Multiple platform build/check report for BioC 3.14 - CHECK results for systemPipeR on tokay2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4137
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: systemPipeR

Version: 2.0.8

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:systemPipeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings systemPipeR_2.0.8.tar.gz

StartedAt: 2022-04-13 03:52:17 -0400 (Wed, 13 Apr 2022)

EndedAt: 2022-04-13 04:01:12 -0400 (Wed, 13 Apr 2022)

EllapsedTime: 535.1 seconds

RetCode: 0

Status: OK

CheckDir: systemPipeR.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:systemPipeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings systemPipeR_2.0.8.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/systemPipeR.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '2.0.8'
* 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  7.4Mb
  sub-directories of 1Mb or more:
    R             1.5Mb
    extdata       2.4Mb
    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
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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  24.60   1.91   26.52
run_DESeq2   17.79   0.04   17.83
renderLogs    6.66   0.95   11.63
loadWorkflow  5.02   0.00    5.01
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
genFeatures 24.15   0.51   24.69
run_DESeq2  17.61   0.09   17.70
renderLogs   7.66   0.34   11.68
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/systemPipeR.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/systemPipeR_2.0.8.tar.gz && rm -rf systemPipeR.buildbin-libdir && mkdir systemPipeR.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=systemPipeR.buildbin-libdir systemPipeR_2.0.8.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL systemPipeR_2.0.8.zip && rm systemPipeR_2.0.8.tar.gz systemPipeR_2.0.8.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
  2 2047k    2 44359    0     0   282k      0  0:00:07 --:--:--  0:00:07  283k
 93 2047k   93 1923k    0     0  1718k      0  0:00:01  0:00:01 --:--:-- 1718k
100 2047k  100 2047k    0     0  1718k      0  0:00:01  0:00:01 --:--:-- 1718k

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  
    LineWise-class                          html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/systemPipeR.buildbin-libdir/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: C:/Users/biocbuild/bbs-3.14-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  
    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  
    writeTargets                            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

install for x64

* installing *source* package 'systemPipeR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'systemPipeR' as systemPipeR_2.0.8.zip
* DONE (systemPipeR)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'systemPipeR' successfully unpacked and MD5 sums checked


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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

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 C:\\Users\\biocbuild\\bbs-3.14-bioc\\tmpdir\\RtmpgB9enH/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 C:\\Users\\biocbuild\\bbs-3.14-bioc\\tmpdir\\RtmpgB9enH/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 C:\\Users\\biocbuild\\bbs-3.14-bioc\\tmpdir\\RtmpgB9enH/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 'C:\Users\biocbuild\bbs-3.14-bioc\tmpdir\RtmpgB9enH\newtest/.SPRproject'
Creating file 'C:\Users\biocbuild\bbs-3.14-bioc\tmpdir\RtmpgB9enH\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 6 | SKIP 11 | PASS 26 ]

== Skipped tests ===============================================================
* On Bioconductor (10)
* On Windows (1)

[ FAIL 0 | WARN 6 | SKIP 11 | PASS 26 ]
> 
> proc.time()
   user  system elapsed 
  11.60    3.60   43.65


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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 C:\\Users\\biocbuild\\bbs-3.14-bioc\\tmpdir\\RtmpWkUxXO/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 C:\\Users\\biocbuild\\bbs-3.14-bioc\\tmpdir\\RtmpWkUxXO/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 C:\\Users\\biocbuild\\bbs-3.14-bioc\\tmpdir\\RtmpWkUxXO/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 'C:\Users\biocbuild\bbs-3.14-bioc\tmpdir\RtmpWkUxXO\newtest/.SPRproject'
Creating file 'C:\Users\biocbuild\bbs-3.14-bioc\tmpdir\RtmpWkUxXO\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 6 | SKIP 11 | PASS 26 ]

== Skipped tests ===============================================================
* On Bioconductor (10)
* On Windows (1)

[ FAIL 0 | WARN 6 | SKIP 11 | PASS 26 ]
> 
> proc.time()
   user  system elapsed 
  13.18    2.64   16.00

