Back to the "Multiple platform build/check report" A  B [C] D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 2.14: CHECK report for chimera on zin2

This page was generated on 2014-10-08 08:49:52 -0700 (Wed, 08 Oct 2014).

Package 139/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chimera 1.6.16
Raffaele A Calogero
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/chimera
Last Changed Rev: 93185 / Revision: 95116
Last Changed Date: 2014-08-05 01:09:55 -0700 (Tue, 05 Aug 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: chimera
Version: 1.6.16
Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings chimera_1.6.16.tar.gz
StartedAt: 2014-10-07 22:27:12 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 22:35:24 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 492.7 seconds
RetCode: 0
Status:  OK 
CheckDir: chimera.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings chimera_1.6.16.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/chimera.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-unknown-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 ‘1.6.16’
* 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’ ‘org.Hs.eg.db’ ‘BSgenome.Hsapiens.UCSC.hg19’
  ‘TxDb.Hsapiens.UCSC.hg19.knownGene’
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 ... [20s/21s] 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.csImport: no visible binding for global variable ‘org.Mm.egCHRLOC’
.csImport: no visible binding for global variable ‘org.Mm.egCHRLOCEND’
.csImport: no visible binding for global variable ‘org.Mm.egSYMBOL’
.csImport: no visible binding for global variable ‘Mmusculus’
.fcImport: no visible binding for global variable ‘org.Mm.egCHRLOC’
.fcImport: no visible binding for global variable ‘org.Mm.egCHRLOCEND’
.fcImport: no visible binding for global variable ‘org.Mm.egSYMBOL’
.fmImport: no visible binding for global variable ‘org.Mm.egCHRLOC’
.fmImport: no visible binding for global variable ‘org.Mm.egCHRLOCEND’
.fmImport: no visible binding for global variable ‘org.Mm.egSYMBOL’
.rsImport: no visible binding for global variable ‘org.Mm.egCHRLOC’
.rsImport: no visible binding for global variable ‘org.Mm.egCHRLOCEND’
.rsImport: no visible binding for global variable ‘org.Mm.egSYMBOL’
.rsImport : .fusionInfo: no visible binding for global variable
  ‘Mmusculus’
.starFset: no visible binding for global variable ‘Mmusculus’
.starImport: no visible binding for global variable ‘org.Mm.egCHRLOC’
.starImport: no visible binding for global variable
  ‘org.Mm.egCHRLOCEND’
.starImport: no visible binding for global variable ‘org.Mm.egSYMBOL’
subreadRun: no visible global function definition for ‘buildindex’
subreadRun: no visible global function definition for ‘align’
subreadRun: no visible global function definition for ‘bowtie_build’
subreadRun: no visible global function definition for ‘bowtie’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [296s/297s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
fusionPeptides   81.801  1.600  83.812
plotCoverage     74.300  0.112  74.786
chimeraSeqSet    47.171  0.680  48.141
class.fSet       24.593  0.152  24.806
chimeraSeqs      23.898  0.140  24.155
filterList        6.777  0.012   6.800
fusionName        6.288  0.004   6.300
is.fSet           6.225  0.000   6.255
supportingReads   6.125  0.004   6.144
importFusionData  6.016  0.004   6.032
* 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

NOTE: There were 4 notes.
See
  ‘/home/biocbuild/bbs-2.14-bioc/meat/chimera.Rcheck/00check.log’
for details.

chimera.Rcheck/00install.out:

* installing *source* package ‘chimera’ ...
** 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)

chimera.Rcheck/chimera-Ex.timings:

nameusersystemelapsed
MHmakeRandomString0.0040.0000.001
bam2fastq000
chimeraSeqSet47.171 0.68048.141
chimeraSeqs23.898 0.14024.155
class.fSet24.593 0.15224.806
filterList6.7770.0126.800
filterSamReads0.0000.0000.001
fusionName6.2880.0046.300
fusionPeptides81.801 1.60083.812
gapfillerInstallation000
gapfillerRun0.0000.0000.001
gapfillerWrap0.0000.0000.001
importFusionData6.0160.0046.032
is.fSet6.2250.0006.255
oncofuseInstallation0.0000.0000.001
oncofuseRun0.0000.0000.001
picardInstallation000
plotCoverage74.300 0.11274.786
prettyPrint0.0040.0000.001
removingErrorLine0.0000.0000.001
starInstallation0.0000.0000.001
starReads0.0000.0000.001
starRun000
subreadRun0.0040.0000.004
supportingReads6.1250.0046.144
tophatInstallation000
tophatRun000
validateSamFile000