Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 2110/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
systemPipeR 2.12.0 (landing page) Thomas Girke
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the systemPipeR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/systemPipeR.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: systemPipeR |
Version: 2.12.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:systemPipeR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings systemPipeR_2.12.0.tar.gz |
StartedAt: 2024-12-20 10:34:20 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 10:46:25 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 725.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: systemPipeR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:systemPipeR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings systemPipeR_2.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/systemPipeR.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘systemPipeR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘systemPipeR’ version ‘2.12.0’ * 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 ... NOTE Found the following hidden files and directories: inst/extdata/.batchtools.conf.R inst/extdata/.batchtools.conf.R.sge inst/extdata/.batchtools.conf.R.torque These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘systemPipeR’ can be installed ... OK * checking installed package size ... NOTE installed size is 6.7Mb sub-directories of 1Mb or more: R 1.6Mb extdata 2.7Mb htmlwidgets 2.0Mb * 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 ... NOTE Problems with news in ‘NEWS’: Cannot process chunk/lines: OVERVIEW * 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 ... NOTE .cmd2cwl2: no visible global function definition for ‘ave’ .getPreprotext: no visible binding for global variable ‘.’ Undefined global functions or variables: . ave Consider adding importFrom("stats", "ave") to your NAMESPACE file. * 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 ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking line endings in Makefiles ... OK * checking for GNU extensions in Makefiles ... OK * checking include directives in Makefiles ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed genFeatures 42.009 1.139 44.456 run_DESeq2 22.136 0.373 23.288 loadWorkflow 10.413 0.307 10.857 renderLogs 7.637 1.508 9.404 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * 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: 4 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/systemPipeR.Rcheck/00check.log’ for details.
systemPipeR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL systemPipeR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘systemPipeR’ ... ** using staged installation ** R ** 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 (systemPipeR)
systemPipeR.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 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(systemPipeR) Loading required package: Rsamtools Loading required package: GenomeInfoDb Loading required package: BiocGenerics Attaching package: 'BiocGenerics' 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, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' 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 Loading required package: GenomicRanges Loading required package: Biostrings Loading required package: XVector Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Loading required package: ShortRead Loading required package: BiocParallel Loading required package: GenomicAlignments Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'MatrixGenerics' The following objects are masked from 'package:matrixStats': colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians > > test_check("systemPipeR") [1] "Generated /tmp/RtmpcG9YF4/rnaseq directory. Next run in rnaseq directory, the R code from *.Rmd template interactively. Alternatively, workflows can be exectued with a single command as instructed in the vignette." [1] "Generated /tmp/RtmpcG9YF4/rnaseq2 directory. Next run in rnaseq directory, the R code from *.Rmd template interactively. Alternatively, workflows can be exectued with a single command as instructed in the vignette." Creating directory '/private/tmp/RtmpcG9YF4/rnaseq2/.SPRproject' Creating file '/private/tmp/RtmpcG9YF4/rnaseq2/.SPRproject/SYSargsList.yml' Running Step: example Running Session: Management | | | 0% | |======================= | 33% | |=============================================== | 67% | |======================================================================| 100% ---- Summary ---- Targets Total_Files Existing_Files Missing_Files example M1 M1 1 1 0 Success M2 M2 1 1 0 Success M3 M3 1 1 0 Success Step Status: Success Done with workflow running, now consider rendering logs & reports To render logs, run: sal <- renderLogs(sal) From command-line: Rscript -e "sal = systemPipeR::SPRproject(resume = TRUE); sal = systemPipeR::renderLogs(sal)" To render reports, run: sal <- renderReport(sal) From command-line: Rscript -e "sal= s ystemPipeR::SPRproject(resume = TRUE); sal = systemPipeR::renderReport(sal)" This message is displayed once per R session Running Step: newStep Running Session: Management | | | 0% | |======================= | 33% | |=============================================== | 