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This page was generated on 2025-08-30 12:09 -0400 (Sat, 30 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4615
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4562
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4541
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 2135/2320HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
systemPipeR 2.15.2  (landing page)
Thomas Girke
Snapshot Date: 2025-08-29 13:45 -0400 (Fri, 29 Aug 2025)
git_url: https://git.bioconductor.org/packages/systemPipeR
git_branch: devel
git_last_commit: a6c070b
git_last_commit_date: 2025-05-26 17:38:10 -0400 (Mon, 26 May 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for systemPipeR on taishan

To the developers/maintainers of the systemPipeR package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: systemPipeR
Version: 2.15.2
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:systemPipeR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings systemPipeR_2.15.2.tar.gz
StartedAt: 2025-08-29 12:13:43 -0000 (Fri, 29 Aug 2025)
EndedAt: 2025-08-29 12:20:45 -0000 (Fri, 29 Aug 2025)
EllapsedTime: 421.5 seconds
RetCode: 0
Status:   OK  
CheckDir: systemPipeR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:systemPipeR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings systemPipeR_2.15.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/systemPipeR.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘systemPipeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘systemPipeR’ version ‘2.15.2’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘systemPipeR’ can be installed ... OK
* checking installed package size ... INFO
  installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R             1.6Mb
    extdata       2.9Mb
    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 ... NOTE
Problems with news in ‘NEWS’:
  Cannot process chunk/lines:
    OVERVIEW
* checking code 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 loading without being on the library search path ... 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
.cmd2cwl2: no visible global function definition for ‘ave’
.getPreprotext: no visible binding for global variable ‘.’
Undefined global functions or variables:
  . ave
Consider adding
  importFrom("stats", "ave")
to your NAMESPACE file.
* 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  29.461  0.758  30.284
run_DESeq2   14.145  1.073  15.257
renderLogs    4.954  0.736   5.733
loadWorkflow  5.131  0.252   5.398
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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
  ‘/home/biocbuild/bbs-3.22-bioc/meat/systemPipeR.Rcheck/00check.log’
for details.


Installation output

systemPipeR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL systemPipeR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘systemPipeR’ ...
** this is package ‘systemPipeR’ version ‘2.15.2’
** 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)

Tests output

systemPipeR.Rcheck/tests/testthat.Rout


R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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: Seqinfo
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
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 /home/biocbuild/tmp/RtmpSRS9Z1/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 /home/biocbuild/tmp/RtmpSRS9Z1/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."
Creating directory '/home/biocbuild/tmp/RtmpSRS9Z1/rnaseq2/.SPRproject'
Creating file '/home/biocbuild/tmp/RtmpSRS9Z1/rnaseq2/.SPRproject/SYSargsList.yml'
Running Step:  example 
Running Session: Management 

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  |===============================================                       |  67%
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---- Summary ---- 
   Targets Total_Files Existing_Files Missing_Files example
M1      M1           1              1             0 Success
M2      M2           1              1             0 Success
M3      M3           1              1             0 Success

Step Status:  Success 
Done with workflow running, now consider rendering logs & reports
To render logs, run:    sal <- renderLogs(sal)
From command-line:      Rscript -e "sal = systemPipeR::SPRproject(resume = TRUE); sal = systemPipeR::renderLogs(sal)"
To render reports, run: sal <- renderReport(sal)
From command-line:      Rscript -e "sal= s ystemPipeR::SPRproject(resume = TRUE); sal = systemPipeR::renderReport(sal)"
This message is displayed once per R session
Running Step:  newStep 
Running Session: Management 

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  |=======================                                               |  33%
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  |===============================================                       |  67%
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  |======================================================================| 100%
---- Summary ---- 
   Targets Total_Files Existing_Files Missing_Files example
M1      M1           1              1             0 Success
M2      M2           1              1             0 Success
M3      M3           1              1             0 Success

