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BioC 2.12: CHECK report for methyAnalysis on moscato2

This page was generated on 2013-10-09 09:39:11 -0700 (Wed, 09 Oct 2013).

Package 406/671HostnameOS / ArchBUILDCHECKBUILD BIN
methyAnalysis 1.2.0
Pan Du
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/methyAnalysis
Last Changed Rev: 75263 / Revision: 81334
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  WARNINGS 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ WARNINGS ] OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  WARNINGS  OK 

Summary

Package: methyAnalysis
Version: 1.2.0
Command: rm -rf methyAnalysis.buildbin-libdir && mkdir methyAnalysis.buildbin-libdir && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=methyAnalysis.buildbin-libdir methyAnalysis_1.2.0.tar.gz >methyAnalysis-install.out 2>&1 && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD check --library=methyAnalysis.buildbin-libdir --install="check:methyAnalysis-install.out" --force-multiarch --no-vignettes --timings methyAnalysis_1.2.0.tar.gz && mv methyAnalysis.buildbin-libdir/* methyAnalysis.Rcheck/ && rmdir methyAnalysis.buildbin-libdir
StartedAt: 2013-10-09 02:59:08 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 03:22:04 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 1375.6 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: methyAnalysis.Rcheck
Warnings: 2

Command output

* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/methyAnalysis.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'methyAnalysis/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'methyAnalysis' version '1.2.0'
* 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 'methyAnalysis' can be installed ... OK
* checking installed package size ... OK
* checking package 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 for unstated 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 ... OK
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ...
** running examples for arch 'i386' ... [399s] WARNING
Found the following significant warnings:

  Warning: 'IlluminaHumanMethylation450k.db' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
                              user system elapsed
plotMethylationHeatmapByGene 57.42   2.38   82.70
buildAnnotationTracks        40.34   1.75   72.01
plotHeatmapByGene            33.38   1.19   46.23
heatmapByChromosome          29.13   1.40   32.20
annotateDMRInfo              27.05   0.27   27.32
export.DMRInfo               25.68   0.19   27.62
createTranscriptTrack        24.26   1.19   28.38
plotTracksWithDataTrackInfo  23.86   0.91   24.82
annotateGRanges              17.05   0.18   17.24
MethyLumiM2GenoSet            8.34   0.20    9.41
** running examples for arch 'x64' ... [364s] WARNING
Found the following significant warnings:

  Warning: 'IlluminaHumanMethylation450k.db' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
                              user system elapsed
plotMethylationHeatmapByGene 55.81   1.73   83.14
buildAnnotationTracks        34.66   1.05   65.30
plotHeatmapByGene            27.93   0.78   41.91
annotateDMRInfo              27.16   0.33   28.11
heatmapByChromosome          24.08   0.77   24.92
plotTracksWithDataTrackInfo  23.79   0.85   24.70
export.DMRInfo               21.61   0.25   21.90
createTranscriptTrack        20.06   0.91   20.97
annotateGRanges              15.85   0.06   15.93
MethyLumiM2GenoSet            7.30   0.19    7.49
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There were 2 warnings.
See
  'E:/biocbld/bbs-2.12-bioc/meat/methyAnalysis.Rcheck/00check.log'
for details.

methyAnalysis.Rcheck/00install.out:


install for i386

* installing *source* package 'methyAnalysis' ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import 'image' when loading 'graphics'
Warning: replacing previous import 'nleqslv' when loading 'nleqslv'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'image' when loading 'graphics'
Warning: replacing previous import 'nleqslv' when loading 'nleqslv'

install for x64

* installing *source* package 'methyAnalysis' ...
** testing if installed package can be loaded
Warning: replacing previous import 'image' when loading 'graphics'
Warning: replacing previous import 'nleqslv' when loading 'nleqslv'
* MD5 sums
packaged installation of 'methyAnalysis' as methyAnalysis_1.2.0.zip
* DONE (methyAnalysis)