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

##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################


* 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.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL chimera
###
##############################################################################
##############################################################################


* 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)

name	user	system	elapsed
MHmakeRandomString	0.004	0.000	0.001
bam2fastq	0	0	0
breakpointOverlaps	3.628	0.100	3.763
chimeraSeqSet	9.704	0.060	9.808
chimeraSeqs	5.880	0.004	5.896
class.fSet	5.644	0.020	5.681
defuseTPTN	6.816	0.000	6.827
filterList	4.336	0.024	4.364
filterSamReads	0	0	0
fusionName	3.600	0.016	3.619
fusionPeptides	31.288	0.112	31.480
gapfillerInstallation	0	0	0
gapfillerRun	0	0	0
gapfillerWrap	0	0	0
importFusionData	3.700	0.016	3.717
is.fSet	4.308	0.004	4.317
newfSet	0.036	0.000	0.037
oncofuseInstallation	0	0	0
oncofuseRun	0	0	0
picardInstallation	0	0	0
plotCoverage	11.272	0.012	11.301
prettyPrint	0	0	0
removingErrorLine	0	0	0
starInstallation	0	0	0
starReads	0	0	0
starRun	0.000	0.000	0.001
subreadRun	2.480	1.380	3.899
supportingReads	4.160	0.056	4.218
tophatInstallation	0	0	0
tophatRun	0	0	0
validateSamFile	0	0	0