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CHECK report for chimera on malbec1

This page was generated on 2019-04-16 11:49:55 -0400 (Tue, 16 Apr 2019).

Package 240/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chimera 1.24.0
Raffaele A Calogero
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/chimera
Branch: RELEASE_3_8
Last Commit: ec9ab96
Last Changed Date: 2018-10-30 11:41:50 -0400 (Tue, 30 Oct 2018)
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: chimera
Version: 1.24.0
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:chimera.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings chimera_1.24.0.tar.gz
StartedAt: 2019-04-15 22:47:39 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 22:53:11 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 332.5 seconds
RetCode: 0
Status:  OK 
CheckDir: chimera.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:chimera.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings chimera_1.24.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/chimera.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 ‘chimera/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘chimera’ version ‘1.24.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘Biobase’ ‘GenomicRanges’ ‘Rsamtools’ ‘GenomicAlignments’
  ‘AnnotationDbi’ ‘BSgenome.Hsapiens.UCSC.hg19’
  ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ ‘Homo.sapiens’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘chimera’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.6Mb
  sub-directories of 1Mb or more:
    examples   5.7Mb
* 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
* 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
'library' or 'require' calls in package code:
  ‘BSgenome.Hsapiens.NCBI.GRCh38’ ‘BSgenome.Mmusculus.UCSC.mm10’
  ‘BSgenome.Mmusculus.UCSC.mm9’ ‘BiocParallel’ ‘Mus.musculus’
  ‘Rsubread’ ‘TxDb.Hsapiens.UCSC.hg38.knownGene’
  ‘TxDb.Mmusculus.UCSC.mm10.knownGene’
  ‘TxDb.Mmusculus.UCSC.mm9.knownGene’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.bfImport: no visible global function definition for ‘read.table’
.bfImport: no visible global function definition for ‘IRanges’
.buildFusion: no visible global function definition for ‘exons’
.buildFusion: no visible global function definition for ‘IRanges’
.buildFusion: no visible global function definition for ‘DNAString’
.csImport: no visible global function definition for ‘read.table’
.csImport: no visible global function definition for ‘IRanges’
.detectIntronic: no visible binding for global variable
  ‘org.Hs.egSYMBOL’
.detectIntronic: no visible global function definition for
  ‘transcripts’
.dfImport: no visible global function definition for ‘read.table’
.dfImport: no visible global function definition for ‘IRanges’
.fcImport: no visible global function definition for ‘read.table’
.fcImport: no visible global function definition for ‘IRanges’
.ffImport: no visible global function definition for ‘read.table’
.ffImport: no visible global function definition for ‘IRanges’
.fhImport: no visible global function definition for ‘read.table’
.fhImport: no visible global function definition for ‘IRanges’
.fmImport: no visible global function definition for ‘read.table’
.fmImport: no visible global function definition for ‘IRanges’
.geneLevelAnnotation: no visible global function definition for ‘genes’
.geneLevelAnnotation: no visible global function definition for
  ‘select’
.geneLevelAnnotation: no visible binding for global variable
  ‘TxDb.Mmusculus.UCSC.mm9.knownGene’
.geneLevelAnnotation: no visible binding for global variable
  ‘Mus.musculus’
.geneLevelAnnotation: no visible binding for global variable
  ‘TxDb.Mmusculus.UCSC.mm10.knownGene’
.geneLevelAnnotation: no visible binding for global variable
  ‘TxDb.Hsapiens.UCSC.hg38.knownGene’
.gfWrap: no visible global function definition for ‘writeXStringSet’
.msImport: no visible global function definition for ‘read.table’
.msImport: no visible global function definition for ‘IRanges’
.onlyExons: no visible global function definition for ‘exons’
