Back to Multiple platform build/check report for BioC 3.15 |
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This page was generated on 2022-03-18 11:08:50 -0400 (Fri, 18 Mar 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
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 |
To the developers/maintainers of the systemPipeR package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1929/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
systemPipeR 2.1.13 (landing page) Thomas Girke
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
Package: systemPipeR |
Version: 2.1.13 |
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:systemPipeR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings systemPipeR_2.1.13.tar.gz |
StartedAt: 2022-03-17 20:26:49 -0400 (Thu, 17 Mar 2022) |
EndedAt: 2022-03-17 20:31:24 -0400 (Thu, 17 Mar 2022) |
EllapsedTime: 275.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: systemPipeR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:systemPipeR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings systemPipeR_2.1.13.tar.gz ### ############################################################################## ############################################################################## * using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/systemPipeR.Rcheck' * using R Under development (unstable) (2021-11-21 r81221) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'systemPipeR/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'systemPipeR' version '2.1.13' * 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 whether package 'systemPipeR' can be installed ... OK * checking installed package size ... NOTE installed size is 7.0Mb sub-directories of 1Mb or more: R 1.5Mb extdata 2.3Mb 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 ... OK * checking R 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 writeTargets: no visible binding for global variable 'sal' Undefined global functions or variables: sal * 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 19.88 0.61 20.48 run_DESeq2 7.44 0.07 7.50 renderLogs 0.94 0.25 8.37 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'testthat.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See 'D:/biocbuild/bbs-3.15-bioc/meat/systemPipeR.Rcheck/00check.log' for details.
systemPipeR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL systemPipeR ### ############################################################################## ############################################################################## * installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library' * installing *source* package 'systemPipeR' ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'systemPipeR' finding HTML links ... done EnvModules-class html GOHyperGAll html INTERSECTset-class html LineWise-class html REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-systemPipeR/00new/systemPipeR/help/linewise.html ParamFiles html SPRproject html SYSargs-class html SYSargs2-class html SYSargsList-class html SYSargsList html REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-systemPipeR/00new/systemPipeR/help/SYSargsList.html VENNset-class html add-methods html alignStats html catDB-class html catmap html check.output html clusterRun html config.param html configWF html countRangeset html createParamFiles html cwlFilesUpdate html evalCode html featureCoverage html featuretypeCounts html filterDEGs html filterVars html genFeatures html importWF html loadWorkflow html mergeBamByFactor html moduleload html olBarplot html olRanges html output_update html overLapper html plotWF html plotfeatureCoverage html plotfeaturetypeCounts html predORF html preprocessReads html readComp html renderLogs html renderReport html returnRPKM html runCommandline html runDiff html runWF html run_DESeq2 html run_edgeR html sal2bash html sal2rmd html scaleRanges html seeFastq html showDF html subsetWF html symLink2bam html sysargs html systemArgs html systemPipeR-package html targets.as.df html tryCMD html tryPath html variantReport html vennPlot html writeTargetsRef html writeTargetsout html write_SYSargsList html ** 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) Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") : DESCRIPTION file of package 'ribor' is missing or broken done
