chimera 1.4.6
Raffaele A Calogero
| Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/chimera | | Last Changed Rev: 87754 / Revision: 88450 | | Last Changed Date: 2014-03-22 16:31:34 -0700 (Sat, 22 Mar 2014) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | [ OK ] | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK |
* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/chimera.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-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 '1.4.6'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'Rsubread'
* 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 ... OK
* 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' call to 'org.Mm.eg.db' which was already attached by Depends.
Please remove these calls from your code.
Packages in Depends field not imported from:
'BSgenome.Hsapiens.UCSC.hg19' 'Biobase' 'Rsamtools'
'TxDb.Hsapiens.UCSC.hg19.knownGene' 'methods' 'org.Hs.eg.db'
'org.Mm.eg.db'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of 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
.detectIntronic: no visible global function definition for '.onlyExons'
subreadRun: no visible global function definition for 'buildindex'
subreadRun: no visible global function definition for 'align'
* 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 for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
'chimera.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [452s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotCoverage 116.95 0.70 117.65
fusionPeptides 104.17 2.09 106.30
chimeraSeqSet 77.18 1.01 78.50
class.fSet 42.60 0.19 42.79
chimeraSeqs 36.60 0.17 36.79
fusionName 11.35 0.00 11.34
prettyPrint 11.25 0.00 11.26
filterList 10.67 0.00 10.67
importFusionData 8.95 0.00 8.95
is.fSet 7.83 0.02 7.85
supportingReads 7.67 0.00 7.68
** running examples for arch 'x64' ... [448s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
fusionPeptides 111.40 2.32 113.81
plotCoverage 108.43 0.43 108.86
chimeraSeqSet 68.61 1.00 69.61
chimeraSeqs 44.07 0.31 44.38
class.fSet 38.94 0.17 39.11
filterList 12.99 0.02 13.01
is.fSet 10.49 0.00 10.49
prettyPrint 10.22 0.00 10.23
fusionName 9.82 0.00 9.82
importFusionData 9.42 0.00 9.42
supportingReads 8.27 0.00 8.27
* checking for unstated dependencies in vignettes ... OK
* 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
'D:/biocbld/bbs-2.13-bioc/meat/chimera.Rcheck/00check.log'
for details.
install for i386
* 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
install for x64
* installing *source* package 'chimera' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'chimera' as chimera_1.4.6.zip
* DONE (chimera)