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BioC 3.4: CHECK report for systemPipeR on moscato1

This page was generated on 2016-09-21 03:46:16 -0700 (Wed, 21 Sep 2016).

Package 1189/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
systemPipeR 1.7.3
Thomas Girke
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/systemPipeR
Last Changed Rev: 120039 / Revision: 121152
Last Changed Date: 2016-08-10 17:47:29 -0700 (Wed, 10 Aug 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: systemPipeR
Version: 1.7.3
Command: rm -rf systemPipeR.buildbin-libdir systemPipeR.Rcheck && mkdir systemPipeR.buildbin-libdir systemPipeR.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=systemPipeR.buildbin-libdir systemPipeR_1.7.3.tar.gz >systemPipeR.Rcheck\00install.out 2>&1 && cp systemPipeR.Rcheck\00install.out systemPipeR-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=systemPipeR.buildbin-libdir --install="check:systemPipeR-install.out" --force-multiarch --no-vignettes --timings systemPipeR_1.7.3.tar.gz
StartedAt: 2016-09-20 17:25:43 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 17:33:05 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 442.1 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 && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=systemPipeR.buildbin-libdir systemPipeR_1.7.3.tar.gz >systemPipeR.Rcheck\00install.out 2>&1 && cp systemPipeR.Rcheck\00install.out systemPipeR-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=systemPipeR.buildbin-libdir --install="check:systemPipeR-install.out" --force-multiarch --no-vignettes --timings systemPipeR_1.7.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-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 '1.7.3'
* 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 ... NOTE
Found the following non-portable file paths:
  systemPipeR/vignettes/systemPipeR_cache/html/align_stats_parallel_cluster_0f051c2b1f70364c102c25e53a23f12e.RData
  systemPipeR/vignettes/systemPipeR_cache/html/align_stats_parallel_cluster_0f051c2b1f70364c102c25e53a23f12e.rdb
  systemPipeR/vignettes/systemPipeR_cache/html/align_stats_parallel_cluster_0f051c2b1f70364c102c25e53a23f12e.rdx
  systemPipeR/vignettes/systemPipeR_cache/html/align_stats_parallel_e41a74f26d017f5fc177af2655e45d55.RData
  systemPipeR/vignettes/systemPipeR_cache/html/align_stats_parallel_e41a74f26d017f5fc177af2655e45d55.rdb
  systemPipeR/vignettes/systemPipeR_cache/html/align_stats_parallel_e41a74f26d017f5fc177af2655e45d55.rdx
  systemPipeR/vignettes/systemPipeR_cache/html/construct_sysargs_a8854172136869af90c5343d9951536e.RData
  systemPipeR/vignettes/systemPipeR_cache/html/custom_preprocessing_e41edaa3ba2719fdfc02ff89b468a9e1.RData
  systemPipeR/vignettes/systemPipeR_cache/html/custom_preprocessing_e41edaa3ba2719fdfc02ff89b468a9e1.rdb
  systemPipeR/vignettes/systemPipeR_cache/html/custom_preprocessing_e41edaa3ba2719fdfc02ff89b468a9e1.rdx
  systemPipeR/vignettes/systemPipeR_cache/html/deseq2_deg_counts_89654aad3b028aaa60cf3b27b7166c34.RData
  systemPipeR/vignettes/systemPipeR_cache/html/fastq_quality_parallel_cluster_981fb1c217635fd948ed528cf5d9f37c.RData
  systemPipeR/vignettes/systemPipeR_cache/html/fastq_quality_parallel_cluster_981fb1c217635fd948ed528cf5d9f37c.rdb
  systemPipeR/vignettes/systemPipeR_cache/html/fastq_quality_parallel_cluster_981fb1c217635fd948ed528cf5d9f37c.rdx
  systemPipeR/vignettes/systemPipeR_cache/html/fastq_quality_parallel_single_87e6e7dcfdfbf7bc314100638c26c52d.RData