systemPipeR.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) 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, 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, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows 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 D:\\biocbuild\\bbs-3.15-bioc\\tmpdir\\RtmpGuJYBw/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 D:\\biocbuild\\bbs-3.15-bioc\\tmpdir\\RtmpGuJYBw/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." [1] "Generated D:\\biocbuild\\bbs-3.15-bioc\\tmpdir\\RtmpGuJYBw/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 'D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpGuJYBw\newtest/.SPRproject' Creating file 'D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpGuJYBw\newtest/.SPRproject/SYSargsList.yml' Reading Rmd fileNow importing step 'load_library' Now importing step 'export_iris' Now importing step 'gzip' Now importing step 'gunzip' Now importing step 'stats' 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 11 | PASS 26 ] == Skipped tests =============================================================== * On Bioconductor (10) * On Windows (1) [ FAIL 0 | WARN 0 | SKIP 11 | PASS 26 ] > > proc.time() user system elapsed 10.90 3.15 14.32
systemPipeR.Rcheck/systemPipeR-Ex.timings
name | user | system | elapsed | |
EnvModules-class | 0 | 0 | 0 | |
GOHyperGAll | 0.02 | 0.00 | 0.01 | |
INTERSECTset-class | 0.05 | 0.00 | 0.05 | |
LineWise-class | 0.23 | 0.00 | 0.55 | |
ParamFiles | 0.06 | 0.00 | 0.06 | |
SPRproject | 0.02 | 0.00 | 0.01 | |
SYSargs-class | 0.00 | 0.02 | 0.02 | |
SYSargs2-class | 0.06 | 0.00 | 0.06 | |
SYSargsList-class | 0.42 | 0.05 | 0.47 | |
SYSargsList | 0.1 | 0.0 | 0.1 | |
VENNset-class | 0 | 0 | 0 | |
alignStats | 1.04 | 0.03 | 1.07 | |
catDB-class | 0 | 0 | 0 | |
catmap | 0 | 0 | 0 | |
check.output | 1.97 | 0.00 | 1.97 | |
clusterRun | 1.11 | 0.00 | 1.11 | |
config.param | 0 | 0 | 0 | |
configWF | 0 | 0 | 0 | |
countRangeset | 0.05 | 0.00 | 0.05 | |
createParamFiles | 0.05 | 0.00 | 0.05 | |
cwlFilesUpdate | 0 | 0 | 0 | |
evalCode | 0.04 | 0.00 | 0.06 | |
featureCoverage | 0.75 | 0.00 | 0.75 | |
featuretypeCounts | 0.02 | 0.00 | 0.01 | |
filterDEGs | 0.77 | 0.00 | 0.77 | |
filterVars | 0.01 | 0.00 | 0.02 | |
genFeatures | 19.88 | 0.61 | 20.48 | |
importWF | 0.02 | 0.01 | 0.03 | |
loadWorkflow | 3.70 | 0.03 | 3.73 | |
mergeBamByFactor | 0.00 | 0.02 | 0.02 | |
moduleload | 0 | 0 | 0 | |
olBarplot | 0.42 | 0.03 | 0.45 | |
olRanges | 0.06 | 0.00 | 0.06 | |
output_update | 0.71 | 0.00 | 0.71 | |
overLapper | 0.23 | 0.02 | 0.25 | |
plotfeatureCoverage | 0 | 0 | 0 | |
plotfeaturetypeCounts | 0 | 0 | 0 | |
predORF | 0.26 | 0.00 | 0.27 | |
preprocessReads | 0.27 | 0.00 | 0.26 | |
readComp | 0.01 | 0.00 | 0.02 | |
renderLogs | 0.94 | 0.25 | 8.37 | |
renderReport | 2.39 | 0.26 | 3.52 | |
returnRPKM | 0 | 0 | 0 | |
runCommandline | 1.21 | 0.00 | 1.21 | |
runDiff | 0.01 | 0.00 | 0.01 | |
runWF | 0.06 | 0.01 | 0.08 | |
run_DESeq2 | 7.44 | 0.07 | 7.50 | |
run_edgeR | 0.58 | 0.01 | 0.64 | |
sal2bash | 0.31 | 0.02 | 0.33 | |
sal2rmd | 0.31 | 0.00 | 0.31 | |
scaleRanges | 0.15 | 0.00 | 0.14 | |
seeFastq | 0 | 0 | 0 | |
showDF | 0.04 | 0.01 | 0.07 | |
subsetWF | 0.85 | 0.00 | 0.84 | |
symLink2bam | 0 | 0 | 0 | |
sysargs | 0.00 | 0.02 | 0.02 | |
systemArgs | 0.01 | 0.00 | 0.01 | |
targets.as.df | 0 | 0 | 0 | |
tryCMD | 0 | 0 | 0 | |
tryPath | 0 | 0 | 0 | |
variantReport | 0 | 0 | 0 | |
vennPlot | 0.20 | 0.02 | 0.22 | |
writeTargetsRef | 0 | 0 | 0 | |
writeTargetsout | 0.85 | 0.00 | 0.84 | |
write_SYSargsList | 0.11 | 0.00 | 0.11 | |