[["vcov"]] not equal to c(0, 79.9668254460519, 306.14928560952). 3/3 mismatches (average diff: 70.4) [1] 14.8 - 0 == 14.8 [2] 221.2 - 80 == 141.2 [3] 250.9 - 306 == -55.2 ── Failure ('test-gxeVarComp.R:37:3'): lme4 model gives the correct output ───── geVCLm$fullRandVC[["vcovPerc"]] not equal to c(0, 0.207105642982462, 0.792894357017538). 3/3 mismatches (average diff: 0.185) [1] 0.0305 - 0.000 == 0.0305 [2] 0.4543 - 0.207 == 0.2471 [3] 0.5153 - 0.793 == -0.2776 ── Failure ('test-gxeVarComp.R:109:3'): predict function functions correctly ─── predVCLm[["predictedValue"]] not equal to c(...). 15/15 mismatches (average diff: 3.33) [1] 76.9 - 79.3 == -2.425 [2] 72.7 - 76.8 == -4.069 [3] 97.9 - 92.0 == 5.840 [4] 81.8 - 82.3 == -0.492 [5] 77.5 - 79.7 == -2.179 [6] 92.5 - 88.8 == 3.749 [7] 69.7 - 74.9 == -5.263 [8] 93.6 - 89.4 == 4.155 [9] 84.0 - 83.6 == 0.364 ... ── Failure ('test-gxeVarComp.R:134:3'): option predictLevel in predict function functions correctly ── predVCLmTr[["predictedValue"]] not equal to c(...). 45/45 mismatches (average diff: 3.33) [1] 75.1 - 77.5 == -2.425 [2] 70.9 - 75.0 == -4.069 [3] 96.1 - 90.2 == 5.840 [4] 80.0 - 80.5 == -0.492 [5] 75.7 - 77.9 == -2.179 [6] 90.7 - 87.0 == 3.749 [7] 67.9 - 73.1 == -5.263 [8] 91.8 - 87.6 == 4.155 [9] 82.2 - 81.8 == 0.364 ... ── Failure ('test-gxeVarComp.R:184:3'): vc function functions correctly ──────── vcVCLm[["Component"]] not equal to c(78.7850079727369, 309.69339127849). 2/2 mismatches (average diff: 93.8) [1] 215 - 78.8 == 136.4 [2] 259 - 309.7 == -51.2 ── Failure ('test-gxeVarComp.R:205:3'): herit function functions correctly ───── `heritVCLm` not equal to 0.202804089299665. 1/1 mismatches [1] 0.454 - 0.203 == 0.251 ── Failure ('test-gxeVarCov.R:66:3'): lme4 model gives correct output ────────── summLm[, "AIC"] not equivalent to 380.14921134723. 1/1 mismatches [1] Inf - 380 == Inf ── Failure ('test-gxeVarCov.R:67:3'): lme4 model gives correct output ────────── summLm[, "BIC"] not equivalent to 383.762536326771. 1/1 mismatches [1] Inf - 384 == Inf ── Failure ('test-gxeVarCov.R:68:3'): lme4 model gives correct output ────────── summLm[, "Deviance"] not equivalent to 376.14921134723. 1/1 mismatches [1] Inf - 376 == Inf ── Failure ('test-gxeVarCov.R:70:3'): lme4 model gives correct output ────────── geVCLm$vcov not equivalent to c(...). 9/9 mismatches (average diff: 7.95) [1] 31.6 - 25.90 == 5.68 [2] 14.3 - 5.25 == 9.09 [3] 14.3 - 5.25 == 9.09 [4] 14.3 - 5.25 == 9.09 [5] 31.6 - 25.90 == 5.68 [6] 14.3 - 5.25 == 9.09 [7] 14.3 - 5.25 == 9.09 [8] 14.3 - 5.25 == 9.09 [9] 31.6 - 25.90 == 5.68 [ FAIL 14 | WARN 47 | SKIP 17 | PASS 434 ] Error: Test failures Execution halted Flavor: r-devel-linux-x86_64-fedora-clang

