| Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-27 12:05 -0400 (Sat, 27 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4832 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4620 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4565 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4563 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1681/2334 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| RAIDS 1.7.2 (landing page) Pascal Belleau
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
|
To the developers/maintainers of the RAIDS package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RAIDS.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: RAIDS |
| Version: 1.7.2 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RAIDS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RAIDS_1.7.2.tar.gz |
| StartedAt: 2025-09-26 23:31:15 -0400 (Fri, 26 Sep 2025) |
| EndedAt: 2025-09-26 23:39:08 -0400 (Fri, 26 Sep 2025) |
| EllapsedTime: 473.6 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: RAIDS.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RAIDS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RAIDS_1.7.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/RAIDS.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RAIDS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RAIDS’ version ‘1.7.2’
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘RAIDS’ can be installed ... OK
* 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 ... 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 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 ... OK
* checking Rd files ... 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 ... NOTE
Documented arguments not in \usage in Rd file 'wrapperAncestry.Rd':
‘pathGeno’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
computeAncestryFromSyntheticFile 7.275 0.218 7.527
readSNVVCF 6.044 0.071 6.138
selParaPCAUpQuartile 5.690 0.036 5.747
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
[7] 0.0881 - 0.0882 == -9.38e-05
[8] 0.0939 - 0.0940 == -1.55e-04
── Failure ('test-gdsWrapper_internal.R:146:5'): runIBDKING() must return expected results ──
result$kinship not equal to `kinship`.
6/9 mismatches (average diff: 0.000713)
[2] 0.01548 - 0.01724 == -0.001756
[3] 0.00108 - 0.00129 == -0.000214
[4] 0.01548 - 0.01724 == -0.001756
[6] -0.01417 - -0.01434 == 0.000168
[7] 0.00108 - 0.00129 == -0.000214
[8] -0.01417 - -0.01434 == 0.000168
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 443 ]
Error: Test failures
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 1 NOTE
See
‘/Users/biocbuild/bbs-3.22-bioc/meat/RAIDS.Rcheck/00check.log’
for details.
RAIDS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL RAIDS ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘RAIDS’ ... ** this is package ‘RAIDS’ version ‘1.7.2’ ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (RAIDS)
RAIDS.Rcheck/tests/testthat.Rout.fail
R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(RAIDS)
Loading required package: gdsfmt
Loading required package: SNPRelate
SNPRelate -- supported by Streaming SIMD Extensions 2 (SSE2)
Loading required package: GENESIS
Loading required package: dplyr
Attaching package: 'dplyr'
The following object is masked from 'package:testthat':
matches
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Loading required package: Rsamtools
Loading required package: Seqinfo
Loading required package: BiocGenerics
Loading required package: generics
Attaching package: 'generics'
The following object is masked from 'package:dplyr':
explain
The following objects are masked from 'package:base':
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
Attaching package: 'BiocGenerics'
The following object is masked from 'package:dplyr':
combine
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
unsplit, which.max, which.min
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:dplyr':
first, rename
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Attaching package: 'IRanges'
The following objects are masked from 'package:dplyr':
collapse, desc, slice
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
>
> ## Run all unit tests
> test_check("RAIDS")
Attaching package: 'Matrix'
The following object is masked from 'package:S4Vectors':
expand
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 443 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-gdsWrapper_internal.R:145:5'): runIBDKING() must return expected results ──
result$IBS0 not equal to `ibs0`.
6/9 mismatches (average diff: 0.000157)
[2] 0.0799 - 0.0797 == 2.22e-04
[3] 0.0881 - 0.0882 == -9.38e-05
[4] 0.0799 - 0.0797 == 2.22e-04
[6] 0.0939 - 0.0940 == -1.55e-04
[7] 0.0881 - 0.0882 == -9.38e-05
[8] 0.0939 - 0.0940 == -1.55e-04
── Failure ('test-gdsWrapper_internal.R:146:5'): runIBDKING() must return expected results ──
result$kinship not equal to `kinship`.
