chimera 1.13.0
Raffaele A Calogero
| Snapshot Date: 2015-10-19 20:20:06 -0400 (Mon, 19 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/chimera | | Last Changed Rev: 109592 / Revision: 109765 | | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ OK ] | |  |
| windows2.bioconductor.org | Windows Server 2012 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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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings chimera_1.13.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/chimera.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* 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 ‘1.13.0’
* 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 ... [18s/18s] 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
Loading required package: DBI
.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 ‘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 ‘IRanges’
.fcImport: no visible global function definition for ‘IRanges’
.ffImport: no visible global function definition for ‘IRanges’
.fhImport: no visible global function definition for ‘IRanges’
.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 ‘IRanges’
.onlyExons: no visible global function definition for ‘exons’
.rsImport: no visible global function definition for ‘MulticoreParam’
.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 ‘IRanges’
.thfImport: no visible global function definition for ‘IRanges’
.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’
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 : .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’
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’
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’
starReads: no visible global function definition for ‘MulticoreParam’
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’
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 bowtie bowtie_build bplapply cdsBy exons extractTranscriptSeqs
genes matchPattern org.Hs.egSYMBOL org.Hs.egUCSCKG pairwiseAlignment
pattern readDNAStringSet select seqlengths seqlengths<-
seqlevelsStyle<- transcripts translate writeXStringSet
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [105s/105s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
fusionPeptides 39.703 0.100 39.830
chimeraSeqSet 10.082 0.040 10.132
plotCoverage 9.500 0.020 9.526
chimeraSeqs 6.977 0.020 6.997
class.fSet 5.762 0.008 5.774
* 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
‘/home/biocbuild/bbs-3.3-bioc/meat/chimera.Rcheck/00check.log’
for details.
* installing *source* package ‘chimera’ ...
** libs
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c StarParser.cpp -o StarParser.o
g++ -shared -L/home/biocbuild/bbs-3.3-bioc/R/lib -L/usr/local/lib -o chimera.so StarParser.o -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-bioc/meat/chimera.Rcheck/chimera/libs
** R
** inst
** preparing package for lazy loading
Now getting the GODb Object directly
Now getting the OrgDb Object directly
Now getting the TxDb Object directly
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Now getting the GODb Object directly
Now getting the OrgDb Object directly
Now getting the TxDb Object directly
* DONE (chimera)