CRAN Package Check Results for Package statgenSTA

Last updated on 2025-03-09 20:52:08 CET.

Flavor	Version	Tinstall	Tcheck	Ttotal	Status	Flags
r-devel-linux-x86_64-debian-clang	1.0.14	11.13	203.11	214.24	OK
r-devel-linux-x86_64-debian-gcc	1.0.14	7.74	141.54	149.28	OK
r-devel-linux-x86_64-fedora-clang	1.0.14			378.99	ERROR
r-devel-linux-x86_64-fedora-gcc	1.0.14			368.63	ERROR
r-devel-macos-arm64	1.0.14			98.00	OK
r-devel-macos-x86_64	1.0.14			217.00	OK
r-devel-windows-x86_64	1.0.14	12.00	193.00	205.00	OK
r-patched-linux-x86_64	1.0.14	10.41	193.79	204.20	NOTE
r-release-linux-x86_64	1.0.14	10.25	191.20	201.45	NOTE
r-release-macos-arm64	1.0.14			96.00	NOTE
r-release-macos-x86_64	1.0.14			182.00	NOTE
r-release-windows-x86_64	1.0.14	12.00	189.00	201.00	NOTE
r-oldrel-macos-arm64	1.0.14				NOTE
r-oldrel-macos-x86_64	1.0.14			168.00	NOTE
r-oldrel-windows-x86_64	1.0.14	15.00	246.00	261.00	NOTE

Check Details

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’ [119s/225s] 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