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BioC 2.13: CHECK report for methVisual on moscato1

This page was generated on 2014-04-05 09:50:01 -0700 (Sat, 05 Apr 2014).

Package 438/750HostnameOS / ArchBUILDCHECKBUILD BIN
methVisual 1.14.0
Arie Zackay
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/methVisual
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
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 

Summary

Package: methVisual
Version: 1.14.0
Command: rm -rf methVisual.buildbin-libdir && mkdir methVisual.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=methVisual.buildbin-libdir methVisual_1.14.0.tar.gz >methVisual-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=methVisual.buildbin-libdir --install="check:methVisual-install.out" --force-multiarch --no-vignettes --timings methVisual_1.14.0.tar.gz && mv methVisual.buildbin-libdir/* methVisual.Rcheck/ && rmdir methVisual.buildbin-libdir
StartedAt: 2014-04-05 05:05:07 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 05:07:51 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 164.1 seconds
RetCode: 0
Status:  OK  
CheckDir: methVisual.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/methVisual.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 'methVisual/DESCRIPTION' ... OK
* this is package 'methVisual' version '1.14.0'
* 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 'methVisual' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'Biostrings' 'grid'
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
Packages in Depends field not imported from:
  'gsubfn' 'plotrix' 'sqldf'
  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 ... 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 for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'methVisual.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [11s] OK
** running examples for arch 'x64' ... [14s] OK
* 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 3 notes.
See
  'D:/biocbld/bbs-2.13-bioc/meat/methVisual.Rcheck/00check.log'
for details.

methVisual.Rcheck/00install.out:


install for i386

* installing *source* package 'methVisual' ...
** R
** data
** 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 'methVisual' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'methVisual' as methVisual_1.14.0.zip
* DONE (methVisual)

methVisual.Rcheck/examples_i386/methVisual-Ex.timings:

nameusersystemelapsed
Cooccurrence0.560.010.57
MethAlignNW1.790.021.90
MethDataInput0.090.020.11
MethLollipops0.020.000.02
MethylQC1.370.001.38
cgInAlign000
cgMethFinder000
coversionGenom000
findNonAligned0.140.000.14
heatMapMeth0.110.000.12
makeDataMethGFF0.190.000.21
makeLocalExpDir0.070.040.11
makeTabFilePath0.020.000.09
matrixSNP0.340.000.34
methCA0.030.000.05
methData0.020.000.02
methFisherTest0.050.000.05
methWhitneyUTest0.020.000.02
plotAbsMethyl000
plotMatrixSNP0.760.000.76
readBisulfFASTA0.090.020.11
selectRefSeq0.060.040.10

methVisual.Rcheck/examples_x64/methVisual-Ex.timings:

nameusersystemelapsed
Cooccurrence0.700.020.71
MethAlignNW1.880.062.01
MethDataInput0.130.000.12
MethLollipops0.030.000.03
MethylQC1.760.011.78
cgInAlign0.020.000.01
cgMethFinder0.020.000.02
coversionGenom000
findNonAligned0.020.000.02
heatMapMeth0.110.020.19
makeDataMethGFF0.200.000.21
makeLocalExpDir0.090.020.11
makeTabFilePath0.020.000.02
matrixSNP0.370.000.38
methCA0.010.010.13
methData0.000.020.02
methFisherTest0.040.000.04
methWhitneyUTest0.010.000.02
plotAbsMethyl0.020.000.02
plotMatrixSNP0.820.010.84
readBisulfFASTA0.090.020.11
selectRefSeq0.060.030.09