Version: 1.0.9
Check: tests
Result: ERROR Running ‘testthat.R’ [56s/75s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(statgenGxE) > > test_check("statgenGxE") [ FAIL 14 | WARN 47 | SKIP 17 | PASS 434 ] ══ Skipped tests (17) ══════════════════════════════════════════════════════════ • On CRAN (17): 'test-gxeMegaEnv.R:72:3', 'test-gxeMegaEnv.R:103:3', 'test-gxeVarComp.R:52:3', 'test-gxeVarComp.R:116:3', 'test-gxeVarComp.R:151:3', 'test-gxeVarComp.R:187:3', 'test-gxeVarComp.R:216:3', 'test-gxeVarCov.R:24:3', 'test-gxeVarCov.R:37:3', 'test-gxeVarCov.R:78:3', 'test-gxeVarCov.R:90:3', 'test-gxeVarCov.R:100:3', 'test-report.R:7:3', 'test-report.R:21:3', 'test-report.R:31:3', 'test-report.R:41:3', 'test-summaries.R:75:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-gxeMegaEnv.R:68:3'): predict.megaEnv functions correctly ───── geTabLm$predictedValue[1, ] not equivalent to c(79.2407761061078, 79.4858110738655). Component 1: Mean relative difference: 0.01361819 Component 2: Mean relative difference: 0.02727539 ── Failure ('test-gxeMegaEnv.R:70:3'): predict.megaEnv functions correctly ───── geTabLm$standardError[1, ] not equivalent to c(6.83087991095342, 6.38912904851271). Component 1: Mean relative difference: 0.2039639 Component 2: Mean relative difference: 0.392072 ── Failure ('test-gxeMegaEnv.R:96:3'): option year in gxeTable functions properly ── megaEnvPred$predictedValue[1, ] not equivalent to c(75.7340426279225, 72.8307799806527). Component 1: Mean relative difference: 0.02866731 Component 2: Mean relative difference: 0.04765296 ── Failure ('test-gxeMegaEnv.R:98:3'): option year in gxeTable functions properly ── megaEnvPred$standardError[1, ] not equivalent to c(5.69948967193805, 7.83055991157765). Component 1: Mean relative difference: 0.3108429 Component 2: Mean relative difference: 0.1233996 ── Failure ('test-gxeVarComp.R:35:3'): lme4 model gives the correct output ───── geVCLm$fullRandVC[["vcov"]] not equal to c(0, 79.9668254460519, 306.14928560952). 3/3 mismatches (average diff: 70.4) [1] 14.8 - 0 == 14.8 [2] 221.2 - 80 == 141.2 [3] 250.9 - 306 == -55.2 ── Failure ('test-gxeVarComp.R:37:3'): lme4 model gives the correct output ───── geVCLm$fullRandVC[["vcovPerc"]] not equal to c(0, 0.207105642982462, 0.792894357017538). 3/3 mismatches (average diff: 0.185) [1] 0.0305 - 0.000 == 0.0305 [2] 0.4543 - 0.207 == 0.2471 [3] 0.5153 - 0.793 == -0.2776 ── Failure ('test-gxeVarComp.R:109:3'): predict function functions correctly ─── predVCLm[["predictedValue"]] not equal to c(...). 