6/9 mismatches (average diff: 0.000713)
[2] 0.01548 - 0.01724 == -0.001756
[3] 0.00108 - 0.00129 == -0.000214
[4] 0.01548 - 0.01724 == -0.001756
[6] -0.01417 - -0.01434 == 0.000168
[7] 0.00108 - 0.00129 == -0.000214
[8] -0.01417 - -0.01434 == 0.000168
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 443 ]
Error: Test failures
Execution halted
RAIDS.Rcheck/RAIDS-Ex.timings
| name | user | system | elapsed | |
| add1KG2SampleGDS | 0.066 | 0.021 | 0.097 | |
| addBlockFromDetFile | 0.003 | 0.004 | 0.007 | |
| addBlockInGDSAnnot | 0.005 | 0.004 | 0.011 | |
| addGDS1KGLDBlock | 0.001 | 0.002 | 0.004 | |
| addGDSRef | 0.003 | 0.003 | 0.008 | |
| addGDSStudyPruning | 0.001 | 0.001 | 0.003 | |
| addGeneBlockGDSRefAnnot | 1.193 | 0.106 | 1.318 | |
| addGeneBlockRefAnnot | 0.002 | 0.002 | 0.004 | |
| addRef2GDS1KG | 0.005 | 0.005 | 0.011 | |
| addStudy1Kg | 0.011 | 0.010 | 0.023 | |
| addStudyGDSSample | 0.008 | 0.004 | 0.014 | |
| addUpdateLap | 0.001 | 0.002 | 0.003 | |
| addUpdateSegment | 0.001 | 0.002 | 0.004 | |
| appendGDSRefSample | 0.008 | 0.004 | 0.012 | |
| appendGDSSampleOnly | 0.001 | 0.001 | 0.004 | |
| appendGDSgenotype | 0.016 | 0.013 | 0.032 | |
| appendGDSgenotypeMat | 0.001 | 0.002 | 0.003 | |
| calcAFMLRNA | 0.004 | 0.002 | 0.007 | |
| computeAlleleFraction | 0.003 | 0.001 | 0.004 | |
| computeAllelicFractionDNA | 0.161 | 0.010 | 0.171 | |
| computeAllelicFractionRNA | 0.264 | 0.008 | 0.273 | |
| computeAllelicImbDNAChr | 0.008 | 0.002 | 0.010 | |
| computeAncestryFromSynthetic | 0.017 | 0.007 | 0.025 | |
| computeAncestryFromSyntheticFile | 7.275 | 0.218 | 7.527 | |
| computeKNNRefSample | 0.016 | 0.005 | 0.021 | |
| computeKNNRefSynthetic | 2.731 | 0.107 | 2.848 | |
| computeLOHBlocksDNAChr | 0.010 | 0.001 | 0.012 | |
| computePCAMultiSynthetic | 0.009 | 0.006 | 0.016 | |
| computePCARefRMMulti | 0.305 | 0.008 | 0.315 | |
| computePCARefSample | 0.356 | 0.005 | 0.362 | |
| computePoolSyntheticAncestryGr | 0.575 | 0.015 | 0.591 | |
| computeSyntheticConfMat | 0.012 | 0.004 | 0.017 | |
| computeSyntheticROC | 0.045 | 0.005 | 0.051 | |
| createAUROCGraph | 1.195 | 0.058 | 1.260 | |
| createAccuracyGraph | 1.049 | 0.009 | 1.062 | |
| createProfile | 0.083 | 0.017 | 0.104 | |
| createStudy2GDS1KG | 0.070 | 0.013 | 0.089 | |
| demoKnownSuperPop1KG | 1.728 | 0.058 | 1.796 | |
| demoPCA1KG | 0.008 | 0.004 | 0.012 | |
| demoPCASyntheticProfiles | 1.760 | 0.027 | 1.796 | |
| demoPedigreeEx1 | 0.021 | 0.004 | 0.025 | |
| estimateAllelicFraction | 0.091 | 0.006 | 0.098 | |
| extractNucleotide | 0 | 0 | 0 | |
| generateGDS1KG | 0.015 | 0.011 | 0.027 | |
| generateGDS1KGgenotypeFromSNPPileup | 0.061 | 0.015 | 0.080 | |
| generateGDSRefSample | 0.005 | 0.003 | 0.009 | |
| generateGDSSNPinfo | 0.005 | 0.004 | 0.011 | |
| generateGDSgenotype | 0.014 | 0.011 | 0.026 | |
| generateGeneBlock | 0.002 | 0.001 | 0.002 | |
| generateMapSnvSel | 0.003 | 0.003 | 0.006 | |
| generatePhase1KG2GDS | 0.016 | 0.014 | 0.031 | |
| generatePhaseRef | 0.014 | 0.009 | 0.024 | |
| generateProfileGDS | 0.063 | 0.014 | 0.080 | |
| getBlockIDs | 0.002 | 0.001 | 0.004 | |
| getRef1KGPop | 0.003 | 0.002 | 0.005 | |
| getRefSuperPop | 0.002 | 0.001 | 0.004 | |
| getTableSNV | 0.014 | 0.004 | 0.018 | |