name	user	system	elapsed
EnvModules-class	0	0	0
GOHyperGAll	0	0	0
INTERSECTset-class	0.02	0.00	0.02
LineWise-class	0.18	0.02	0.20
ParamFiles	0.05	0.04	0.09
SPRproject	0	0	0
SYSargs-class	0.03	0.00	0.04
SYSargs2-class	0.10	0.00	0.09
SYSargsList-class	0.70	0.29	0.98
SYSargsList	0.11	0.09	0.21
VENNset-class	0.01	0.00	0.01
alignStats	1.13	0.25	1.38
catDB-class	0	0	0
catmap	0	0	0
check.output	1.11	0.00	1.11
clusterRun	1.08	0.00	1.08
config.param	0	0	0
configWF	0	0	0
countRangeset	0.06	0.00	0.06
createParamFiles	0.06	0.00	0.06
cwlFilesUpdate	0	0	0
evalCode	0.05	0.00	0.23
featureCoverage	1.01	0.00	1.02
featuretypeCounts	0.02	0.00	0.02
filterDEGs	1.86	0.09	1.95
filterVars	0.02	0.00	0.01
genFeatures	24.60	1.91	26.52
importWF	0.05	0.00	0.05
loadWorkflow	5.02	0.00	5.01
mergeBamByFactor	0.01	0.00	0.02
moduleload	0	0	0
olBarplot	0.46	0.00	0.45
olRanges	0.14	0.00	0.14
output_update	1.20	0.00	1.21
overLapper	0.28	0.05	0.32
plotfeatureCoverage	0.02	0.00	0.02
plotfeaturetypeCounts	0	0	0
predORF	0.18	0.00	0.19
preprocessReads	0.55	0.00	0.54
readComp	0.03	0.00	0.03
renderLogs	6.66	0.95	11.63
renderReport	2.91	0.23	3.51
returnRPKM	0	0	0
runCommandline	1.17	0.00	1.17
runDiff	0.02	0.02	0.03
runWF	0.10	0.01	0.11
run_DESeq2	17.79	0.04	17.83
run_edgeR	0.68	0.00	0.67
sal2bash	0.71	0.02	0.74
sal2rmd	0.5	0.0	0.5
scaleRanges	0.25	0.00	0.25
seeFastq	0	0	0
showDF	0.05	0.03	0.08
subsetWF	1.28	0.00	1.28
symLink2bam	0.02	0.00	0.01
sysargs	0.01	0.00	0.02
systemArgs	0	0	0
targets.as.df	0.02	0.00	0.02
tryCMD	0	0	0
tryPath	0	0	0
variantReport	0.02	0.00	0.01
vennPlot	0.31	0.00	0.31
writeTargets	0.09	0.01	0.11
writeTargetsRef	0	0	0
writeTargetsout	1.3	0.0	1.3
write_SYSargsList	0.26	0.02	0.28

name	user	system	elapsed
EnvModules-class	0	0	0
GOHyperGAll	0	0	0
INTERSECTset-class	0.01	0.00	0.02
LineWise-class	0.19	0.00	0.19
ParamFiles	0.08	0.00	0.08
SPRproject	0	0	0
SYSargs-class	0.01	0.00	0.01
SYSargs2-class	0.08	0.01	0.10
SYSargsList-class	0.44	0.05	0.48
SYSargsList	0.09	0.00	0.09
VENNset-class	0.02	0.00	0.02
alignStats	1.11	0.03	1.14
catDB-class	0	0	0
catmap	0	0	0
check.output	1.15	0.00	1.16
clusterRun	1.05	0.00	1.04
config.param	0	0	0
configWF	0	0	0
countRangeset	0.08	0.00	0.08
createParamFiles	0.06	0.00	0.06
cwlFilesUpdate	0	0	0
evalCode	0.05	0.02	0.07
featureCoverage	1.09	0.00	1.09
featuretypeCounts	0	0	0
filterDEGs	1.36	0.00	1.36
filterVars	0.02	0.00	0.01
genFeatures	24.15	0.51	24.69
importWF	0.05	0.00	0.05
loadWorkflow	4.69	0.02	4.70
mergeBamByFactor	0.00	0.02	0.02
moduleload	0	0	0
olBarplot	0.37	0.01	0.39
olRanges	0.13	0.00	0.12
output_update	1.33	0.00	1.33
overLapper	0.32	0.00	0.33
plotfeatureCoverage	0	0	0
plotfeaturetypeCounts	0.02	0.00	0.02
predORF	0.45	0.00	0.45
preprocessReads	0.39	0.00	0.39
readComp	0.02	0.00	0.01
renderLogs	7.66	0.34	11.68
renderReport	4.35	0.19	4.98
returnRPKM	0	0	0
runCommandline	0.99	0.00	0.99
runDiff	0.03	0.00	0.03
runWF	0.08	0.02	0.09
run_DESeq2	17.61	0.09	17.70
run_edgeR	0.67	0.02	0.69
sal2bash	0.77	0.00	0.77
sal2rmd	0.57	0.03	0.61
scaleRanges	0.27	0.00	0.26
seeFastq	0	0	0
showDF	0.06	0.03	0.10
subsetWF	1.30	0.00	1.29
symLink2bam	0.00	0.02	0.02
sysargs	0.00	0.01	0.01
systemArgs	0.00	0.02	0.02
targets.as.df	0	0	0
tryCMD	0	0	0
tryPath	0	0	0
variantReport	0.01	0.00	0.01
vennPlot	0.32	0.01	0.33
writeTargets	0.11	0.00	0.11
writeTargetsRef	0	0	0
writeTargetsout	1.26	0.00	1.27
write_SYSargsList	0.13	0.00	0.12

CHECK results for systemPipeR on tokay2

Summary

Command output

Installation output

Tests output

Example timings