Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:25 -0400 (Fri, 15 Oct 2021).
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 1888/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
systemPipeR 1.26.3 (landing page) Thomas Girke
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: systemPipeR |
Version: 1.26.3 |
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:systemPipeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings systemPipeR_1.26.3.tar.gz |
StartedAt: 2021-10-15 06:25:33 -0400 (Fri, 15 Oct 2021) |
EndedAt: 2021-10-15 06:37:35 -0400 (Fri, 15 Oct 2021) |
EllapsedTime: 721.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: systemPipeR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:systemPipeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings systemPipeR_1.26.3.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/systemPipeR.Rcheck' * using R version 4.1.1 (2021-08-10) * 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 '1.26.3' * 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 ... 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 R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 ... NOTE Namespace in Imports field not imported from: 'testthat' 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 ... NOTE .change_branch: no visible binding for global variable '.' .cmdToCwl: no visible binding for global variable 'slash_line' .find_long_branch: no visible binding for global variable '.' .parse_step : <anonymous>: no visible binding for global variable '.' .parse_step: no visible binding for global variable '.' GOHyperGAll_Subset: no visible binding for global variable 'test_sample' GOHyperGAll_Subset: no visible binding for global variable 'GO_CC_DF' SPRdata: no visible global function definition for 'SimpleList' appendParam: no visible binding for global variable 'commandline' countRangeset: no visible global function definition for 'import.bed' countRangeset: no visible global function definition for 'summarizeOverlaps' featureCoverage: no visible global function definition for 'Rle' featuretypeCounts: no visible global function definition for 'first' genFeatures: no visible global function definition for 'seqlengths<-' goBarplot: no visible binding for global variable 'SampleMatch' goBarplot: no visible binding for global variable 'Sample' loadWF: no visible global function definition for 'metadata' loadWorkflow: no visible global function definition for 'metadata' olRanges: no visible global function definition for 'seqlengths<-' olRanges: no visible global function definition for 'seqlengths' olRanges: no visible global function definition for 'Rle' renameParam: no visible binding for global variable 'commandline' replaceParam: no visible binding for global variable 'commandline' replaceParam: no visible binding for global variable 'replacing' subsetParam: no visible binding for global variable 'commandline' subsetRmd: no visible binding for global variable '.' addAssay,SummarizedExperiment: no visible global function definition for 'SimpleList' addMetadata,SummarizedExperiment: no visible global function definition for 'metadata' Undefined global functions or variables: . GO_CC_DF Rle Sample SampleMatch SimpleList commandline first import.bed metadata replacing seqlengths seqlengths<- slash_line summarizeOverlaps test_sample * 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 ... ** running examples for arch 'i386' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed genFeatures 21.17 2.26 23.49 run_DESeq2 15.68 0.24 15.92 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed genFeatures 23.72 0.30 24.01 run_DESeq2 18.03 0.03 18.06 * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'testthat.R' OK ** running tests for arch 'x64' ... 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 'C:/Users/biocbuild/bbs-3.13-bioc/meat/systemPipeR.Rcheck/00check.log' for details.
systemPipeR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/systemPipeR_1.26.3.tar.gz && rm -rf systemPipeR.buildbin-libdir && mkdir systemPipeR.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=systemPipeR.buildbin-libdir systemPipeR_1.26.3.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL systemPipeR_1.26.3.zip && rm systemPipeR_1.26.3.tar.gz systemPipeR_1.26.3.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 97 1652k 97 1615k 0 0 2700k 0 --:--:-- --:--:-- --:--:-- 2700k 100 1652k 100 1652k 0 0 2749k 0 --:--:-- --:--:-- --:--:-- 2748k install for i386 * 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 ParamFiles html SPRdata html SYSargs-class html SYSargs2-class html SYSargsList-class html SYSargsList html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/systemPipeR.buildbin-libdir/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 evalCode html featureCoverage html featuretypeCounts html filterDEGs html filterVars html genFeatures html getQsubargs html initWF 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 qsubRun html readComp html renderReport html renderWF html returnRPKM html runCommandline html runDiff html runWF html run_DESeq2 html run_edgeR html scaleRanges html seeFastq html subsetWF html symLink2bam html sysargs html systemArgs html systemPipeR-package html targets.as.df html tryCL html tryPath html variantReport html vennPlot html writeTargetsRef html writeTargetsout 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 install for x64 * installing *source* package 'systemPipeR' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'systemPipeR' as systemPipeR_1.26.3.zip * DONE (systemPipeR) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'systemPipeR' successfully unpacked and MD5 sums checked
systemPipeR.Rcheck/tests_i386/testthat.Rout R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: i386-w64-mingw32/i386 (32-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 Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB 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 C:\\Users\\biocbuild\\bbs-3.13-bioc\\tmpdir\\RtmpW4aj31/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] "Running `cmdlist` for defaultid" Missing expected outputs files: 0 Existing expected outputs files: 1 defaultid TRUE /usr/bin/ln: failed to create symbolic link 'C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpW4aj31/rnaseq/somedir/.bam.bai': No such file or directory Creating directory 'C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpW4aj31\rnaseq\.SPRproject' Project started with success: ./SPRproject and SPRconfig.yml were created.[ FAIL 0 | WARN 2 | SKIP 0 | PASS 8 ] > > proc.time() user system elapsed 15.12 2.34 103.31 |
systemPipeR.Rcheck/tests_x64/testthat.Rout R version 4.1.1 (2021-08-10) -- "Kick Things" 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 Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB 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 C:\\Users\\biocbuild\\bbs-3.13-bioc\\tmpdir\\RtmpyYtg8d/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] "Running `cmdlist` for defaultid" Missing expected outputs files: 0 Existing expected outputs files: 1 defaultid TRUE /usr/bin/ln: failed to create symbolic link 'C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpyYtg8d/rnaseq/somedir/.bam.bai': No such file or directory Creating directory 'C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpyYtg8d\rnaseq\.SPRproject' Project started with success: ./SPRproject and SPRconfig.yml were created.[ FAIL 0 | WARN 2 | SKIP 0 | PASS 8 ] > > proc.time() user system elapsed 16.50 1.17 33.76 |
systemPipeR.Rcheck/examples_i386/systemPipeR-Ex.timings
|
systemPipeR.Rcheck/examples_x64/systemPipeR-Ex.timings
|