| groupChr1KGSNV | 0.065 | 0.096 | 0.197 | |
| identifyRelative | 0.010 | 0.004 | 0.015 | |
| identifyRelativeRef | 0.007 | 0.003 | 0.011 | |
| inferAncestry | 0.015 | 0.002 | 0.017 | |
| inferAncestryDNA | 0.012 | 0.001 | 0.014 | |
| inferAncestryGeneAware | 0.017 | 0.002 | 0.019 | |
| matKNNSynthetic | 0.052 | 0.005 | 0.057 | |
| pedSynthetic | 0.045 | 0.006 | 0.051 | |
| prepPed1KG | 0.004 | 0.002 | 0.006 | |
| prepPedSynthetic1KG | 0.005 | 0.002 | 0.007 | |
| prepSynthetic | 0.013 | 0.005 | 0.020 | |
| processBlockChr | 0.003 | 0.001 | 0.003 | |
| processPileupChrBin | 3.592 | 0.081 | 3.708 | |
| profileAncestry | 0.024 | 0.004 | 0.028 | |
| pruning1KGbyChr | 0.003 | 0.002 | 0.006 | |
| pruningSample | 0.044 | 0.010 | 0.055 | |
| readSNVBAM | 0.001 | 0.001 | 0.001 | |
| readSNVFileGeneric | 0.005 | 0.002 | 0.005 | |
| readSNVPileupFile | 0.051 | 0.002 | 0.054 | |
| readSNVVCF | 6.044 | 0.071 | 6.138 | |
| runExomeAncestry | 0.016 | 0.004 | 0.020 | |
| runIBDKING | 0.043 | 0.005 | 0.050 | |
| runLDPruning | 0.022 | 0.010 | 0.033 | |
| runProfileAncestry | 0.021 | 0.004 | 0.024 | |
| runRNAAncestry | 0.013 | 0.003 | 0.016 | |
| runWrapperAncestry | 0.014 | 0.003 | 0.018 | |
| selParaPCAUpQuartile | 5.690 | 0.036 | 5.747 | |
| select1KGPop | 0.006 | 0.002 | 0.007 | |
| select1KGPopForSynthetic | 0.006 | 0.001 | 0.007 | |
| snpPositionDemo | 0.003 | 0.002 | 0.006 | |
| snvListVCF | 0.005 | 0.002 | 0.007 | |
| splitSelectByPop | 0.001 | 0.001 | 0.001 | |
| syntheticGeno | 0.027 | 0.005 | 0.033 | |
| tableBlockAF | 0.024 | 0.002 | 0.026 | |
| testAlleleFractionChange | 0.001 | 0.000 | 0.002 | |
| testEmptyBox | 0.001 | 0.000 | 0.002 | |
| validateAdd1KG2SampleGDS | 0.001 | 0.001 | 0.002 | |
| validateAddStudy1Kg | 0.002 | 0.001 | 0.003 | |
| validateCharacterString | 0.001 | 0.000 | 0.000 | |
| validateComputeAncestryFromSyntheticFile | 0.002 | 0.001 | 0.004 | |
| validateComputeKNNRefSample | 0.003 | 0.003 | 0.006 | |
| validateComputeKNNRefSynthetic | 0.005 | 0.004 | 0.009 | |
| validateComputePCAMultiSynthetic | 0.002 | 0.002 | 0.005 | |
| validateComputePCARefSample | 0.002 | 0.001 | 0.002 | |
| validateComputePoolSyntheticAncestryGr | 0.001 | 0.000 | 0.001 | |
| validateComputeSyntheticRoc | 0.010 | 0.003 | 0.013 | |
| validateCreateAccuracyGraph | 0.001 | 0.001 | 0.002 | |
| validateCreateStudy2GDS1KG | 0.002 | 0.001 | 0.003 | |
| validateDataRefSynParameter | 0.001 | 0.001 | 0.001 | |
| validateEstimateAllelicFraction | 0.004 | 0.001 | 0.005 | |
| validateGDSClass | 0.001 | 0.000 | 0.002 | |
| validateGenerateGDS1KG | 0.001 | 0.000 | 0.002 | |
| validateLogical | 0 | 0 | 0 | |
| validatePEDStudyParameter | 0.001 | 0.001 | 0.001 | |
| validatePepSynthetic | 0.002 | 0.001 | 0.003 | |
| validatePositiveIntegerVector | 0 | 0 | 0 | |
| validatePrepPed1KG | 0.001 | 0.000 | 0.001 | |
| validateProfileGDSExist | 0.001 | 0.000 | 0.002 | |
| validatePruningSample | 0.002 | 0.001 | 0.002 | |
| validateRunExomeOrRNAAncestry | 0.004 | 0.001 | 0.005 | |
| validateSingleRatio | 0.000 | 0.001 | 0.000 | |
| validateStudyDataFrameParameter | 0.000 | 0.000 | 0.001 | |
| validateSyntheticGeno | 0.002 | 0.002 | 0.003 | |
| validatecreateProfile | 0.002 | 0.001 | 0.003 | |
| wrapperAncestry | 0.016 | 0.003 | 0.020 | |