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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:systemPipeR.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings systemPipeR_1.22.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/systemPipeR.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (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 ‘1.22.0’
* 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
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 ... OK
* 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 ... NOTE
countRangeset: warning in read.delim(infile1(args)[i], comment = "#"):
  partial argument match of 'comment' to 'comment.char'
vennPlot : ellipseVenn: warning in close.screen(all = TRUE): partial
  argument match of 'all' to 'all.screens'
writeTargetsRef: warning in read.delim(infile, comment = "#"): partial
  argument match of 'comment' to 'comment.char'
.change_branch: no visible binding for global variable ‘.’
.checkOutArgs2: no visible binding for global variable ‘dir.name’
.find_long_branch: no visible binding for global variable ‘.’
.makeBam: no visible binding for global variable ‘i’
.makeBam: no visible binding for global variable ‘j’
.parse_step : <anonymous>: no visible binding for global variable ‘.’
.parse_step: no visible binding for global variable ‘.’
.resizeFeature: no visible global function definition for ‘DataFrame’
.subsetReadsByMappingRegion: no visible global function definition for
  ‘IRanges’
.subsetReadsByMappingRegion: no visible global function definition for
  ‘seqlengths’
.subsetReadsByMappingRegion: no visible global function definition for
  ‘readGAlignments’
GOHyperGAll_Subset: no visible binding for global variable
  ‘test_sample’
assembleCommandlineList: no visible binding for global variable ‘WF’
countRangeset: no visible global function definition for ‘import.bed’
countRangeset: no visible global function definition for
  ‘summarizeOverlaps’
featureCoverage: no visible global function definition for
  ‘readGAlignments’
featureCoverage: no visible global function definition for ‘qwidth’
featureCoverage: no visible global function definition for
  ‘subsetByOverlaps’
featureCoverage: no visible global function definition for ‘Rle’
featuretypeCounts: no visible global function definition for
  ‘readGAlignments’
featuretypeCounts: no visible global function definition for
  ‘readGAlignmentPairs’
featuretypeCounts: no visible global function definition for
  ‘subsetByOverlaps’
featuretypeCounts: no visible global function definition for ‘qwidth’
featuretypeCounts: no visible global function definition for ‘last’
featuretypeCounts: no visible global function definition for ‘first’
filterDEGs: no visible binding for global variable ‘Comparisons’
filterDEGs: no visible binding for global variable ‘Counts’
filterDEGs: no visible binding for global variable ‘Type’
genFeatures: no visible global function definition for ‘DataFrame’
genFeatures: no visible global function definition for ‘seqlengths<-’
getQsubargs: no visible binding for global variable ‘tophatargs’
goBarplot: no visible binding for global variable ‘SampleMatch’
goBarplot: no visible binding for global variable ‘Sample’
olBarplot: no visible binding for global variable ‘Intersect_Sets’
olBarplot: no visible binding for global variable ‘Counts’
olBarplot: no visible binding for global variable ‘Level’
olRanges: no visible global function definition for ‘seqlengths<-’
olRanges: no visible global function definition for ‘seqlengths’
olRanges: no visible global function definition for ‘Rle’
olRanges: no visible global function definition for ‘IRanges’
plotfeatureCoverage: no visible binding for global variable ‘Coverage’
plotfeatureCoverage: no visible binding for global variable ‘Strand’
plotfeaturetypeCounts: no visible binding for global variable ‘Feature’
plotfeaturetypeCounts: no visible binding for global variable ‘Counts’
plotfeaturetypeCounts: no visible binding for global variable ‘Strand’
plotfeaturetypeCounts: no visible binding for global variable ‘Length’
predORF : .predORF: no visible global function definition for ‘IRanges’
readComp: no visible binding for global variable ‘args_bam’
renderInputs: no visible binding for global variable ‘WF’
renderOutputs: no visible binding for global variable ‘WF’
scaleRanges : .scaleRanges: no visible global function definition for
  ‘IRanges’
scaleRanges: no visible global function definition for ‘DataFrame’
seeFastqPlot : fastqPlot: no visible binding for global variable
  ‘Cycle’
seeFastqPlot : fastqPlot: no visible binding for global variable ‘low’
seeFastqPlot : fastqPlot: no visible binding for global variable ‘mid’
seeFastqPlot : fastqPlot: no visible binding for global variable ‘top’
seeFastqPlot : fastqPlot: no visible binding for global variable
  ‘Frequency’
seeFastqPlot : fastqPlot: no visible binding for global variable ‘Base’
seeFastqPlot : fastqPlot: no visible binding for global variable
  ‘Quality’
seeFastqPlot : fastqPlot: no visible binding for global variable
  ‘RelDiv’
seeFastqPlot : fastqPlot: no visible binding for global variable
  ‘Method’
seeFastqPlot : fastqPlot: no visible binding for global variable
  ‘minQuality’
seeFastqPlot : fastqPlot: no visible binding for global variable
  ‘Percent’
seeFastqPlot : fastqPlot: no visible binding for global variable
  ‘Outliers’
subsetRmd: no visible binding for global variable ‘.’
Undefined global functions or variables:
  . Base Comparisons Counts Coverage Cycle DataFrame Feature Frequency
  IRanges Intersect_Sets Length Level Method Outliers Percent Quality
  RelDiv Rle Sample SampleMatch Strand Type WF args_bam dir.name first
  i import.bed j last low mid minQuality qwidth readGAlignmentPairs
  readGAlignments seqlengths seqlengths<- subsetByOverlaps
  summarizeOverlaps test_sample top tophatargs
* 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 21.199  0.279  21.479
run_DESeq2   9.593  0.020   9.612
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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
  ‘/home/biocbuild/bbs-3.11-bioc/meat/systemPipeR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL systemPipeR
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.11-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)

R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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.

> BiocGenerics:::testPackage("systemPipeR")

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, which.max, which.min


Attaching package: 'S4Vectors'

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

    expand.grid


Attaching package: 'Biostrings'

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

    strsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'matrixStats'

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

    anyMissing, rowMedians


Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    aperm, apply, rowsum




RUNIT TEST PROTOCOL -- Sat Oct 17 06:06:41 2020 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
systemPipeR RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In normalizePath(infile1) :
  path[1]="SRR446027_1.fastq": No such file or directory
2: In normalizePath(infile1) :
  path[2]="SRR446028_1.fastq": No such file or directory
3: In normalizePath(infile1) :
  path[3]="SRR446029_1.fastq": No such file or directory
4: In normalizePath(infile1) :
  path[4]="SRR446030_1.fastq": No such file or directory
> 
> proc.time()
   user  system elapsed 
 18.481   0.424  21.849