  systemPipeR/vignettes/systemPipeR_cache/html/fastq_quality_parallel_single_87e6e7dcfdfbf7bc314100638c26c52d.rdb
  systemPipeR/vignettes/systemPipeR_cache/html/fastq_quality_parallel_single_87e6e7dcfdfbf7bc314100638c26c52d.rdx
  systemPipeR/vignettes/systemPipeR_cache/html/genChip_workflow_single_6eee2576b65a48f51e1dd54432ac8ea0.RData
  systemPipeR/vignettes/systemPipeR_cache/html/genChip_workflow_single_6eee2576b65a48f51e1dd54432ac8ea0.rdb
  systemPipeR/vignettes/systemPipeR_cache/html/genChip_workflow_single_6eee2576b65a48f51e1dd54432ac8ea0.rdx
  systemPipeR/vignettes/systemPipeR_cache/html/genRibo_workflow_single_a7ee40491d0f82a7209ce7f20aa1bce9.RData
  systemPipeR/vignettes/systemPipeR_cache/html/genRibo_workflow_single_a7ee40491d0f82a7209ce7f20aa1bce9.rdb
  systemPipeR/vignettes/systemPipeR_cache/html/genRibo_workflow_single_a7ee40491d0f82a7209ce7f20aa1bce9.rdx
  systemPipeR/vignettes/systemPipeR_cache/html/genRna_workflow_single_865fbdca4c56e8ae4f6295e250ab220b.RData
  systemPipeR/vignettes/systemPipeR_cache/html/genRna_workflow_single_865fbdca4c56e8ae4f6295e250ab220b.rdb
  systemPipeR/vignettes/systemPipeR_cache/html/genRna_workflow_single_865fbdca4c56e8ae4f6295e250ab220b.rdx
  systemPipeR/vignettes/systemPipeR_cache/html/genVar_workflow_single_85369033487573758c368e1b18c2e939.RData
  systemPipeR/vignettes/systemPipeR_cache/html/genVar_workflow_single_85369033487573758c368e1b18c2e939.rdb
  systemPipeR/vignettes/systemPipeR_cache/html/genVar_workflow_single_85369033487573758c368e1b18c2e939.rdx
  systemPipeR/vignettes/systemPipeR_cache/html/hierarchical_clustering_26f264bb871fd0c2f342b0c079aee49e.RData
  systemPipeR/vignettes/systemPipeR_cache/html/hierarchical_clustering_26f264bb871fd0c2f342b0c079aee49e.rdb
  systemPipeR/vignettes/systemPipeR_cache/html/hierarchical_clustering_26f264bb871fd0c2f342b0c079aee49e.rdx
  systemPipeR/vignettes/systemPipeR_cache/html/plot_go_enrichment_a4a220bf9eb7f1125e3a802cedd67c24.RData
  systemPipeR/vignettes/systemPipeR_cache/html/process_monitoring_0e49b11e73810c66c83bdcd6bcd3e394.RData
  systemPipeR/vignettes/systemPipeR_cache/html/read_counting_mirna_4195067fd0942be85d1decde3da75c3e.RData
  systemPipeR/vignettes/systemPipeR_cache/html/read_counting_mirna_4195067fd0942be85d1decde3da75c3e.rdb
  systemPipeR/vignettes/systemPipeR_cache/html/read_counting_mirna_4195067fd0942be85d1decde3da75c3e.rdx
  systemPipeR/vignettes/systemPipeR_cache/html/read_counting_multicore_8f4bae011588aec1419eb6f86f683f9b.RData
  systemPipeR/vignettes/systemPipeR_cache/html/read_counting_multicore_8f4bae011588aec1419eb6f86f683f9b.rdb
  systemPipeR/vignettes/systemPipeR_cache/html/read_counting_multicore_8f4bae011588aec1419eb6f86f683f9b.rdx
  systemPipeR/vignettes/systemPipeR_cache/html/read_counting_multinode_83ec3b9d8967b28eed8957801d322dda.RData
  systemPipeR/vignettes/systemPipeR_cache/html/read_counting_multinode_83ec3b9d8967b28eed8957801d322dda.rdb
  systemPipeR/vignettes/systemPipeR_cache/html/read_counting_multinode_83ec3b9d8967b28eed8957801d322dda.rdx
  systemPipeR/vignettes/systemPipeR_cache/html/run_bowtie_parallel_5bfc0855d4e02f149c5d7aedcfa6ac7b.RData
  systemPipeR/vignettes/systemPipeR_cache/html/run_bowtie_parallel_5bfc0855d4e02f149c5d7aedcfa6ac7b.rdb
  systemPipeR/vignettes/systemPipeR_cache/html/run_bowtie_parallel_5bfc0855d4e02f149c5d7aedcfa6ac7b.rdx
  systemPipeR/vignettes/systemPipeR_cache/html/run_bowtie_single_c498a76143c61cef609d9c01a7de3243.RData

