chimera 1.13.1
Raffaele A Calogero
| Snapshot Date: 2016-04-20 17:20:35 -0700 (Wed, 20 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/chimera | | Last Changed Rev: 115833 / Revision: 116626 | | Last Changed Date: 2016-04-05 16:03:15 -0700 (Tue, 05 Apr 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK | |
| morelia | 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_1.13.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/chimera.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* 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 ‘1.13.1’
* 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 ... [21s/33s] 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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [150s/157s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
fusionPeptides 51.255 1.220 52.817
chimeraSeqSet 14.074 0.224 14.835
plotCoverage 13.289 0.209 13.767
class.fSet 8.760 0.132 9.711
chimeraSeqs 8.537 0.144 9.091
defuseTPTN 8.104 0.016 8.812
fusionName 5.431 0.103 5.573
subreadRun 2.472 2.488 5.615
* 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-3.3-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-3.3-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)