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BioC 3.6: CHECK report for chimera on tokay1

This page was generated on 2017-08-16 13:31:13 -0400 (Wed, 16 Aug 2017).

Package 205/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chimera 1.19.0
Raffaele A Calogero
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/chimera
Last Changed Rev: 129129 / Revision: 131943
Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: chimera
Version: 1.19.0
Command: rm -rf chimera.buildbin-libdir chimera.Rcheck && mkdir chimera.buildbin-libdir chimera.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=chimera.buildbin-libdir chimera_1.19.0.tar.gz >chimera.Rcheck\00install.out 2>&1 && cp chimera.Rcheck\00install.out chimera-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=chimera.buildbin-libdir --install="check:chimera-install.out" --force-multiarch --no-vignettes --timings chimera_1.19.0.tar.gz
StartedAt: 2017-08-15 22:18:42 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 22:27:07 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 505.3 seconds
RetCode: 0
Status:  OK  
CheckDir: chimera.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf chimera.buildbin-libdir chimera.Rcheck && mkdir chimera.buildbin-libdir chimera.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=chimera.buildbin-libdir chimera_1.19.0.tar.gz >chimera.Rcheck\00install.out 2>&1 && cp chimera.Rcheck\00install.out chimera-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=chimera.buildbin-libdir --install="check:chimera-install.out" --force-multiarch --no-vignettes --timings chimera_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/chimera.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'chimera/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'chimera' version '1.19.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'Rsubread'

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 whether package 'chimera' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.7Mb
  sub-directories of 1Mb or more:
    examples   5.7Mb
    libs       1.4Mb
* 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
'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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.6-bioc/meat/chimera.buildbin-libdir/chimera/libs/i386/chimera.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* 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
fusionPeptides 26.62   0.23   27.90
plotCoverage   10.04   0.04   10.10
chimeraSeqSet   9.66   0.24    9.89
chimeraSeqs     5.14   0.12    5.26
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
fusionPeptides     29.19   0.27   29.45
plotCoverage       11.17   0.06   11.24
chimeraSeqSet      10.64   0.12   10.77
chimeraSeqs         6.11   0.07    6.17
breakpointOverlaps  5.86   0.19    6.05
class.fSet          5.22   0.04    5.26
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: 'xtable'
* 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
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/chimera.Rcheck/00check.log'
for details.


chimera.Rcheck/00install.out:


install for i386

* installing *source* package 'chimera' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c StarParser.cpp -o StarParser.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o chimera.dll tmp.def StarParser.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/chimera.buildbin-libdir/chimera/libs/i386
** R
** inst
** preparing package for lazy loading
No methods found in "RSQLite" for requests: dbGetQuery
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "RSQLite" for requests: dbGetQuery

install for x64

* installing *source* package 'chimera' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c StarParser.cpp -o StarParser.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o chimera.dll tmp.def StarParser.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/chimera.buildbin-libdir/chimera/libs/x64
** testing if installed package can be loaded
No methods found in "RSQLite" for requests: dbGetQuery
* MD5 sums
packaged installation of 'chimera' as chimera_1.19.0.zip
* DONE (chimera)

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

nameusersystemelapsed
MHmakeRandomString000
bam2fastq000
breakpointOverlaps4.060.114.18
chimeraSeqSet9.660.249.89
chimeraSeqs5.140.125.26
class.fSet4.780.064.85
defuseTPTN3.90.03.9
filterList2.910.042.94
filterSamReads000
fusionName2.910.032.94
fusionPeptides26.62 0.2327.90
gapfillerInstallation000
gapfillerRun000
gapfillerWrap000
importFusionData2.840.173.02
is.fSet2.690.072.75
newfSet0.050.000.04
oncofuseInstallation000
oncofuseRun000
picardInstallation000
plotCoverage10.04 0.0410.10
prettyPrint000
removingErrorLine000
starInstallation000
starReads000
starRun000
subreadRun000
supportingReads2.660.072.71
tophatInstallation000
tophatRun000
validateSamFile000

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

nameusersystemelapsed
MHmakeRandomString000
bam2fastq000
breakpointOverlaps5.860.196.05
chimeraSeqSet10.64 0.1210.77
chimeraSeqs6.110.076.17
class.fSet5.220.045.26
defuseTPTN4.130.004.13
filterList3.260.003.26
filterSamReads000
fusionName2.810.002.82
fusionPeptides29.19 0.2729.45
gapfillerInstallation000
gapfillerRun000
gapfillerWrap000
importFusionData3.160.023.17
is.fSet3.640.063.70
newfSet0.050.000.05
oncofuseInstallation000
oncofuseRun0.020.000.01
picardInstallation000
plotCoverage11.17 0.0611.24
prettyPrint000
removingErrorLine000
starInstallation000
starReads000
starRun000
subreadRun000
supportingReads3.110.053.16
tophatInstallation000
tophatRun000
validateSamFile000