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BioC 3.1: CHECK report for chimera on petty

This page was generated on 2015-10-09 09:35:31 -0700 (Fri, 09 Oct 2015).

Package 155/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chimera 1.10.0
Raffaele A Calogero
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/chimera
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: chimera
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings chimera_1.10.0.tar.gz
StartedAt: 2015-10-08 22:00:07 -0700 (Thu, 08 Oct 2015)
EndedAt: 2015-10-08 22:13:53 -0700 (Thu, 08 Oct 2015)
EllapsedTime: 826.3 seconds
RetCode: 0
Status:  OK 
CheckDir: chimera.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings chimera_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/chimera.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.10.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘chimera’ can be installed ... [32s/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:
  ‘BiocParallel’ ‘BSgenome.Hsapiens.NCBI.GRCh38’
  ‘BSgenome.Mmusculus.UCSC.mm10’ ‘BSgenome.Mmusculus.UCSC.mm9’
  ‘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
.buildFusion: no visible global function definition for ‘DNAString’
.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’
.rsImport: no visible global function definition for ‘MulticoreParam’
.rsImport : .fusionInfo: no visible binding for global variable
  ‘BSgenome.Hsapiens.NCBI.GRCh38’
.rsImport: no visible global function definition for ‘bplapply’
bam2fastq: no visible global function definition for ‘MulticoreParam’
bam2fastq: no visible global function definition for ‘bplapply’
chimeraSeqs: no visible global function definition for ‘DNAStringSet’
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’
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 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 ‘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’
starReads: no visible global function definition for ‘MulticoreParam’
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’
* 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 ... [518s/519s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
fusionPeptides     122.596  1.388 124.108
plotCoverage       114.777  0.368 115.221
chimeraSeqSet       64.339  0.335  64.733
class.fSet          44.452  0.178  44.641
chimeraSeqs         40.394  0.168  40.581
breakpointOverlaps  24.847  0.439  25.314
filterList          18.345  0.141  18.496
supportingReads     15.754  0.203  15.974
fusionName          14.804  0.164  14.974
importFusionData    14.360  0.254  14.629
is.fSet             13.808  0.206  14.022
defuseTPTN           9.845  0.011   9.859
* 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-3.1-bioc/meat/chimera.Rcheck/00check.log’
for details.


chimera.Rcheck/00install.out:

* installing *source* package ‘chimera’ ...
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c StarParser.cpp -o StarParser.o
llvm-g++-4.2 -arch x86_64 -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 -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-3.1-bioc/meat/chimera.Rcheck/chimera/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (chimera)

chimera.Rcheck/chimera-Ex.timings:

nameusersystemelapsed
MHmakeRandomString0.0020.0000.002
bam2fastq0.0020.0010.001
breakpointOverlaps24.847 0.43925.314
chimeraSeqSet64.339 0.33564.733
chimeraSeqs40.394 0.16840.581
class.fSet44.452 0.17844.641
defuseTPTN9.8450.0119.859
filterList18.345 0.14118.496
filterSamReads0.0010.0000.000
fusionName14.804 0.16414.974
fusionPeptides122.596 1.388124.108
gapfillerInstallation0.0010.0000.001
gapfillerRun0.0010.0000.001
gapfillerWrap0.0010.0000.001
importFusionData14.360 0.25414.629
is.fSet13.808 0.20614.022
newfSet0.0560.0010.057
oncofuseInstallation0.0010.0000.000
oncofuseRun0.0010.0000.001
picardInstallation0.0010.0000.001
plotCoverage114.777 0.368115.221
prettyPrint0.0010.0000.001
removingErrorLine0.0010.0000.001
starInstallation0.0010.0000.002
starReads0.0010.0000.001
starRun0.0010.0000.001
subreadRun0.0030.0000.004
supportingReads15.754 0.20315.974
tophatInstallation0.0010.0000.001
tophatRun0.0010.0000.001
validateSamFile000