MethylSeekR 1.9.0
Lukas Burger
| Snapshot Date: 2015-08-19 16:24:33 -0700 (Wed, 19 Aug 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MethylSeekR | | Last Changed Rev: 102594 / Revision: 107602 | | Last Changed Date: 2015-04-16 13:02:44 -0700 (Thu, 16 Apr 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | [ OK ] | OK | |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### rm -rf MethylSeekR.buildbin-libdir MethylSeekR.Rcheck && mkdir MethylSeekR.buildbin-libdir MethylSeekR.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MethylSeekR.buildbin-libdir MethylSeekR_1.9.0.tar.gz >MethylSeekR.Rcheck\00install.out 2>&1 && cp MethylSeekR.Rcheck\00install.out MethylSeekR-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=MethylSeekR.buildbin-libdir --install="check:MethylSeekR-install.out" --force-multiarch --no-vignettes --timings MethylSeekR_1.9.0.tar.gz
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/MethylSeekR.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 'MethylSeekR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MethylSeekR' version '1.9.0'
* 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 'MethylSeekR' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
'parallel'
A package should be listed in only one of these fields.
* 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
Namespace in Imports field not imported from: 'geneplotter'
All declared Imports should be used.
Package in Depends field not imported from: 'rtracklayer'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
PMDviterbiSegmentation : <anonymous>: no visible global function
definition for 'Rle'
PMDviterbiSegmentation : <anonymous>: no visible global function
definition for 'runValue'
calculateAlphaDistr : <anonymous>: no visible global function
definition for 'Rle'
calculateFDRs : <anonymous>: no visible global function definition for
'Rle'
calculateFDRs : <anonymous>: no visible global function definition for
'runValue'
createGRangesObjectPMDSegmentation : <anonymous>: no visible global
function definition for 'Rle'
createGRangesObjectPMDSegmentation : <anonymous>: no visible global
function definition for 'nrun'
createGRangesObjectPMDSegmentation : <anonymous>: no visible global
function definition for 'runValue'
plotFinalSegmentation: no visible global function definition for 'Rle'
segmentUMRsLMRs : <anonymous>: no visible global function definition
for 'Rle'
segmentUMRsLMRs : <anonymous>: no visible global function definition
for 'runValue'
segmentUMRsLMRs: no visible global function definition for 'Rle'
segmentUMRsLMRs: no visible global function definition for 'DataFrame'
* 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' ... [308s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
MethylSeekR-package 85.94 3.42 98.86
plotPMDSegmentation 52.15 1.92 54.07
savePMDSegments 48.50 1.40 49.93
segmentPMDs 45.67 1.04 46.71
calculateFDRs 13.94 0.48 23.23
plotAlphaDistributionOneChr 11.50 0.25 11.75
plotFinalSegmentation 4.46 0.23 5.15
** running examples for arch 'x64' ... [342s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
MethylSeekR-package 94.21 3.85 106.50
plotPMDSegmentation 59.79 1.59 61.39
savePMDSegments 56.02 1.11 57.12
segmentPMDs 53.63 1.11 54.74
plotAlphaDistributionOneChr 12.50 0.41 12.91
calculateFDRs 11.79 0.84 21.67
plotFinalSegmentation 6.59 0.31 6.89
* 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: 3 NOTEs
See
'D:/biocbld/bbs-3.2-bioc/meat/MethylSeekR.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'MethylSeekR' ...
** 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 'MethylSeekR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MethylSeekR' as MethylSeekR_1.9.0.zip
* DONE (MethylSeekR)