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BioC 3.2: CHECK report for methVisual on oaxaca

This page was generated on 2016-04-23 10:24:35 -0700 (Sat, 23 Apr 2016).

Package 630/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
methVisual 1.22.0
Arie Zackay
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/methVisual
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: methVisual
Version: 1.22.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings methVisual_1.22.0.tar.gz
StartedAt: 2016-04-23 01:59:08 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 02:00:57 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 109.3 seconds
RetCode: 0
Status:  OK 
CheckDir: methVisual.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings methVisual_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/methVisual.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘methVisual/DESCRIPTION’ ... OK
* this is package ‘methVisual’ version ‘1.22.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘methVisual’ can be installed ... [9s/13s] 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
* 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 ... 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.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
makeDataMethGFF: no visible binding for global variable ‘fn’
plotMatrixSNP: no visible global function definition for ‘color.legend’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [10s/10s] 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
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/methVisual.Rcheck/00check.log’
for details.


methVisual.Rcheck/00install.out:

* 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
* DONE (methVisual)

methVisual.Rcheck/methVisual-Ex.timings:

nameusersystemelapsed
Cooccurrence0.4690.0690.539
MethAlignNW1.4470.0921.553
MethDataInput0.0230.0050.029
MethLollipops0.0130.0030.017
MethylQC1.0840.0721.277
cgInAlign0.0030.0020.005
cgMethFinder0.0000.0000.001
coversionGenom0.0010.0000.001
findNonAligned0.0040.0030.006
heatMapMeth0.0860.0090.094
makeDataMethGFF0.1280.0120.140
makeLocalExpDir0.0160.0040.020
makeTabFilePath0.0120.0030.097
matrixSNP0.2960.0620.356
methCA0.0140.0040.017
methData0.0030.0020.004
methFisherTest0.0470.0050.052
methWhitneyUTest0.0060.0020.009
plotAbsMethyl0.0050.0020.007
plotMatrixSNP0.6250.1230.798
readBisulfFASTA0.0650.0080.072
selectRefSeq0.0130.0040.017