• using R Under development (unstable) (2025-02-15 r87723)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)     GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
• running under: Fedora Linux 40 (Workstation Edition)
• using session charset: UTF-8
• using option ‘--no-stop-on-test-error’
• checking for file ‘statgenSTA/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘statgenSTA’ version ‘1.0.14’
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... INFO Package suggested but not available for checking: ‘asreml’
• 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 ‘statgenSTA’ can be installed ... [18s/24s] OK See the install log for details.
• 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 ... OK
• checking whether the package can be loaded with stated dependencies ... OK
• checking whether the package can be unloaded cleanly ... OK
• checking whether the namespace can be loaded with stated dependencies ... OK
• checking whether the namespace can be unloaded cleanly ... OK
• checking loading without being on the library search path ... OK
• checking whether startup messages can be suppressed ... OK
• checking use of S3 registration ... OK
• checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘mapproj’   All declared Imports should be used.
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... [33s/42s] OK
• checking Rd files ... 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 ... OK
• checking LazyData ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking R/sysdata.rda ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [23s/29s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [117s/149s] ERROR   Running ‘testthat.R’ [116s/148s] 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
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [87s/115s] OK
• checking PDF version of manual ... [10s/15s] OK
• checking HTML version of manual ... 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