Back to Multiple platform build/check report for BioC 3.16
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

This page was generated on 2022-06-29 11:05:41 -0400 (Wed, 29 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4343
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" 4159
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

CHECK results for systemPipeR on lconway


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? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1960/2124HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
systemPipeR 2.3.2  (landing page)
Thomas Girke
Snapshot Date: 2022-06-28 14:00:02 -0400 (Tue, 28 Jun 2022)
git_url: https://git.bioconductor.org/packages/systemPipeR
git_branch: master
git_last_commit: e802523
git_last_commit_date: 2022-04-29 19:42:47 -0400 (Fri, 29 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: systemPipeR
Version: 2.3.2
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:systemPipeR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings systemPipeR_2.3.2.tar.gz
StartedAt: 2022-06-28 23:32:22 -0400 (Tue, 28 Jun 2022)
EndedAt: 2022-06-28 23:38:05 -0400 (Tue, 28 Jun 2022)
EllapsedTime: 342.2 seconds
RetCode: 0
Status:   OK  
CheckDir: systemPipeR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:systemPipeR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings systemPipeR_2.3.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/systemPipeR.Rcheck’
* using R version 4.2.0 Patched (2022-05-29 r82424)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘systemPipeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘systemPipeR’ version ‘2.3.2’
* 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 ... NOTE
  installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R             1.5Mb
    extdata       2.7Mb
    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
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
genFeatures  26.979  0.529  27.616
run_DESeq2   11.864  0.096  11.988
loadWorkflow  6.014  0.141   6.173
renderLogs    4.784  0.727   5.904
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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
  ‘/Users/biocbuild/bbs-3.16-bioc/meat/systemPipeR.Rcheck/00check.log’
for details.



Installation output

systemPipeR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL systemPipeR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/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 4.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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
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 /tmp/Rtmp3dZlMo/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 /tmp/Rtmp3dZlMo/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 '/private/tmp/Rtmp3dZlMo/rnaseq2/.SPRproject'
Creating file '/private/tmp/Rtmp3dZlMo/rnaseq2/.SPRproject/SYSargsList.yml'
Running Step:  example 
Running Session: Management 

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=======================                                               |  33%
  |                                                                            
  |===============================================                       |  67%
  |                                                                            
  |======================================================================| 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 
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 

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=======================                                               |  33%
  |                                                                            
  |===============================================                       |  67%
  |                                                                            
  |======================================================================| 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%
  |                                                                            
  |======================================================================| 100%
Step Status:  Warning 
[1] "Generated /tmp/Rtmp3dZlMo/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 '/private/tmp/Rtmp3dZlMo/newtest/.SPRproject'
Creating file '/private/tmp/Rtmp3dZlMo/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 0 | SKIP 10 | PASS 47 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• On Bioconductor (10)

[ FAIL 0 | WARN 0 | SKIP 10 | PASS 47 ]
> 
> proc.time()
   user  system elapsed 
 12.285   3.730  16.240 

Example timings

systemPipeR.Rcheck/systemPipeR-Ex.timings

nameusersystemelapsed
EnvModules-class0.0020.0000.002
GOHyperGAll0.0000.0000.002
INTERSECTset-class0.0080.0080.016
LineWise-class0.1970.0210.218
ParamFiles0.0820.0030.085
SPRproject0.0020.0020.005
SYSargs-class0.0210.0070.029
SYSargs2-class0.1030.0080.113
SYSargsList-class1.1410.0281.174
SYSargsList0.0940.0080.103
VENNset-class0.0040.0030.007
alignStats0.9570.0421.005
catDB-class0.0010.0000.001
catmap0.0000.0000.001
check.output1.1510.0111.166
clusterRun1.1240.0101.138
config.param000
configWF000
countRangeset0.0690.0030.072
createParamFiles0.0660.0010.066
cwlFilesUpdate000
evalCode0.0480.0050.055
featureCoverage0.9940.0051.001
featuretypeCounts1.0420.0061.053
filterDEGs1.0620.0271.092
filterVars0.0090.0040.013
genFeatures26.979 0.52927.616
importWF0.0280.0070.036
loadWorkflow6.0140.1416.173
mergeBamByFactor0.0070.0020.009
moduleload0.0000.0010.001
olBarplot0.4190.0380.462
olRanges0.1090.0040.113
output_update1.3000.0111.313
overLapper0.3050.0310.340
plotfeatureCoverage1.2660.0081.277
plotfeaturetypeCounts1.2400.0071.251
predORF0.1990.0050.205
preprocessReads0.3530.0050.360
readComp1.2300.0071.240
renderLogs4.7840.7275.904
renderReport1.6170.1591.825
returnRPKM0.0000.0010.000
runCommandline1.2290.0271.260
runDiff0.0420.0030.045
runWF0.0920.0090.104
run_DESeq211.864 0.09611.988
run_edgeR0.5760.0110.590
sal2bash0.4970.0230.523
sal2rmd0.4760.0210.500
scaleRanges0.2130.0020.216
seeFastq0.0010.0000.001
showDF0.0580.0250.083
subsetWF1.3090.0081.322
symLink2bam1.3680.0081.379
sysargs0.0090.0040.013
systemArgs0.0100.0040.014
targets.as.df0.0040.0010.005
trimbatch0.1910.0020.194
tryCMD000
tryPath0.0010.0000.001
variantReport0.0080.0040.012
vennPlot0.3200.0300.355
writeTargets0.0970.0080.107
writeTargetsRef0.0000.0010.001
writeTargetsout1.2600.0081.273
write_SYSargsList0.1130.0080.123