Package: systemPipeR

Version: 1.16.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:systemPipeR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings systemPipeR_1.16.1.tar.gz

StartedAt: 2019-04-16 03:04:47 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 03:10:54 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 366.8 seconds

RetCode: 0

Status:  OK

CheckDir: systemPipeR.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:systemPipeR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings systemPipeR_1.16.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/systemPipeR.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.16.1’
* 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/.BatchJobs.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 ... NOTE
Namespaces in Imports field not imported from:
  ‘BiocGenerics’ ‘VariantAnnotation’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.AffyID2GeneID: no visible global function definition for ‘read.delim’
.readGOorg: no visible global function definition for ‘read.delim’
.readGOorg: no visible global function definition for ‘na.omit’
.resizeFeature: no visible global function definition for ‘DataFrame’
.sampleDFgene2GO: no visible global function definition for ‘na.omit’
.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: no visible global function definition for ‘phyper’
GOHyperGAll_Simplify: no visible global function definition for
  ‘na.omit’
GOHyperGAll_Subset: no visible binding for global variable
  ‘test_sample’
clusterRun: no visible global function definition for ‘chunk’
combineVarReports: no visible global function definition for
  ‘read.delim’
countRangeset: no visible global function definition for ‘read.delim’
countRangeset: no visible global function definition for ‘import.bed’
countRangeset: no visible global function definition for
  ‘summarizeOverlaps’
countRangeset: no visible global function definition for ‘write.table’
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’
featureCoverage: no visible global function definition for ‘na.omit’
featureCoverage: no visible global function definition for
  ‘write.table’
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’
filterVars: no visible global function definition for ‘readVcf’
filterVars: no visible global function definition for ‘totalDepth<-’
filterVars: no visible global function definition for ‘refDepth<-’
filterVars: no visible global function definition for ‘altDepth<-’
filterVars: no visible global function definition for ‘asVCF’
filterVars: no visible global function definition for ‘writeVcf’
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’
overLapper : <anonymous>: no visible global function definition for
  ‘combn’
plotfeatureCoverage: no visible global function definition for
  ‘aggregate’
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 global function definition for
  ‘dev.off’
plotfeaturetypeCounts: no visible binding for global variable ‘Length’
predORF : .predORF: no visible global function definition for ‘na.omit’
predORF : .predORF: no visible global function definition for ‘IRanges’
readComp: no visible global function definition for ‘read.delim’
readComp: no visible global function definition for ‘combn’
runDiff: no visible global function definition for ‘read.delim’
runDiff: no visible global function definition for ‘write.table’
runDiff: no visible global function definition for ‘pdf’
runDiff: no visible global function definition for ‘dev.off’
run_edgeR: no visible global function definition for ‘model.matrix’
run_edgeR: no visible global function definition for ‘pdf’
run_edgeR: no visible global function definition for ‘dev.off’
scaleRanges : .scaleRanges: no visible global function definition for
  ‘IRanges’
scaleRanges: no visible global function definition for ‘DataFrame’
seeFastq : seeFastqSingle: no visible global function definition for
  ‘boxplot’
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’
systemArgs: no visible global function definition for ‘read.delim’
varSummary: no visible global function definition for ‘read.delim’
variantReport: no visible global function definition for ‘readVcf’
variantReport: no visible global function definition for
  ‘locateVariants’
variantReport: no visible global function definition for ‘AllVariants’
variantReport: no visible global function definition for
  ‘predictCoding’
variantReport: no visible global function definition for ‘ref’
variantReport: no visible global function definition for ‘alt’
variantReport: no visible global function definition for ‘write.table’
vennPlot: no visible global function definition for ‘symbols’
vennPlot: no visible global function definition for ‘text’
vennPlot : plotellipse: no visible global function definition for
  ‘plot’
vennPlot : ellipseVenn: no visible global function definition for
  ‘split.screen’
vennPlot : ellipseVenn: no visible global function definition for
  ‘screen’
vennPlot : ellipseVenn: no visible global function definition for
  ‘text’
vennPlot : ellipseVenn: no visible global function definition for
  ‘close.screen’
writeTargetsRef: no visible global function definition for ‘read.delim’
show,INTERSECTset: no visible binding for global variable ‘vennset’
Undefined global functions or variables:
  AllVariants Base Comparisons Counts Coverage Cycle DataFrame Feature
  Frequency IRanges Intersect_Sets Length Level Method Outliers Percent
  Quality RelDiv Rle Sample SampleMatch Strand Type aggregate alt
  altDepth<- asVCF boxplot chunk close.screen combn dev.off first
  import.bed last locateVariants low mid minQuality model.matrix
  na.omit pdf phyper plot predictCoding qwidth read.delim
  readGAlignmentPairs readGAlignments readVcf ref refDepth<- screen
  seqlengths seqlengths<- split.screen subsetByOverlaps
  summarizeOverlaps symbols test_sample text top tophatargs
  totalDepth<- vennset write.table writeVcf
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "boxplot", "close.screen", "plot", "screen",
             "split.screen", "symbols", "text")
  importFrom("stats", "aggregate", "model.matrix", "na.omit", "phyper")
  importFrom("utils", "combn", "read.delim", "write.table")
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
genFeatures 21.447  0.622  22.325
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/systemPipeR.Rcheck/00check.log’
for details.

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL systemPipeR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘systemPipeR’ ...
** 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
* DONE (systemPipeR)

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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.

> 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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, 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 object is masked from 'package:Biostrings':

    type

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

    aperm, apply




RUNIT TEST PROTOCOL -- Tue Apr 16 03:10:47 2019 
*********************************************** 
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 
 16.365   0.733  17.271 

name	user	system	elapsed
GOHyperGAll	0.001	0.000	0.001
INTERSECTset-class	0.013	0.004	0.017
SYSargs-class	0.043	0.005	0.048
VENNset-class	0.012	0.005	0.017
alignStats	0.016	0.002	0.020
catDB-class	0.000	0.000	0.001
catmap	0	0	0
clusterRun	0.016	0.002	0.019
countRangeset	0.109	0.001	0.111
featureCoverage	0.010	0.001	0.011
featuretypeCounts	0.015	0.001	0.016
filterDEGs	1.081	0.035	1.128
filterVars	0.014	0.002	0.017
genFeatures	21.447	0.622	22.325
getQsubargs	0.014	0.002	0.017
mergeBamByFactor	0.011	0.001	0.012
moduleload	0	0	0
olBarplot	0.651	0.021	0.679
overLapper	0.549	0.020	0.571
plotfeatureCoverage	0.013	0.002	0.015
plotfeaturetypeCounts	0.015	0.001	0.016
predORF	0.267	0.004	0.275
preprocessReads	0.027	0.004	0.031
qsubRun	0.017	0.002	0.019
readComp	0.022	0.003	0.024
returnRPKM	0	0	0
runCommandline	0.021	0.003	0.023
runDiff	0.047	0.002	0.049
run_DESeq2	4.679	0.061	4.775
run_edgeR	1.181	0.032	1.221
scaleRanges	0.171	0.001	0.174
seeFastq	0.000	0.000	0.001
symLink2bam	0.014	0.002	0.016
sysargs	0.016	0.002	0.018
systemArgs	0.018	0.002	0.019
variantReport	0.010	0.002	0.012
vennPlot	0.578	0.015	0.597
writeTargetsRef	0.001	0.000	0.001
writeTargetsout	0.012	0.002	0.013