##############################################################################
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###
### 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_2.16.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/systemPipeR.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘systemPipeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘systemPipeR’ version ‘2.16.0’
* 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  6.7Mb
  sub-directories of 1Mb or more:
    R             1.6Mb
    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 ... 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     43.954  1.191  62.948
run_DESeq2      22.306  0.444  36.807
loadWorkflow    10.463  0.501  15.571
renderLogs       7.707  1.574  12.217
renderReport     3.596  0.822   5.959
runCommandline   3.640  0.462   5.731
filterDEGs       3.778  0.080   5.360
subsetWF         3.431  0.307   7.732
symLink2bam      3.541  0.104   6.184
writeTargetsout  3.446  0.020   5.590
run_edgeR        2.769  0.113   6.740
scaleRanges      1.272  1.050   5.989
* 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
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/systemPipeR.Rcheck/00check.log’
for details.

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘systemPipeR’ ...
** this is package ‘systemPipeR’ version ‘2.16.0’
** 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)

R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 /tmp/RtmpNQlbht/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/RtmpNQlbht/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/RtmpNQlbht/rnaseq2/.SPRproject'
Creating file '/private/tmp/RtmpNQlbht/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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Step Status:  Warning 
[1] "Generated /tmp/RtmpNQlbht/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/RtmpNQlbht/newtest/.SPRproject'
Creating file '/private/tmp/RtmpNQlbht/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 
 /private/tmp/RtmpNQlbht/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 
 27.854   7.844  59.982