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 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch chimera_1.6.16.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/chimera.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘1.6.16’
* 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 ... [44s/48s] OK
* checking installed package size ... NOTE
installed size is 6.2Mb
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [12m/12m] OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotCoverage 192.276 0.707 194.923
fusionPeptides 182.200 7.117 190.651
chimeraSeqSet 109.137 3.399 113.069
class.fSet 61.695 0.795 63.659
chimeraSeqs 60.872 0.773 62.016
filterList 16.573 0.104 16.969
fusionName 16.264 0.060 16.408
supportingReads 15.729 0.057 15.892
is.fSet 15.405 0.049 15.561
importFusionData 14.791 0.105 14.919
* 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
‘/Users/biocbuild/bbs-2.14-bioc/meat/chimera.Rcheck/00check.log’
for details.