Thomas Girke
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/systemPipeR |
| git_branch: RELEASE_3_13 |
| git_last_commit: 08593cd |
| git_last_commit_date: 2021-06-26 12:23:40 -0400 (Sat, 26 Jun 2021) |
| 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 |
##############################################################################
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###
### 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
###
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* 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
###
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% 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
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systemPipeR.Rcheck/examples_i386/systemPipeR-Ex.timings
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systemPipeR.Rcheck/examples_x64/systemPipeR-Ex.timings
|