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BioC 3.3: CHECK report for systemPipeR on moscato2

This page was generated on 2016-10-13 12:53:05 -0700 (Thu, 13 Oct 2016).

Package 1144/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
systemPipeR 1.6.4
Thomas Girke
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/systemPipeR
Last Changed Rev: 119926 / Revision: 122332
Last Changed Date: 2016-08-06 14:17:03 -0700 (Sat, 06 Aug 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: systemPipeR
Version: 1.6.4
Command: rm -rf systemPipeR.buildbin-libdir systemPipeR.Rcheck && mkdir systemPipeR.buildbin-libdir systemPipeR.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=systemPipeR.buildbin-libdir systemPipeR_1.6.4.tar.gz >systemPipeR.Rcheck\00install.out 2>&1 && cp systemPipeR.Rcheck\00install.out systemPipeR-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=systemPipeR.buildbin-libdir --install="check:systemPipeR-install.out" --force-multiarch --no-vignettes --timings systemPipeR_1.6.4.tar.gz
StartedAt: 2016-10-13 09:32:10 -0700 (Thu, 13 Oct 2016)
EndedAt: 2016-10-13 09:41:42 -0700 (Thu, 13 Oct 2016)
EllapsedTime: 572.0 seconds
RetCode: 0
Status:  OK  
CheckDir: systemPipeR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf systemPipeR.buildbin-libdir systemPipeR.Rcheck && mkdir systemPipeR.buildbin-libdir systemPipeR.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=systemPipeR.buildbin-libdir systemPipeR_1.6.4.tar.gz >systemPipeR.Rcheck\00install.out 2>&1 && cp systemPipeR.Rcheck\00install.out systemPipeR-install.out  && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=systemPipeR.buildbin-libdir --install="check:systemPipeR-install.out" --force-multiarch --no-vignettes --timings systemPipeR_1.6.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/systemPipeR.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'systemPipeR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'systemPipeR' version '1.6.4'
* 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 whether package 'systemPipeR' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc       3.1Mb
    extdata   1.7Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
genFeatures 18.03   0.56   20.34
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
genFeatures 18.40   0.58   18.99
run_edgeR    5.74   0.00    5.74
run_DESeq2   5.24   0.02    5.26
filterDEGs   4.46   0.00    5.15
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.R'
 OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: 'GenomicAlignments'
* 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: 5 NOTEs
See
  'E:/biocbld/bbs-3.3-bioc/meat/systemPipeR.Rcheck/00check.log'
for details.


systemPipeR.Rcheck/00install.out:


install for i386

* installing *source* package 'systemPipeR' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'systemPipeR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'systemPipeR' as systemPipeR_1.6.4.zip
* DONE (systemPipeR)

systemPipeR.Rcheck/examples_i386/systemPipeR-Ex.timings:

nameusersystemelapsed
GOHyperGAll000
INTERSECTset-class0.010.000.02
SYSargs-class0.030.000.03
VENNset-class000
alignStats0.010.000.01
catDB-class000
catmap0.020.000.02
clusterRun0.020.000.01
countRangeset0.060.000.07
featureCoverage0.010.000.01
featuretypeCounts0.020.000.02
filterDEGs3.630.003.63
filterVars0.020.000.02
genFeatures18.03 0.5620.34
getQsubargs0.030.000.03
mergeBamByFactor0.040.000.03
moduleload000
olBarplot1.010.021.05
overLapper0.720.010.73
plotfeatureCoverage0.010.000.02
plotfeaturetypeCounts0.020.000.02
predORF0.650.000.65
preprocessReads0.050.000.05
qsubRun0.030.000.03
readComp0.030.000.03
returnRPKM000
runCommandline0.010.000.01
runDiff0.080.000.08
run_DESeq24.680.014.70
run_edgeR3.960.023.97
scaleRanges0.160.000.16
seeFastq000
symLink2bam0.010.000.01
sysargs0.020.000.02
systemArgs0.020.000.02
variantReport0.020.000.02
vennPlot0.890.030.92
writeTargetsRef0.000.010.02
writeTargetsout0.010.000.01

systemPipeR.Rcheck/examples_x64/systemPipeR-Ex.timings:

nameusersystemelapsed
GOHyperGAll000
INTERSECTset-class0.010.000.01
SYSargs-class0.050.000.05
VENNset-class000
alignStats0.030.000.03
catDB-class000
catmap000
clusterRun0.020.000.02
countRangeset0.070.000.08
featureCoverage0.040.000.06
featuretypeCounts0.030.000.03
filterDEGs4.460.005.15
filterVars0.010.000.01
genFeatures18.40 0.5818.99
getQsubargs0.010.000.01
mergeBamByFactor0.020.000.02
moduleload000
olBarplot0.670.010.68
overLapper1.110.001.11
plotfeatureCoverage0.020.000.01
plotfeaturetypeCounts0.010.000.02
predORF0.330.000.32
preprocessReads0.030.020.05
qsubRun0.010.000.02
readComp0.030.000.03
returnRPKM000
runCommandline0.020.000.01
runDiff0.090.000.09
run_DESeq25.240.025.26
run_edgeR5.740.005.74
scaleRanges0.280.010.29
seeFastq000
symLink2bam0.030.000.03
sysargs0.010.000.02
systemArgs0.020.000.02
variantReport0.010.000.01
vennPlot1.040.061.10
writeTargetsRef0.020.000.02
writeTargetsout0.010.000.02