.plotCoverage: no visible global function definition for ‘window’
.plotCoverage: no visible global function definition for ‘plot’
.plotCoverage: no visible global function definition for ‘polygon’
.plotCoverage: no visible global function definition for ‘abline’
.rsImport: no visible global function definition for ‘MulticoreParam’
.rsImport: no visible global function definition for ‘read.table’
.rsImport : .fusionInfo: no visible global function definition for
  ‘IRanges’
.rsImport : .fusionInfo: no visible binding for global variable
  ‘BSgenome.Hsapiens.NCBI.GRCh38’
.rsImport : .fusionInfo: no visible global function definition for
  ‘seqlevelsStyle<-’
.rsImport: no visible global function definition for ‘bplapply’
.starImport: no visible global function definition for ‘read.table’
.starImport: no visible global function definition for ‘IRanges’
.thfImport: no visible global function definition for ‘read.table’
.thfImport: no visible global function definition for ‘IRanges’
.thfPostImport: no visible global function definition for ‘read.table’
.thfPostImport: no visible global function definition for ‘IRanges’
bam2fastq: no visible global function definition for ‘MulticoreParam’
bam2fastq: no visible global function definition for ‘bplapply’
breakpointOverlaps: no visible global function definition for ‘IRanges’
breakpointOverlaps: no visible global function definition for
  ‘seqlengths<-’
breakpointOverlaps: no visible global function definition for
  ‘seqlengths’
breakpointOverlaps: no visible global function definition for
  ‘subjectHits’
chimeraSeqSet: no visible global function definition for
  ‘MulticoreParam’
chimeraSeqSet: no visible global function definition for ‘bplapply’
chimeraSeqSet : <anonymous>: no visible global function definition for
  ‘DNAStringSet’
chimeraSeqs: no visible binding for global variable ‘org.Hs.egSYMBOL’
chimeraSeqs: no visible global function definition for ‘transcripts’
chimeraSeqs: no visible global function definition for ‘DNAStringSet’
defuseTPTN: no visible global function definition for ‘read.table’
defuseTPTN : .my.newfset: no visible global function definition for
  ‘IRanges’
defuseTPTN : .my.newfset: no visible global function definition for
  ‘DNAStringSet’
filterList: no visible global function definition for ‘MulticoreParam’
filterList: no visible global function definition for ‘bplapply’
fusionName: no visible global function definition for ‘MulticoreParam’
fusionName: no visible global function definition for ‘bplapply’
fusionPeptides: no visible binding for global variable
  ‘org.Hs.egUCSCKG’
fusionPeptides: no visible binding for global variable
  ‘org.Hs.egSYMBOL’
fusionPeptides: no visible global function definition for ‘cdsBy’
fusionPeptides: no visible global function definition for
  ‘extractTranscriptSeqs’
fusionPeptides: no visible global function definition for ‘translate’
fusionPeptides: no visible global function definition for ‘AAStringSet’
fusionPeptides : <anonymous>: no visible global function definition for
  ‘pairwiseAlignment’
fusionPeptides: no visible global function definition for ‘pattern’
fusionPeptides: no visible global function definition for
  ‘matchPattern’
gapfillerInstallation: no visible global function definition for
  ‘download.file’
gapfillerRun: no visible global function definition for
  ‘readDNAStringSet’
gapfillerRun: no visible global function definition for
  ‘pairwiseAlignment’
gapfillerRun: no visible global function definition for ‘Views’
gapfillerRun: no visible global function definition for ‘DNAStringSet’
gapfillerWrap: no visible global function definition for
  ‘MulticoreParam’
gapfillerWrap: no visible global function definition for ‘bplapply’
newfSet: no visible global function definition for ‘DNAStringSet’
oncofuseInstallation: no visible global function definition for
  ‘download.file’
oncofuseRun: no visible global function definition for ‘write.table’
oncofuseRun: no visible global function definition for ‘read.table’
oncofuseRun: no visible global function definition for ‘smoothScatter’