15/15 mismatches (average diff: 3.33) [1] 76.9 - 79.3 == -2.425 [2] 72.7 - 76.8 == -4.069 [3] 97.9 - 92.0 == 5.840 [4] 81.8 - 82.3 == -0.492 [5] 77.5 - 79.7 == -2.179 [6] 92.5 - 88.8 == 3.749 [7] 69.7 - 74.9 == -5.263 [8] 93.6 - 89.4 == 4.155 [9] 84.0 - 83.6 == 0.364 ... ── Failure ('test-gxeVarComp.R:134:3'): option predictLevel in predict function functions correctly ── predVCLmTr[["predictedValue"]] not equal to c(...). 45/45 mismatches (average diff: 3.33) [1] 75.1 - 77.5 == -2.425 [2] 70.9 - 75.0 == -4.069 [3] 96.1 - 90.2 == 5.840 [4] 80.0 - 80.5 == -0.492 [5] 75.7 - 77.9 == -2.179 [6] 90.7 - 87.0 == 3.749 [7] 67.9 - 73.1 == -5.263 [8] 91.8 - 87.6 == 4.155 [9] 82.2 - 81.8 == 0.364 ... ── Failure ('test-gxeVarComp.R:184:3'): vc function functions correctly ──────── vcVCLm[["Component"]] not equal to c(78.7850079727369, 309.69339127849). 2/2 mismatches (average diff: 93.8) [1] 215 - 78.8 == 136.4 [2] 259 - 309.7 == -51.2 ── Failure ('test-gxeVarComp.R:205:3'): herit function functions correctly ───── `heritVCLm` not equal to 0.202804089299665. 1/1 mismatches [1] 0.454 - 0.203 == 0.251 ── Failure ('test-gxeVarCov.R:66:3'): lme4 model gives correct output ────────── summLm[, "AIC"] not equivalent to 380.14921134723. 1/1 mismatches [1] Inf - 380 == Inf ── Failure ('test-gxeVarCov.R:67:3'): lme4 model gives correct output ────────── summLm[, "BIC"] not equivalent to 383.762536326771. 1/1 mismatches [1] Inf - 384 == Inf ── Failure ('test-gxeVarCov.R:68:3'): lme4 model gives correct output ────────── summLm[, "Deviance"] not equivalent to 376.14921134723. 1/1 mismatches [1] Inf - 376 == Inf ── Failure ('test-gxeVarCov.R:70:3'): lme4 model gives correct output ────────── geVCLm$vcov not equivalent to c(...). 9/9 mismatches (average diff: 7.95) [1] 31.6 - 25.90 == 5.68 [2] 14.3 - 5.25 == 9.09 [3] 14.3 - 5.25 == 9.09 [4] 14.3 - 5.25 == 9.09 [5] 31.6 - 25.90 == 5.68 [6] 14.3 - 5.25 == 9.09 [7] 14.3 - 5.25 == 9.09 [8] 14.3 - 5.25 == 9.09 [9] 31.6 - 25.90 == 5.68 [ FAIL 14 | WARN 47 | SKIP 17 | PASS 434 ] Error: Test failures Execution halted Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 1.0.9
Check: package dependencies
Result: NOTE Package suggested but not available for checking: ‘asreml’ Flavors: r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64

