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This page was generated on 2024-12-23 11:47 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4372
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 2094/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
systemPipeR 2.13.0  (landing page)
Thomas Girke
Snapshot Date: 2024-12-22 13:40 -0500 (Sun, 22 Dec 2024)
git_url: https://git.bioconductor.org/packages/systemPipeR
git_branch: devel
git_last_commit: 94357f2
git_last_commit_date: 2024-10-29 09:54:41 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    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 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for systemPipeR on kunpeng2

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: 2.13.0
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_2.13.0.tar.gz
StartedAt: 2024-12-23 12:41:42 -0000 (Mon, 23 Dec 2024)
EndedAt: 2024-12-23 12:49:03 -0000 (Mon, 23 Dec 2024)
EllapsedTime: 440.6 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_2.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/systemPipeR.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* 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 ‘2.13.0’
* 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 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  31.645  0.887  32.587
run_DESeq2   13.014  0.168  13.210
renderLogs    5.873  0.682   6.599
loadWorkflow  5.077  0.103   5.190
* 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-3.21-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-devel_2024-11-24/site-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 Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 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: GenomeInfoDb
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: 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
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 /home/biocbuild/tmp/Rtmptdvloz/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/Rtmptdvloz/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/Rtmptdvloz/rnaseq2/.SPRproject'
Creating file '/home/biocbuild/tmp/Rtmptdvloz/rnaseq2/.SPRproject/SYSargsList.yml'
Running Step:  example 
Running Session: Management 

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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 

  |                                                                            
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  |======================================================================| 100%
Step Status:  Warning 
[1] "Generated /home/biocbuild/tmp/Rtmptdvloz/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/Rtmptdvloz/newtest/.SPRproject'
Creating file '/home/biocbuild/tmp/Rtmptdvloz/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/Rtmptdvloz/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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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 
 15.964   1.433  18.460 

Example timings

systemPipeR.Rcheck/systemPipeR-Ex.timings

nameusersystemelapsed
EnvModules-class0.0000.0010.002
GOHyperGAll000
INTERSECTset-class0.0060.0020.008
LineWise-class0.1760.0130.191
ParamFiles0.1470.0000.147
ParamFiles20.1840.0000.184
SPRproject0.0050.0000.005
SYSargs-class0.0210.0000.022
SYSargs2-class0.0730.0000.076
SYSargsList-class0.5430.0240.570
SYSargsList0.1100.0080.120
VENNset-class0.0060.0000.007
alignStats2.6820.1082.800
catDB-class000
catmap000
check.output1.7190.0081.732
clusterRun1.6030.0001.608
config.param000
configWF000
countRangeset0.0510.0000.052
createParamFiles0.1920.0110.205
cwlFilesUpdate000
evalCode0.0310.0040.039
featureCoverage1.5970.0081.609
featuretypeCounts1.6060.0151.626
filterDEGs2.0830.0562.145
filterVars0.0100.0000.011
genFeatures31.645 0.88732.587
importWF0.0450.0040.049
listCmdTools000
loadWorkflow5.0770.1035.190
mergeBamByFactor0.0000.0100.011
moduleload0.0000.0000.001
olBarplot0.5690.0160.585
olRanges0.130.000.13
output_update1.8190.0041.827
overLapper0.4630.0080.472
plotfeatureCoverage1.5880.0481.639
plotfeaturetypeCounts1.8260.0001.828
predORF0.2410.0040.245
preprocessReads0.5430.0150.561
readComp1.8540.0481.904
renderLogs5.8730.6826.599
renderReport2.1110.4342.566
returnRPKM000
runCommandline1.5580.3521.912
runDiff0.0380.0120.050
runWF0.1150.0110.128
run_DESeq213.014 0.16813.210
run_edgeR1.4890.0271.518
sal2bash0.5920.2570.852
sal2rmd0.9050.3131.224
scaleRanges0.2290.0480.278
seeFastq000
showDF0.0580.0200.078
subsetWF1.6740.2311.911
symLink2bam1.8740.0831.962
sysargs0.010.000.01
systemArgs0.010.000.01
targets.as.df0.0050.0000.005
trimbatch0.3460.0000.348
tryCMD000
tryPath0.0010.0000.002
variantReport0.010.000.01
vennPlot0.4780.0000.479
writeTargets0.1180.0000.119
writeTargetsRef0.0010.0000.001
writeTargetsout1.8540.0081.867
write_SYSargsList0.1320.0040.138