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section 'Package structure' in the 'Writing R Extensions' manual.
* checking whether package 'systemPipeR' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.4Mb
  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 11.37   0.33   11.94
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
genFeatures 10.95   0.36   11.32
* 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: 6 NOTEs
See
  'D:/biocbld/bbs-3.4-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_1.7.3.zip
* DONE (systemPipeR)

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

nameusersystemelapsed
GOHyperGAll000
INTERSECTset-class000
SYSargs-class0.030.000.03
VENNset-class0.020.000.01
alignStats0.020.000.02
catDB-class000
catmap000
clusterRun0.010.000.01
countRangeset0.060.000.07
featureCoverage0.000.010.01
featuretypeCounts0.020.000.02
filterDEGs2.750.002.74
filterVars0.010.000.01
genFeatures11.37 0.3311.94
getQsubargs0.010.000.02
mergeBamByFactor0.020.000.01
moduleload000
olBarplot0.580.010.60
overLapper1.180.001.18
plotfeatureCoverage0.020.000.02
plotfeaturetypeCounts0.010.000.01
predORF0.240.020.25
preprocessReads0.030.000.04
qsubRun0.010.000.01
readComp0.040.000.03
returnRPKM000
runCommandline0.010.000.02
runDiff0.050.000.04
run_DESeq23.060.013.08
run_edgeR2.660.002.67
scaleRanges0.130.000.12
seeFastq000
symLink2bam000
sysargs0.020.000.01
systemArgs0.030.000.03
variantReport0.020.000.02
vennPlot0.570.000.58
writeTargetsRef000
writeTargetsout0.020.000.01

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

nameusersystemelapsed
GOHyperGAll000
INTERSECTset-class0.010.000.02
SYSargs-class0.030.030.06
VENNset-class0.000.010.01
alignStats0.020.000.02
catDB-class000
catmap000
clusterRun0.020.020.03
countRangeset0.080.000.07
featureCoverage0.000.010.02
featuretypeCounts000
filterDEGs2.760.002.91
filterVars0.020.000.02
genFeatures10.95 0.3611.32
getQsubargs0.020.000.02
mergeBamByFactor0.010.000.02
moduleload000
olBarplot0.610.000.60
overLapper0.770.000.77
plotfeatureCoverage0.010.000.01
plotfeaturetypeCounts0.020.000.02
predORF0.280.000.28
preprocessReads0.030.000.03
qsubRun0.000.020.02
readComp0.030.000.03
returnRPKM000
runCommandline0.020.000.01
runDiff0.060.000.07
run_DESeq23.710.053.76
run_edgeR3.450.013.46
scaleRanges0.170.000.17
seeFastq000
symLink2bam0.020.000.02
sysargs0.010.000.01
systemArgs0.020.000.02
variantReport0.010.000.01
vennPlot0.740.000.74
writeTargetsRef000
writeTargetsout0.010.000.01