Package statgenHTP

Current CRAN status: NOTE: 8, OK: 7

Version: 1.0.7
Check: package dependencies
Result: NOTE Package suggested but not available for checking: ‘asreml’ Flavors: r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64

Version: 1.0.7
Check: installed package size
Result: NOTE installed size is 5.0Mb sub-directories of 1Mb or more: data 3.5Mb Flavor: r-release-macos-arm64

Package statgenIBD

Current CRAN status: NOTE: 6, OK: 9

Version: 1.0.8
Check: dependencies in R code
Result: NOTE Namespace in Imports field not imported from: ‘statgenGWAS’ All declared Imports should be used. Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 1.0.8
Check: installed package size
Result: NOTE installed size is 7.5Mb sub-directories of 1Mb or more: extdata 2.4Mb libs 4.2Mb Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64

Package statgenMPP

Current CRAN status: OK: 15

Package statgenQTLxT

Current CRAN status: NOTE: 7, OK: 8

Version: 1.0.2
Check: Rd cross-references
Result: NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: runMultiTraitGwas.Rd: GWAS Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-windows-x86_64

Version: 1.0.2
Check: installed package size
Result: NOTE installed size is 7.4Mb sub-directories of 1Mb or more: libs 6.4Mb Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64

Package statgenSTA

Current CRAN status: ERROR: 2, NOTE: 8, OK: 5

Version: 1.0.14
Check: dependencies in R code
Result: NOTE Namespace in Imports field not imported from: ‘mapproj’ All declared Imports should be used. Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 1.0.14
Check: tests
Result: ERROR Running ‘testthat.R’ [135s/364s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(statgenSTA) > > test_check("statgenSTA") [ FAIL 21 | WARN 19 | SKIP 6 | PASS 757 ] ══ Skipped tests (6) ═══════════════════════════════════════════════════════════ • On CRAN (2): 'test-STA.R:200:3', 'test-STA.R:219:3' • empty test (1): 'test-fitTDSpATS.R:67:1' • {asreml} is not installed (3): 'test-STA.R:43:3', 'test-STA.R:57:3', 'test-STA.R:113:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-ExtractLme4.R:37:3'): BLUPs are computed correctly ─────────── extLm$BLUPs$t1 not equal to c(...). 15/15 mismatches (average diff: 7.36) [1] 83.5 - 79.4 == 4.17 [2] 68.7 - 79.4 == -10.63 [3] 87.5 - 79.4 == 8.14 [4] 76.4 - 79.4 == -2.95 [5] 85.4 - 79.4 == 6.03 [6] 72.3 - 79.4 == -7.05 [7] 72.6 - 79.4 == -6.77 [8] 70.8 - 79.4 == -8.63 [9] 83.6 - 79.4 == 4.23 ... ── Failure ('test-ExtractLme4.R:49:3'): SE of BLUPs are computed correctly ───── extLm$seBLUPs$t1 not equal to rep(x = 0, times = 15). 15/15 mismatches (average diff: 11.8) [1] 11.8 - 0 == 11.8 [2] 11.8 - 0 == 11.8 [3] 11.8 - 0 == 11.8 [4] 11.8 - 0 == 11.8 [5] 11.8 - 0 == 11.8 [6] 11.8 - 0 == 11.8 [7] 11.8 - 0 == 11.8 [8] 11.8 - 0 == 11.8 [9] 11.8 - 0 == 11.8 ... ── Failure ('test-ExtractLme4.R:63:3'): heritability is computed correctly ───── extLm$heritability not equivalent to 0. 1/1 mismatches [1] 0.55 - 0 == 0.55 ── Failure ('test-ExtractLme4.R:70:3'): heritability can be coerced to data.frame correctly ── herit[1, 2] not equal to 0. 1/1 mismatches [1] 0.55 - 0 == 0.55 ── Failure ('test-ExtractLme4.R:77:3'): varGen is computed correctly ─────────── extLm$varGen not equivalent to 0. 1/1 mismatches [1] 309 - 0 == 309 ── Failure ('test-ExtractLme4.R:84:3'): varErr is computed correctly ─────────── extLm$varErr not equivalent to 638.590646884335. 