chimera 1.19.0
Raffaele A Calogero
| Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/chimera | | Last Changed Rev: 129129 / Revision: 131943 | | Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | |
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### rm -rf chimera.buildbin-libdir chimera.Rcheck && mkdir chimera.buildbin-libdir chimera.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=chimera.buildbin-libdir chimera_1.19.0.tar.gz >chimera.Rcheck\00install.out 2>&1 && cp chimera.Rcheck\00install.out chimera-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=chimera.buildbin-libdir --install="check:chimera-install.out" --force-multiarch --no-vignettes --timings chimera_1.19.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/chimera.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'chimera/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'chimera' version '1.19.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'Rsubread'
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 whether package 'chimera' can be installed ... OK
* checking installed package size ... NOTE
installed size is 7.7Mb
sub-directories of 1Mb or more:
examples 5.7Mb
libs 1.4Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.6-bioc/meat/chimera.buildbin-libdir/chimera/libs/i386/chimera.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
fusionPeptides 26.62 0.23 27.90
plotCoverage 10.04 0.04 10.10
chimeraSeqSet 9.66 0.24 9.89
chimeraSeqs 5.14 0.12 5.26
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
fusionPeptides 29.19 0.27 29.45
plotCoverage 11.17 0.06 11.24
chimeraSeqSet 10.64 0.12 10.77
chimeraSeqs 6.11 0.07 6.17
breakpointOverlaps 5.86 0.19 6.05
class.fSet 5.22 0.04 5.26
* 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: 6 NOTEs
See
'C:/Users/biocbuild/bbs-3.6-bioc/meat/chimera.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'chimera' ...
** libs
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -mtune=core2 -c StarParser.cpp -o StarParser.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o chimera.dll tmp.def StarParser.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/chimera.buildbin-libdir/chimera/libs/i386
** R
** inst
** preparing package for lazy loading
No methods found in "RSQLite" for requests: dbGetQuery
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "RSQLite" for requests: dbGetQuery
install for x64
* installing *source* package 'chimera' ...
** libs
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -mtune=core2 -c StarParser.cpp -o StarParser.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o chimera.dll tmp.def StarParser.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/chimera.buildbin-libdir/chimera/libs/x64
** testing if installed package can be loaded
No methods found in "RSQLite" for requests: dbGetQuery
* MD5 sums
packaged installation of 'chimera' as chimera_1.19.0.zip
* DONE (chimera)