chimera 1.17.0
Raffaele A Calogero
| Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/chimera | | Last Changed Rev: 122712 / Revision: 127142 | | Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |
| toluca2 | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | [ OK ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings chimera_1.17.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/chimera.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.17.0’
* 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 6.4Mb
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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
fusionPeptides 31.499 0.636 63.177
plotCoverage 11.281 0.147 11.519
chimeraSeqSet 9.103 0.158 9.875
defuseTPTN 5.153 0.006 5.161
chimeraSeqs 4.843 0.080 5.083
subreadRun 2.254 1.903 6.303
* 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: 5 NOTEs
See
‘/Users/biocbuild/bbs-3.5-bioc/meat/chimera.Rcheck/00check.log’
for details.
* installing *source* package ‘chimera’ ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c StarParser.cpp -o StarParser.o
clang++ -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 /Users/biocbuild/bbs-3.5-bioc/meat/chimera.Rcheck/chimera/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (chimera)