67% | |======================================================================| 100% ---- Summary ---- Targets Total_Files Existing_Files Missing_Files example M1 M1 1 1 0 Success M2 M2 1 1 0 Success M3 M3 1 1 0 Success Step Status: Success Running Step: R_code Running Session: Management | | | 0% | |======================================================================| 100% Step Status: Warning [1] "Generated /tmp/RtmpcG9YF4/newtest directory. Next run in new directory, the R code from *.Rmd template interactively. Alternatively, workflows can be exectued with a single command as instructed in the vignette." Creating directory '/private/tmp/RtmpcG9YF4/newtest/.SPRproject' Creating file '/private/tmp/RtmpcG9YF4/newtest/.SPRproject/SYSargsList.yml' Reading Rmd file Now importing step 'load_library' Now importing step 'export_iris' Now importing step 'gzip' Now importing step 'gunzip' Now importing step 'stats' Now back up current Rmd file as template for `renderReport` Template for renderReport is stored at /private/tmp/RtmpcG9YF4/newtest/.SPRproject/workflow_template.Rmd Edit this file manually is not recommended Now check if required tools are installed Check if they are in path: Checking path for gzip PASS Checking path for gunzip PASS step_name tool in_path 1 gzip gzip TRUE 2 gunzip gunzip TRUE All required tools in PATH, skip module check. If you want to check modules use `listCmdModules`Import done Instance of 'LineWise' Code Chunk length: 1 mapply(function(x, y) write.csv(x, y), split(iris, factor(iris$Species)), file.path("results", paste0(names(split(iris, factor(iris$Species))), ".csv"))) load_library 5 + 5 load_library 5 + 5 66 + 55 Running Step: load_library Running Session: Management | | | 0% | |======================================================================| 100% Step Status: Success Running Step: export_iris Running Session: Management | | | 0% | |======================================================================| 100% Step Status: Success Skipping Step: gzip Skipping Step: gunzip Skipping Step: stats [ FAIL 0 | WARN 0 | SKIP 10 | PASS 47 ] ══ Skipped tests (10) ══════════════════════════════════════════════════════════ • On Bioconductor (10): 'test-01-SYSargs.R:2:1', 'test-02-SYSargs2.R:9:5', 'test-02-SYSargs2.R:55:5', 'test-03-SYSargsList.R:63:5', 'test-05-catDB.R:3:1', 'test-06-VENNset.R:3:1', 'test-07-features.R:3:1', 'test-08-cmd2cwl.R:2:1', 'test-10-chipSeq.R:4:1', 'test-utilities.R:2:1' [ FAIL 0 | WARN 0 | SKIP 10 | PASS 47 ] > > proc.time() user system elapsed 25.620 6.779 33.710
systemPipeR.Rcheck/systemPipeR-Ex.timings
name | user | system | elapsed | |
EnvModules-class | 0.002 | 0.002 | 0.003 | |
GOHyperGAll | 0.000 | 0.001 | 0.003 | |
INTERSECTset-class | 0.016 | 0.025 | 0.040 | |
LineWise-class | 0.324 | 0.037 | 0.363 | |
ParamFiles | 0.238 | 0.007 | 0.246 | |
ParamFiles2 | 0.351 | 0.008 | 0.361 | |
SPRproject | 0.007 | 0.004 | 0.011 | |
SYSargs-class | 0.039 | 0.017 | 0.057 | |
SYSargs2-class | 0.131 | 0.012 | 0.143 | |
SYSargsList-class | 1.111 | 0.077 | 1.209 | |
SYSargsList | 0.210 | 0.012 | 0.224 | |
VENNset-class | 0.013 | 0.015 | 0.028 | |
alignStats | 4.235 | 0.090 | 4.444 | |
catDB-class | 0.001 | 0.001 | 0.003 | |
catmap | 0.000 | 0.001 | 0.001 | |
check.output | 3.487 | 0.054 | 3.720 | |
clusterRun | 3.279 | 0.025 | 3.338 | |
config.param | 0.000 | 0.001 | 0.001 | |
configWF | 0.000 | 0.001 | 0.001 | |
countRangeset | 0.092 | 0.006 | 0.097 | |
createParamFiles | 0.376 | 0.005 | 0.384 | |
cwlFilesUpdate | 0.000 | 0.001 | 0.000 | |
evalCode | 0.047 | 0.007 | 0.056 | |
featureCoverage | 3.264 | 0.017 | 3.343 | |
featuretypeCounts | 3.230 | 0.011 | 3.261 | |
filterDEGs | 3.454 | 0.077 | 3.567 | |
filterVars | 0.016 | 0.009 | 0.026 | |
genFeatures | 42.009 | 1.139 | 44.456 | |
importWF | 0.081 | 0.010 | 0.092 | |
listCmdTools | 0.000 | 0.000 | 0.001 | |
loadWorkflow | 10.413 | 0.307 | 10.857 | |
mergeBamByFactor | 0.017 | 0.007 | 0.023 | |
moduleload | 0.000 | 0.002 | 0.002 | |
olBarplot | 1.024 | 0.100 | 1.147 | |
olRanges | 0.235 | 0.008 | 0.253 | |
output_update | 3.533 | 0.019 | 3.570 | |
overLapper | 0.785 | 0.067 | 0.860 | |
plotfeatureCoverage | 3.217 | 0.011 | 3.258 | |
plotfeaturetypeCounts | 3.469 | 0.012 | 3.510 | |
predORF | 0.408 | 0.010 | 0.423 | |
preprocessReads | 1.051 | 0.009 | 1.065 | |
readComp | 3.487 | 0.015 | 3.524 | |
renderLogs | 7.637 | 1.508 | 9.404 | |
renderReport | 3.534 | 0.792 | 4.412 | |
returnRPKM | 0.000 | 0.001 | 0.001 | |
runCommandline | 3.605 | 0.450 | 4.277 | |
runDiff | 0.093 | 0.017 | 0.115 | |
runWF | 0.226 | 0.038 | 0.286 | |
run_DESeq2 | 22.136 | 0.373 | 23.288 | |
run_edgeR | 2.595 | 0.061 | 2.678 | |
sal2bash | 1.120 | 0.261 | 1.447 | |
sal2rmd | 1.559 | 0.408 | 1.986 | |
scaleRanges | 0.434 | 0.089 | 0.529 | |
seeFastq | 0.000 | 0.001 | 0.001 | |
showDF | 0.116 | 0.066 | 0.188 | |
subsetWF | 3.627 | 0.504 | 4.160 | |
symLink2bam | 3.629 | 0.147 | 3.800 | |
sysargs | 0.019 | 0.010 | 0.030 | |
systemArgs | 0.020 | 0.012 | 0.032 | |
targets.as.df | 0.009 | 0.005 | 0.014 | |
trimbatch | 0.681 | 0.005 | 0.691 | |
tryCMD | 0.000 | 0.001 | 0.001 | |
tryPath | 0.002 | 0.001 | 0.003 | |
variantReport | 0.018 | 0.010 | 0.028 | |
vennPlot | 0.811 | 0.080 | 0.899 | |
writeTargets | 0.201 | 0.014 | 0.216 | |
writeTargetsRef | 0.002 | 0.001 | 0.003 | |
writeTargetsout | 3.479 | 0.017 | 3.523 | |
write_SYSargsList | 0.237 | 0.013 | 0.252 | |