1/1 mismatches [1] 504 - 639 == -134 ── Failure ('test-ExtractLme4.R:142:3'): rMeans are computed correctly ───────── extLm$rMeans$t1 not equal to c(...). 30/30 mismatches (average diff: 7.36) [1] 99.3 - 81.3 == 17.99 [2] 89.4 - 81.3 == 8.14 [3] 83.5 - 77.5 == 6.03 [4] 70.0 - 81.3 == -11.24 [5] 81.4 - 77.5 == 3.96 [6] 79.8 - 77.5 == 2.32 [7] 70.7 - 81.3 == -10.63 [8] 68.8 - 77.5 == -8.63 [9] 95.5 - 77.5 == 17.99 ... ── Failure ('test-ExtractLme4.R:159:3'): random effects are computed correctly ── extLm$ranEf$t1 not equal to c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0). 15/15 mismatches (average diff: 7.36) [1] 4.17 - 0 == 4.17 [2] -10.63 - 0 == -10.63 [3] 8.14 - 0 == 8.14 [4] -2.95 - 0 == -2.95 [5] 6.03 - 0 == 6.03 [6] -7.05 - 0 == -7.05 [7] -6.77 - 0 == -6.77 [8] -8.63 - 0 == -8.63 [9] 4.23 - 0 == 4.23 ... ── Failure ('test-ExtractLme4.R:167:3'): residuals are computed correctly for genotype random ── extLm$residR$t1 not equal to c(...). 30/30 mismatches (average diff: 7.36) [1] 7.07 - 25.1 == -17.99 [2] -1.04 - 7.1 == -8.14 [3] 13.73 - 19.8 == -6.03 [4] -32.05 - -43.3 == 11.24 [5] 36.02 - 40.0 == -3.96 [6] 6.78 - 9.1 == -2.32 [7] -18.65 - -29.3 == 10.63 [8] -8.92 - -17.5 == 8.63 [9] 22.34 - 40.3 == -17.99 ... ── Failure ('test-ExtractLme4.R:184:3'): standardized residuals are computed correctly ── extLm$stdResR$t1 not equal to c(...). 30/30 mismatches (average diff: 0.264) [1] 0.3147 - 0.992 == -0.6769 [2] -0.0462 - 0.281 == -0.3273 [3] 0.6115 - 0.782 == -0.1708 [4] -1.4272 - -1.713 == 0.2860 [5] 1.6039 - 1.582 == 0.0219 [6] 0.3017 - 0.360 == -0.0584 [7] -0.8303 - -1.159 == 0.3283 [8] -0.3972 - -0.694 == 0.2972 [9] 0.9945 - 1.596 == -0.6012 ... ── Failure ('test-STA.R:36:3'): summary.STA produces correct output for lme4 ─── sumLm$heritability not equivalent to 0. 1/1 mismatches [1] 0.52 - 0 == 0.52 ── Failure ('test-fitTDLme4.R:112:3'): Fitting models functions properly when trait contains space ── `... <- NULL` did not produce any messages. ── Failure ('test-outliers.R:56:3'): option rLimit funtions properly ─────────── out1$indicator[["E1"]][["t1"]] has length 4, not length 6. ── Failure ('test-outliers.R:57:3'): option rLimit funtions properly ─────────── nrow(out1$outliers) not equal to 6. 1/1 mismatches [1] 4 - 6 == -2 ── Failure ('test-outliers.R:58:3'): option rLimit funtions properly ─────────── out1$outliers$res not equal to c(...). Lengths differ: 4 is not 6 ── Failure ('test-outliers.R:66:3'): option rLimit funtions properly for multiple traits ── sapply(X = out14$indicator[["E1"]], FUN = length) not equivalent to c(6, 10, 0, 2). 2/4 mismatches (average diff: 3) [1] 4 - 6 == -2 [2] 6 - 10 == -4 ── Failure ('test-outliers.R:68:3'): option rLimit funtions properly for multiple traits ── nrow(out14$outliers) not equal to 18. 1/1 mismatches [1] 12 - 18 == -6 ── Failure ('test-outliers.R:74:3'): option commonFactors functions properly ─── out1$indicator[["E1"]][["t1"]] has length 4, not length 6. ── Failure ('test-outliers.R:75:3'): option commonFactors functions properly ─── nrow(out1$outliers) not equal to 18. 1/1 mismatches [1] 12 - 18 == -6 ── Failure ('test-outliers.R:76:3'): option commonFactors functions properly ─── sum(out1$outliers$outlier) not equal to 6. 1/1 mismatches [1] 4 - 6 == -2 ── Failure ('test-outliers.R:87:3'): option verbose functions properly ───────── any(grepl(pattern = "1.082710", x = printOut2)) is not TRUE `actual`: FALSE `expected`: TRUE [ FAIL 21 | WARN 19 | SKIP 6 | PASS 757 ] Error: Test failures Execution halted Flavor: r-devel-linux-x86_64-fedora-clang

