compEpiTools 1.3.4
Kamal Kishore
| Snapshot Date: 2015-08-19 16:24:33 -0700 (Wed, 19 Aug 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/compEpiTools | | Last Changed Rev: 104774 / Revision: 107602 | | Last Changed Date: 2015-06-10 02:38:18 -0700 (Wed, 10 Jun 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ OK ] | OK | |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### rm -rf compEpiTools.buildbin-libdir compEpiTools.Rcheck && mkdir compEpiTools.buildbin-libdir compEpiTools.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=compEpiTools.buildbin-libdir compEpiTools_1.3.4.tar.gz >compEpiTools.Rcheck\00install.out 2>&1 && cp compEpiTools.Rcheck\00install.out compEpiTools-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=compEpiTools.buildbin-libdir --install="check:compEpiTools-install.out" --force-multiarch --no-vignettes --timings compEpiTools_1.3.4.tar.gz
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/compEpiTools.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'compEpiTools/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'compEpiTools' version '1.3.4'
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 'compEpiTools' 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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
TSS: no visible global function definition for 'end<-'
TSS: no visible global function definition for 'start<-'
findLncRNA: no visible global function definition for 'start<-'
findLncRNA: no visible global function definition for 'end<-'
findLncRNA: no visible global function definition for 'IRanges'
stallingIndex : getBound: no visible global function definition for
'start<-'
stallingIndex : getBound: no visible global function definition for
'end<-'
stallingIndex: no visible global function definition for 'IRanges'
topGOres: no visible global function definition for 'ggplot'
topGOres: no visible global function definition for 'aes'
topGOres: no visible binding for global variable 'Significant'
topGOres: no visible binding for global variable 'P_val'
topGOres: no visible global function definition for 'geom_bar'
topGOres: no visible global function definition for 'coord_flip'
topGOres: no visible global function definition for 'ylab'
ucsc2GRanges: no visible global function definition for 'IRanges'
GR2fasta,GRanges: no visible global function definition for
'seqlengths'
GR2fasta,GRanges: no visible global function definition for
'seqlengths<-'
GR2fasta,GRanges: no visible global function definition for 'trim'
GRangesInPromoters,GRanges: no visible global function definition for
'start<-'
GRannotate,GRanges: no visible global function definition for 'start<-'
GRannotate,GRanges: no visible global function definition for 'end<-'
GRcoverageSummit,GRanges: no visible global function definition for
'start<-'
GRcoverageSummit,GRanges: no visible global function definition for
'end<-'
GRmidpoint,GRanges: no visible global function definition for 'start<-'
GRmidpoint,GRanges: no visible global function definition for 'end<-'
GRsetwidth,GRanges: no visible global function definition for 'start<-'
GRsetwidth,GRanges: no visible global function definition for 'end<-'
countOverlapsInBins,GRanges: no visible global function definition for
'IRanges'
featuresLength,TxDb: no visible global function definition for 'reduce'
getPromoterClass,TxDb: no visible binding for global variable 'txdb'
getPromoterClass,TxDb: no visible global function definition for
'start<-'
getPromoterClass,TxDb: no visible global function definition for
'stopCluster'
makeGtfFromDb,TxDb: no visible global function definition for 'reduce'
matchEnhancers,GRanges: no visible global function definition for
'distanceToNearest'
matchEnhancers,GRanges: no visible global function definition for
'IRanges'
* 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 ...
** running examples for arch 'i386' ... [189s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
topGOres 50.88 0.04 54.36
GRangesInPromoters-methods 7.91 0.02 7.97
GRannotate-methods 6.27 0.09 10.59
matchEnhancers 4.99 0.03 5.02
heatmapPlot 3.28 0.09 9.41
makeGtfFromDb 3.15 0.16 35.12
simplifyGOterms 1.64 0.12 7.91
getPromoterClass-methods 0.89 0.03 17.74
** running examples for arch 'x64' ... [156s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
topGOres 60.54 0.08 60.65
GRangesInPromoters-methods 8.55 0.04 8.60
GRannotate-methods 6.55 0.03 6.60
matchEnhancers 5.52 0.08 5.60
distanceFromTSS-methods 4.74 0.03 5.03
getPromoterClass-methods 1.08 0.02 20.94
* 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
* DONE
Status: 1 NOTE
See
'D:/biocbld/bbs-3.2-bioc/meat/compEpiTools.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'compEpiTools' ...
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import by 'graph::.__C__dist' when loading 'topGO'
groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import by 'graph::.__C__dist' when loading 'topGO'
groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
install for x64
* installing *source* package 'compEpiTools' ...
** testing if installed package can be loaded
Warning: replacing previous import by 'graph::.__C__dist' when loading 'topGO'
groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
* MD5 sums
packaged installation of 'compEpiTools' as compEpiTools_1.3.4.zip
* DONE (compEpiTools)