picardInstallation: no visible global function definition for
  ‘download.file’
plotCoverage: no visible binding for global variable ‘org.Hs.egSYMBOL’
plotCoverage: no visible global function definition for ‘transcripts’
plotCoverage: no visible global function definition for ‘exons’
plotCoverage: no visible global function definition for ‘IRanges’
plotCoverage: no visible global function definition for ‘window’
plotCoverage: no visible global function definition for ‘plot’
plotCoverage: no visible global function definition for ‘polygon’
plotCoverage: no visible global function definition for ‘abline’
plotCoverage: no visible global function definition for ‘rect’
prettyPrint: no visible global function definition for ‘write.table’
starInstallation: no visible global function definition for
  ‘download.file’
starReads: no visible global function definition for ‘MulticoreParam’
starReads: no visible global function definition for ‘read.table’
starReads: no visible global function definition for ‘IRanges’
subreadRun: no visible global function definition for ‘bowtie_build’
subreadRun: no visible global function definition for ‘bowtie’
supportingReads: no visible global function definition for
  ‘MulticoreParam’
supportingReads: no visible global function definition for ‘bplapply’
tophatInstallation: no visible global function definition for
  ‘download.file’
tophatInstallation: no visible global function definition for ‘unzip’
Undefined global functions or variables:
  AAStringSet BSgenome.Hsapiens.NCBI.GRCh38 DNAString DNAStringSet
  IRanges MulticoreParam Mus.musculus TxDb.Hsapiens.UCSC.hg38.knownGene
  TxDb.Mmusculus.UCSC.mm10.knownGene TxDb.Mmusculus.UCSC.mm9.knownGene
  Views abline bowtie bowtie_build bplapply cdsBy download.file exons
  extractTranscriptSeqs genes matchPattern org.Hs.egSYMBOL
  org.Hs.egUCSCKG pairwiseAlignment pattern plot polygon read.table
  readDNAStringSet rect select seqlengths seqlengths<- seqlevelsStyle<-
  smoothScatter subjectHits transcripts translate unzip window
  write.table writeXStringSet
Consider adding
  importFrom("graphics", "abline", "plot", "polygon", "rect",
             "smoothScatter")
  importFrom("stats", "window")
  importFrom("utils", "download.file", "read.table", "unzip",
             "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 C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
fusionPeptides 31.288  0.112  31.480
plotCoverage   11.272  0.012  11.301
chimeraSeqSet   9.704  0.060   9.808
defuseTPTN      6.816  0.000   6.827
chimeraSeqs     5.880  0.004   5.896
class.fSet      5.644  0.020   5.681
* 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: 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.8-bioc/meat/chimera.Rcheck/00check.log’
for details.



Installation output

chimera.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL chimera
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘chimera’ ...
** libs
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c StarParser.cpp -o StarParser.o
g++ -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o chimera.so StarParser.o -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/library/chimera/libs
** 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 (chimera)

Tests output


Example timings

chimera.Rcheck/chimera-Ex.timings

nameusersystemelapsed
MHmakeRandomString0.0040.0000.001
bam2fastq000
breakpointOverlaps3.6280.1003.763
chimeraSeqSet9.7040.0609.808
chimeraSeqs5.8800.0045.896
class.fSet5.6440.0205.681
defuseTPTN6.8160.0006.827
filterList4.3360.0244.364
filterSamReads000
fusionName3.6000.0163.619
fusionPeptides31.288 0.11231.480
gapfillerInstallation000
gapfillerRun000
gapfillerWrap000
importFusionData3.7000.0163.717
is.fSet4.3080.0044.317
newfSet0.0360.0000.037
oncofuseInstallation000
oncofuseRun000
picardInstallation000
plotCoverage11.272 0.01211.301
prettyPrint000
removingErrorLine000
starInstallation000
starReads000
starRun0.0000.0000.001
subreadRun2.4801.3803.899
supportingReads4.1600.0564.218
tophatInstallation000
tophatRun000
validateSamFile000