Version: 1.0.14
Check: tests
Result: ERROR Running ‘testthat.R’ [116s/155s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(statgenSTA) > > test_check("statgenSTA") [ FAIL 21 | WARN 19 | SKIP 6 | PASS 757 ] ══ Skipped tests (6) ═══════════════════════════════════════════════════════════ • On CRAN (2): 'test-STA.R:200:3', 'test-STA.R:219:3' • empty test (1): 'test-fitTDSpATS.R:67:1' • {asreml} is not installed (3): 'test-STA.R:43:3', 'test-STA.R:57:3', 'test-STA.R:113:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-ExtractLme4.R:37:3'): BLUPs are computed correctly ─────────── extLm$BLUPs$t1 not equal to c(...). 15/15 mismatches (average diff: 7.36) [1] 83.5 - 79.4 == 4.17 [2] 68.7 - 79.4 == -10.63 [3] 87.5 - 79.4 == 8.14 [4] 76.4 - 79.4 == -2.95 [5] 85.4 - 79.4 == 6.03 [6] 72.3 - 79.4 == -7.05 [7] 72.6 - 79.4 == -6.77 [8] 70.8 - 79.4 == -8.63 [9] 83.6 - 79.4 == 4.23 ... ── Failure ('test-ExtractLme4.R:49:3'): SE of BLUPs are computed correctly ───── extLm$seBLUPs$t1 not equal to rep(x = 0, times = 15). 15/15 mismatches (average diff: 11.8) [1] 11.8 - 0 == 11.8 [2] 11.8 - 0 == 11.8 [3] 11.8 - 0 == 11.8 [4] 11.8 - 0 == 11.8 [5] 11.8 - 0 == 11.8 [6] 11.8 - 0 == 11.8 [7] 11.8 - 0 == 11.8 [8] 11.8 - 0 == 11.8 [9] 11.8 - 0 == 11.8 ... ── Failure ('test-ExtractLme4.R:63:3'): heritability is computed correctly ───── extLm$heritability not equivalent to 0. 1/1 mismatches [1] 0.55 - 0 == 0.55 ── Failure ('test-ExtractLme4.R:70:3'): heritability can be coerced to data.frame correctly ── herit[1, 2] not equal to 0. 1/1 mismatches [1] 0.55 - 0 == 0.55 ── Failure ('test-ExtractLme4.R:77:3'): varGen is computed correctly ─────────── extLm$varGen not equivalent to 0. 1/1 mismatches [1] 309 - 0 == 309 ── Failure ('test-ExtractLme4.R:84:3'): varErr is computed correctly ─────────── extLm$varErr not equivalent to 638.590646884335. 1/1 mismatches [1] 504 - 639 == -134 ── Failure ('test-ExtractLme4.R:142:3'): rMeans are computed correctly ───────── extLm$rMeans$t1 not equal to c(...). 30/30 mismatches (average diff: 7.36) [1] 99.3 - 81.3 == 17.99 [2] 89.4 - 81.3 == 8.14 [3] 83.5 - 77.5 == 6.03 [4] 70.0 - 81.3 == -11.24 [5] 81.4 - 77.5 == 3.96 [6] 79.8 - 77.5 == 2.32 [7] 70.7 - 81.3 == -10.63 [8] 68.8 - 77.5 == -8.63 [9] 95.5 - 77.5 == 17.99 ... ── Failure ('test-ExtractLme4.R:159:3'): random effects are computed correctly ── extLm$ranEf$t1 not equal to c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0). 15/15 mismatches (average diff: 7.36) [1] 4.17 - 0 == 4.17 [2] -10.63 - 0 == -10.63 [3] 8.14 - 0 == 8.14 [4] -2.95 - 0 == -2.95 [5] 6.03 - 0 == 6.03 [6] -7.05 - 0 == -7.05 [7] -6.77 - 0 == -6.77 [8] -8.63 - 0 == -8.63 [9] 4.23 - 0 == 4.23 ... ── Failure ('test-ExtractLme4.R:167:3'): residuals are computed correctly for genotype random ── extLm$residR$t1 not equal to c(...). 