Back to Multiple platform build/check report for BioC 3.8
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

CHECK report for systemPipeR on malbec1

This page was generated on 2019-04-16 11:50:49 -0400 (Tue, 16 Apr 2019).

Package 1541/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
systemPipeR 1.16.1
Thomas Girke
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/systemPipeR
Branch: RELEASE_3_8
Last Commit: 6f1a478
Last Changed Date: 2019-01-04 13:07:22 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: systemPipeR
Version: 1.16.1
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:systemPipeR.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings systemPipeR_1.16.1.tar.gz
StartedAt: 2019-04-16 03:21:55 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 03:27:30 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 335.0 seconds
RetCode: 0
Status:  OK 
CheckDir: systemPipeR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:systemPipeR.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings systemPipeR_1.16.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/systemPipeR.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.16.1’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
genFeatures 21.904  0.336  22.282
run_DESeq2   5.276  0.020   5.303
* 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
  ‘/home/biocbuild/bbs-3.8-bioc/meat/systemPipeR.Rcheck/00check.log’
for details.



Installation output

systemPipeR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL systemPipeR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/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)

Tests output

systemPipeR.Rcheck/tests/runTests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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, 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 03:27:26 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 
 15.716   0.448  16.219 

Example timings

systemPipeR.Rcheck/systemPipeR-Ex.timings

nameusersystemelapsed
GOHyperGAll000
INTERSECTset-class0.0160.0000.014
SYSargs-class0.0480.0000.060
VENNset-class0.0120.0000.010
alignStats0.0160.0000.017
catDB-class0.0000.0000.001
catmap000
clusterRun0.0160.0000.016
countRangeset0.0760.0000.074
featureCoverage0.0040.0040.008
featuretypeCounts0.0080.0000.008
filterDEGs1.1960.0281.225
filterVars0.0160.0000.014
genFeatures21.904 0.33622.282
getQsubargs0.0120.0040.017
mergeBamByFactor0.0120.0000.028
moduleload000
olBarplot0.6960.0120.711
overLapper0.6320.0080.643
plotfeatureCoverage0.0160.0000.014
plotfeaturetypeCounts0.0160.0000.013
predORF0.2880.0000.288
preprocessReads0.0320.0000.119
qsubRun0.0160.0000.017
readComp0.0160.0080.024
returnRPKM000
runCommandline0.0160.0000.017
runDiff0.0560.0000.056
run_DESeq25.2760.0205.303
run_edgeR1.0160.0041.023
scaleRanges0.2120.0000.215
seeFastq0.0000.0000.001
symLink2bam0.0120.0000.014
sysargs0.0160.0000.017
systemArgs0.0160.0000.017
variantReport0.0160.0000.016
vennPlot0.6000.0080.610
writeTargetsRef0.0040.0000.001
writeTargetsout0.0120.0000.014