Package: chimera

Version: 1.25.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:chimera.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings chimera_1.25.0.tar.gz

StartedAt: 2019-04-08 23:48:01 -0400 (Mon, 08 Apr 2019)

EndedAt: 2019-04-08 23:54:31 -0400 (Mon, 08 Apr 2019)

EllapsedTime: 390.7 seconds

RetCode: 0

Status:  OK

CheckDir: chimera.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:chimera.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings chimera_1.25.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/chimera.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.25.0’
* 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  6.3Mb
  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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
fusionPeptides 34.198  0.501  35.184
plotCoverage   10.331  0.143  10.595
subreadRun      6.753  3.404  10.291
chimeraSeqSet   9.370  0.207   9.694
defuseTPTN      8.432  0.012   8.547
chimeraSeqs     6.827  0.132   7.042
class.fSet      5.953  0.126   6.154
* 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
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/chimera.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL chimera
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘chimera’ ...
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c StarParser.cpp -o StarParser.o
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o chimera.so StarParser.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/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)

name	user	system	elapsed
MHmakeRandomString	0.001	0.000	0.001
bam2fastq	0.001	0.000	0.001
breakpointOverlaps	3.384	0.178	3.597
chimeraSeqSet	9.370	0.207	9.694
chimeraSeqs	6.827	0.132	7.042
class.fSet	5.953	0.126	6.154
defuseTPTN	8.432	0.012	8.547
filterList	3.828	0.083	3.935
filterSamReads	0	0	0
fusionName	3.902	0.085	4.020
fusionPeptides	34.198	0.501	35.184
gapfillerInstallation	0	0	0
gapfillerRun	0	0	0
gapfillerWrap	0	0	0
importFusionData	4.528	0.111	4.691
is.fSet	3.569	0.080	3.691
newfSet	0.061	0.000	0.062
oncofuseInstallation	0	0	0
oncofuseRun	0.000	0.000	0.001
picardInstallation	0	0	0
plotCoverage	10.331	0.143	10.595
prettyPrint	0	0	0
removingErrorLine	0	0	0
starInstallation	0.001	0.001	0.000
starReads	0.001	0.000	0.000
starRun	0.001	0.000	0.001
subreadRun	6.753	3.404	10.291
supportingReads	3.608	0.107	3.757
tophatInstallation	0.000	0.000	0.001
tophatRun	0	0	0
validateSamFile	0.001	0.001	0.000