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This page was generated on 2024-06-28 17:42 -0400 (Fri, 28 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4760
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4494
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4508
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4466
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4362
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 2125/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
systemPipeR 2.10.0  (landing page)
Thomas Girke
Snapshot Date: 2024-06-26 14:00 -0400 (Wed, 26 Jun 2024)
git_url: https://git.bioconductor.org/packages/systemPipeR
git_branch: RELEASE_3_19
git_last_commit: 4521e19
git_last_commit_date: 2024-04-30 10:38:46 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  


CHECK results for systemPipeR on palomino3

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.

raw results


Summary

Package: systemPipeR
Version: 2.10.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:systemPipeR.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings systemPipeR_2.10.0.tar.gz
StartedAt: 2024-06-27 06:50:00 -0400 (Thu, 27 Jun 2024)
EndedAt: 2024-06-27 06:57:21 -0400 (Thu, 27 Jun 2024)
EllapsedTime: 440.5 seconds
RetCode: 0
Status:   OK  
CheckDir: systemPipeR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:systemPipeR.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings systemPipeR_2.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/systemPipeR.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'systemPipeR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'systemPipeR' version '2.10.0'
* 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  6.3Mb
  sub-directories of 1Mb or more:
    R             1.6Mb
    extdata       2.3Mb
    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 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 33.34   0.83   34.21
run_DESeq2  10.22   0.04   10.28
renderLogs   2.73   0.50   12.81
* 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: 4 NOTEs
See
  'F:/biocbuild/bbs-3.19-bioc/meat/systemPipeR.Rcheck/00check.log'
for details.


Installation output

systemPipeR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL systemPipeR
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/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)

Tests output

systemPipeR.Rcheck/tests/testthat.Rout


R version 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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, aperm, 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, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

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

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 F:\\biocbuild\\bbs-3.19-bioc\\tmpdir\\RtmpYVt5XC/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 F:\\biocbuild\\bbs-3.19-bioc\\tmpdir\\RtmpYVt5XC/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 F:\\biocbuild\\bbs-3.19-bioc\\tmpdir\\RtmpYVt5XC/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 'F:\biocbuild\bbs-3.19-bioc\tmpdir\RtmpYVt5XC\newtest/.SPRproject'
Creating file 'F:\biocbuild\bbs-3.19-bioc\tmpdir\RtmpYVt5XC\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 
 F:\biocbuild\bbs-3.19-bioc\tmpdir\RtmpYVt5XC\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
ERROR
  step_name   tool in_path
1      gzip   gzip    TRUE
2    gunzip gunzip   FALSE
Now check if modular system:
No module is listed, check your CWL yaml configuration files, skip.
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 

  |                                                                            
  |                                                                      |   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 
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
[ FAIL 0 | WARN 0 | SKIP 11 | PASS 26 ]

══ Skipped tests (11) ══════════════════════════════════════════════════════════
• 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'
• On Windows (1): 'test-03-SYSargsList.R:9:5'

[ FAIL 0 | WARN 0 | SKIP 11 | PASS 26 ]
> 
> proc.time()
   user  system elapsed 
  14.50    2.60   23.06 

Example timings

systemPipeR.Rcheck/systemPipeR-Ex.timings

nameusersystemelapsed
EnvModules-class000
GOHyperGAll000
INTERSECTset-class0.010.000.01
LineWise-class0.130.080.27
ParamFiles0.190.000.19
ParamFiles20.140.030.17
SPRproject0.010.000.01
SYSargs-class0.020.010.05
SYSargs2-class0.080.000.10
SYSargsList-class0.600.070.67
SYSargsList0.130.000.13
VENNset-class0.000.020.01
alignStats2.090.072.19
catDB-class0.020.000.02
catmap000
check.output1.700.051.76
clusterRun1.140.031.17
config.param000
configWF000
countRangeset0.070.000.07
createParamFiles0.170.020.18
cwlFilesUpdate000
evalCode0.030.000.08
featureCoverage1.480.001.49
featuretypeCounts1.350.081.42
filterDEGs2.250.072.34
filterVars0.020.000.01
genFeatures33.34 0.8334.21
importWF0.060.000.08
listCmdTools000
loadWorkflow4.060.144.20
mergeBamByFactor0.020.000.02
moduleload000
olBarplot0.360.070.42
olRanges0.290.000.30
output_update1.190.031.22
overLapper0.50.00.5
plotfeatureCoverage1.910.001.90
plotfeaturetypeCounts1.750.031.78
predORF0.230.000.25
preprocessReads0.440.030.47
readComp1.500.021.52
renderLogs 2.73 0.5012.81
renderReport2.210.184.13
returnRPKM000
runCommandline1.590.031.64
runDiff0.030.000.04
runWF0.140.000.14
run_DESeq210.22 0.0410.28
run_edgeR1.940.092.23
sal2bash0.830.051.20
sal2rmd0.560.090.75
scaleRanges0.270.000.27
seeFastq000
showDF0.090.060.86
subsetWF1.640.051.72
symLink2bam1.530.051.58
sysargs0.020.000.03
systemArgs0.010.010.03
targets.as.df0.020.000.01
trimbatch0.300.000.36
tryCMD000
tryPath0.000.020.02
variantReport0.010.000.03
vennPlot0.660.030.69
writeTargets0.120.010.19
writeTargetsRef000
writeTargetsout1.320.041.34
write_SYSargsList0.140.010.17