Step Status:  Success 
Running Step:  R_code 
Running Session: Management 

  |                                                                            
  |                                                                      |   0%
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  |======================================================================| 100%
Step Status:  Warning 
[1] "Generated /home/biocbuild/tmp/RtmpSRS9Z1/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 '/home/biocbuild/tmp/RtmpSRS9Z1/newtest/.SPRproject'
Creating file '/home/biocbuild/tmp/RtmpSRS9Z1/newtest/.SPRproject/SYSargsList.yml'
Reading Rmd file
Now importing step 'load_library' 
Now importing step 'export_iris' 
Now importing step 'gzip' 
Now importing step 'gunzip' 
Now importing step 'stats' 
Now back up current Rmd file as template for `renderReport`
Template for renderReport is stored at 
 /home/biocbuild/tmp/RtmpSRS9Z1/newtest/.SPRproject/workflow_template.Rmd 
 Edit this file manually is not recommended 
Now check if required tools are installed 
Check if they are in path:
Checking path for gzip
PASS
Checking path for gunzip
PASS
  step_name   tool in_path
1      gzip   gzip    TRUE
2    gunzip gunzip    TRUE
All required tools in PATH, skip module check. If you want to check modules use `listCmdModules`Import  done
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 

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  |======================================================================| 100%
Step Status:  Success 
Running Step:  export_iris 
Running Session: Management 

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  |======================================================================| 100%
Step Status:  Success 
Skipping Step:  gzip 
Skipping Step:  gunzip 
Skipping Step:  stats 
[ FAIL 0 | WARN 0 | SKIP 10 | PASS 47 ]

══ Skipped tests (10) ══════════════════════════════════════════════════════════
• On Bioconductor (10): 'test-01-SYSargs.R:2:1', 'test-02-SYSargs2.R:9:5',
  'test-02-SYSargs2.R:55:5', 'test-03-SYSargsList.R:63:5',
  'test-05-catDB.R:3:1', 'test-06-VENNset.R:3:1', 'test-07-features.R:3:1',
  'test-08-cmd2cwl.R:2:1', 'test-10-chipSeq.R:4:1', 'test-utilities.R:2:1'

[ FAIL 0 | WARN 0 | SKIP 10 | PASS 47 ]
> 
> proc.time()
   user  system elapsed 
 16.134   1.801  19.051 

Example timings

systemPipeR.Rcheck/systemPipeR-Ex.timings

nameusersystemelapsed
EnvModules-class0.0020.0000.001
GOHyperGAll000
INTERSECTset-class0.0080.0000.008
LineWise-class0.1780.0120.192
ParamFiles0.1140.0000.114
ParamFiles20.1780.0040.182
SPRproject0.0060.0000.005
SYSargs-class0.0190.0040.024
SYSargs2-class0.0790.0000.082
SYSargsList-class0.7270.0160.749
SYSargsList0.1190.0000.121
VENNset-class0.0060.0000.006
alignStats2.2430.0602.311
catDB-class0.0000.0010.001
catmap000
check.output1.6690.0011.674
clusterRun1.5750.0431.624
config.param0.0000.0000.001
configWF000
countRangeset0.0490.0040.053
createParamFiles0.1920.0040.196
cwlFilesUpdate000
evalCode0.0460.0000.051
featureCoverage1.5300.0001.534
featuretypeCounts1.5430.0281.575
filterDEGs2.0090.0322.047
filterVars0.0100.0000.011
genFeatures29.461 0.75830.284
importWF0.0490.0080.058
listCmdTools000
loadWorkflow5.1310.2525.398
mergeBamByFactor0.0100.0000.011
moduleload000
olBarplot0.6580.0080.668
olRanges0.1410.0040.145
output_update1.8090.0111.827
overLapper0.4810.0080.490
plotfeatureCoverage1.8490.0201.873
plotfeaturetypeCounts1.5770.0081.589
predORF0.2600.0000.261
preprocessReads0.5440.0000.550
readComp1.8060.0041.815
renderLogs4.9540.7365.733
renderReport2.1260.5392.681
returnRPKM000
runCommandline1.6630.3592.027
runDiff0.0550.0000.055
runWF0.1170.0280.145
run_DESeq214.145 1.07315.257
run_edgeR1.5480.0561.608
sal2bash0.6370.2750.914
sal2rmd0.6190.3961.018
scaleRanges0.5500.0910.642
seeFastq000
showDF0.0640.0230.087
subsetWF1.6440.2911.939
symLink2bam1.8530.1962.053
sysargs0.0110.0000.010
systemArgs0.0110.0000.010
targets.as.df0.0050.0000.004
trimbatch0.3510.0000.352
tryCMD000
tryPath0.0010.0000.001
variantReport0.010.000.01
vennPlot0.4670.0320.500
writeTargets0.1240.0040.129
writeTargetsRef0.0010.0000.001
writeTargetsout1.8720.0481.925
write_SYSargsList0.1440.0080.154