Thomas Girke
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/systemPipeR |
| Branch: RELEASE_3_12 |
| Last Commit: a9dc042 |
| Last Changed Date: 2021-05-01 02:53:49 -0400 (Sat, 01 May 2021) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:37:07 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the systemPipeR package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1832/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| systemPipeR 1.24.6 (landing page) Thomas Girke
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: systemPipeR |
| Version: 1.24.6 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:systemPipeR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings systemPipeR_1.24.6.tar.gz |
| StartedAt: 2021-05-06 06:45:38 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 06:54:01 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 503.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: systemPipeR.Rcheck |
| Warnings: 0 |
##############################################################################
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### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:systemPipeR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings systemPipeR_1.24.6.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/systemPipeR.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘systemPipeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘systemPipeR’ version ‘1.24.6’
* 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
.github
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 ... 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
* 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
.change_branch: no visible binding for global variable ‘.’
.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 ‘.’
.resizeFeature: no visible global function definition for ‘DataFrame’
.subsetReadsByMappingRegion: no visible global function definition for
‘seqlengths’
.subsetReadsByMappingRegion: no visible global function definition for
‘readGAlignments’
GOHyperGAll_Subset: no visible binding for global variable
‘test_sample’
assembleCommandlineList: no visible binding for global variable ‘WF’
countRangeset: no visible global function definition for ‘import.bed’
countRangeset: no visible global function definition for
‘summarizeOverlaps’
featureCoverage: no visible global function definition for
‘readGAlignments’
featureCoverage: no visible global function definition for ‘qwidth’
featureCoverage: no visible global function definition for ‘Rle’
featuretypeCounts: no visible global function definition for
‘readGAlignments’
featuretypeCounts: no visible global function definition for
‘readGAlignmentPairs’
featuretypeCounts: no visible global function definition for ‘qwidth’
featuretypeCounts: no visible global function definition for ‘last’
featuretypeCounts: no visible global function definition for ‘first’
filterDEGs: no visible binding for global variable ‘Comparisons’
filterDEGs: no visible binding for global variable ‘Counts’
filterDEGs: no visible binding for global variable ‘Type’
genFeatures: no visible global function definition for ‘DataFrame’
genFeatures: no visible global function definition for ‘seqlengths<-’
getQsubargs: no visible binding for global variable ‘tophatargs’
goBarplot: no visible binding for global variable ‘SampleMatch’
goBarplot: no visible binding for global variable ‘Sample’
olBarplot: no visible binding for global variable ‘Intersect_Sets’
olBarplot: no visible binding for global variable ‘Counts’
olBarplot: no visible binding for global variable ‘Level’
olRanges: no visible global function definition for ‘seqlengths<-’
olRanges: no visible global function definition for ‘seqlengths’
olRanges: no visible global function definition for ‘Rle’
plotfeatureCoverage: no visible binding for global variable ‘Coverage’
plotfeatureCoverage: no visible binding for global variable ‘Strand’
plotfeaturetypeCounts: no visible binding for global variable ‘Feature’
plotfeaturetypeCounts: no visible binding for global variable ‘Counts’
plotfeaturetypeCounts: no visible binding for global variable ‘Strand’
plotfeaturetypeCounts: no visible binding for global variable ‘Length’
readComp: no visible binding for global variable ‘args_bam’
renderInputs: no visible binding for global variable ‘WF’
renderOutputs: no visible binding for global variable ‘WF’
scaleRanges: no visible global function definition for ‘DataFrame’
subsetRmd: no visible binding for global variable ‘.’
Undefined global functions or variables:
. Comparisons Counts Coverage DataFrame Feature Intersect_Sets Length
Level Rle Sample SampleMatch Strand Type WF args_bam first import.bed
last qwidth readGAlignmentPairs readGAlignments seqlengths
seqlengths<- summarizeOverlaps test_sample tophatargs
* 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 19.741 0.406 20.151
run_DESeq2 10.046 0.040 10.089
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.12-bioc/meat/systemPipeR.Rcheck/00check.log’
for details.
systemPipeR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL systemPipeR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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/runTests.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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.