30/30 mismatches (average diff: 7.36) [1] 7.07 - 25.1 == -17.99 [2] -1.04 - 7.1 == -8.14 [3] 13.73 - 19.8 == -6.03 [4] -32.05 - -43.3 == 11.24 [5] 36.02 - 40.0 == -3.96 [6] 6.78 - 9.1 == -2.32 [7] -18.65 - -29.3 == 10.63 [8] -8.92 - -17.5 == 8.63 [9] 22.34 - 40.3 == -17.99 ... ── Failure ('test-ExtractLme4.R:184:3'): standardized residuals are computed correctly ── extLm$stdResR$t1 not equal to c(...). 30/30 mismatches (average diff: 0.264) [1] 0.3147 - 0.992 == -0.6769 [2] -0.0462 - 0.281 == -0.3273 [3] 0.6115 - 0.782 == -0.1708 [4] -1.4272 - -1.713 == 0.2860 [5] 1.6039 - 1.582 == 0.0219 [6] 0.3017 - 0.360 == -0.0584 [7] -0.8303 - -1.159 == 0.3283 [8] -0.3972 - -0.694 == 0.2972 [9] 0.9945 - 1.596 == -0.6012 ... ── Failure ('test-STA.R:36:3'): summary.STA produces correct output for lme4 ─── sumLm$heritability not equivalent to 0. 1/1 mismatches [1] 0.52 - 0 == 0.52 ── Failure ('test-fitTDLme4.R:112:3'): Fitting models functions properly when trait contains space ── `... <- NULL` did not produce any messages. ── Failure ('test-outliers.R:56:3'): option rLimit funtions properly ─────────── out1$indicator[["E1"]][["t1"]] has length 4, not length 6. ── Failure ('test-outliers.R:57:3'): option rLimit funtions properly ─────────── nrow(out1$outliers) not equal to 6. 1/1 mismatches [1] 4 - 6 == -2 ── Failure ('test-outliers.R:58:3'): option rLimit funtions properly ─────────── out1$outliers$res not equal to c(...). Lengths differ: 4 is not 6 ── Failure ('test-outliers.R:66:3'): option rLimit funtions properly for multiple traits ── sapply(X = out14$indicator[["E1"]], FUN = length) not equivalent to c(6, 10, 0, 2). 2/4 mismatches (average diff: 3) [1] 4 - 6 == -2 [2] 6 - 10 == -4 ── Failure ('test-outliers.R:68:3'): option rLimit funtions properly for multiple traits ── nrow(out14$outliers) not equal to 18. 1/1 mismatches [1] 12 - 18 == -6 ── Failure ('test-outliers.R:74:3'): option commonFactors functions properly ─── out1$indicator[["E1"]][["t1"]] has length 4, not length 6. ── Failure ('test-outliers.R:75:3'): option commonFactors functions properly ─── nrow(out1$outliers) not equal to 18. 1/1 mismatches [1] 12 - 18 == -6 ── Failure ('test-outliers.R:76:3'): option commonFactors functions properly ─── sum(out1$outliers$outlier) not equal to 6. 1/1 mismatches [1] 4 - 6 == -2 ── Failure ('test-outliers.R:87:3'): option verbose functions properly ───────── any(grepl(pattern = "1.082710", x = printOut2)) is not TRUE `actual`: FALSE `expected`: TRUE [ FAIL 21 | WARN 19 | SKIP 6 | PASS 757 ] Error: Test failures Execution halted Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 1.0.14
Check: package dependencies
Result: NOTE Package suggested but not available for checking: ‘asreml’ Flavors: r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64