> BiocGenerics:::testPackage("systemPipeR")
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
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
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
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
RUNIT TEST PROTOCOL -- Thu May 6 06:53:51 2021
***********************************************
Number of test functions: 1
Number of errors: 0
Number of failures: 0
1 Test Suite :
systemPipeR RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1
Number of errors: 0
Number of failures: 0
Warning messages:
1: In normalizePath(infile1) :
path[1]="SRR446027_1.fastq": No such file or directory
2: In normalizePath(infile1) :
path[2]="SRR446028_1.fastq": No such file or directory
3: In normalizePath(infile1) :
path[3]="SRR446029_1.fastq": No such file or directory
4: In normalizePath(infile1) :
path[4]="SRR446030_1.fastq": No such file or directory
>
> proc.time()
user system elapsed
19.061 0.757 21.153
systemPipeR.Rcheck/systemPipeR-Ex.timings
| name | user | system | elapsed | |
| EnvModules-class | 0.001 | 0.001 | 0.002 | |
| GOHyperGAll | 0.000 | 0.000 | 0.001 | |
| INTERSECTset-class | 0.011 | 0.009 | 0.019 | |
| SYSargs-class | 0.035 | 0.007 | 0.043 | |
| SYSargs2-class | 2.013 | 0.179 | 2.193 | |
| SYSargs2Pipe-class | 0.001 | 0.001 | 0.001 | |
| SYSargs2Pipe-methods | 0.000 | 0.001 | 0.001 | |
| SYSargsList-class | 0.000 | 0.001 | 0.001 | |
| VENNset-class | 0.008 | 0.005 | 0.012 | |
| alignStats | 1.892 | 0.012 | 1.905 | |
| catDB-class | 0.000 | 0.000 | 0.001 | |
| catmap | 0.000 | 0.001 | 0.000 | |
| clusterRun | 1.858 | 0.009 | 1.868 | |
| config.param | 0 | 0 | 0 | |
| configWF | 0.001 | 0.001 | 0.000 | |
| countRangeset | 0.084 | 0.002 | 0.087 | |
| createWF | 0.001 | 0.000 | 0.001 | |
| evalCode | 0.001 | 0.000 | 0.001 | |
| featureCoverage | 0.011 | 0.002 | 0.012 | |
| featuretypeCounts | 0.010 | 0.002 | 0.013 | |
| filterDEGs | 0.781 | 0.027 | 0.807 | |
| filterVars | 0.011 | 0.003 | 0.014 | |
| genFeatures | 19.741 | 0.406 | 20.151 | |
| getQsubargs | 0.014 | 0.005 | 0.019 | |
| initWF | 0.000 | 0.000 | 0.001 | |
| loadWorkflow | 3.640 | 0.089 | 3.732 | |
| mergeBamByFactor | 0.011 | 0.002 | 0.013 | |
| module | 0.000 | 0.000 | 0.001 | |
| moduleload | 0.001 | 0.000 | 0.000 | |
| olBarplot | 0.467 | 0.044 | 0.512 | |
| olRanges | 0.134 | 0.003 | 0.138 | |
| output_update | 1.966 | 0.013 | 1.979 | |
| overLapper | 0.359 | 0.033 | 0.394 | |
| plotWF | 0.000 | 0.000 | 0.001 | |
| plotfeatureCoverage | 0.010 | 0.002 | 0.012 | |
| plotfeaturetypeCounts | 0.010 | 0.002 | 0.012 | |
| predORF | 0.210 | 0.002 | 0.212 | |
| preprocessReads | 0.022 | 0.005 | 0.027 | |
| qsubRun | 0.014 | 0.002 | 0.016 | |
| readComp | 0.016 | 0.003 | 0.021 | |
| renderReport | 0 | 0 | 0 | |
| renderWF | 1.955 | 0.003 | 1.957 | |
| returnRPKM | 0.001 | 0.000 | 0.000 | |
| runCommandline | 1.965 | 0.010 | 1.976 | |
| runDiff | 0.038 | 0.002 | 0.040 | |
| runWF | 0 | 0 | 0 | |
| run_DESeq2 | 10.046 | 0.040 | 10.089 | |
| run_edgeR | 0.623 | 0.012 | 0.636 | |
| run_track | 0.000 | 0.001 | 0.001 | |
| scaleRanges | 0.392 | 0.004 | 0.396 | |
| seeFastq | 0.000 | 0.001 | 0.000 | |
| subsetWF | 1.807 | 0.002 | 1.809 | |
| symLink2bam | 0.011 | 0.002 | 0.012 | |
| sysargs | 0.014 | 0.004 | 0.017 | |
| sysargs2-methods | 1.976 | 0.015 | 1.993 | |
| sysargslist-methods | 0.000 | 0.000 | 0.001 | |
| systemArgs | 0.014 | 0.003 | 0.016 | |
| targets.as.df | 1.980 | 0.003 | 1.983 | |
| tryCL | 0.000 | 0.001 | 0.000 | |
| tryPath | 0 | 0 | 0 | |
| variantReport | 0.010 | 0.003 | 0.014 | |
| vennPlot | 0.352 | 0.026 | 0.380 | |
| writeTargetsRef | 0.001 | 0.000 | 0.001 | |
| writeTargetsout | 1.989 | 0.005 | 1.994 | |