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BioC 3.0: CHECK report for motifRG on moscato1

This page was generated on 2015-04-10 09:47:57 -0700 (Fri, 10 Apr 2015).

Package 574/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
motifRG 1.10.0
Zizhen Yao
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/motifRG
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 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 

Summary

Package: motifRG
Version: 1.10.0
Command: rm -rf motifRG.buildbin-libdir motifRG.Rcheck && mkdir motifRG.buildbin-libdir motifRG.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=motifRG.buildbin-libdir motifRG_1.10.0.tar.gz >motifRG.Rcheck\00install.out 2>&1 && cp motifRG.Rcheck\00install.out motifRG-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=motifRG.buildbin-libdir --install="check:motifRG-install.out" --force-multiarch --no-vignettes --timings motifRG_1.10.0.tar.gz
StartedAt: 2015-04-10 03:22:19 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 03:30:31 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 492.2 seconds
RetCode: 0
Status:  OK  
CheckDir: motifRG.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf motifRG.buildbin-libdir motifRG.Rcheck && mkdir motifRG.buildbin-libdir motifRG.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=motifRG.buildbin-libdir motifRG_1.10.0.tar.gz >motifRG.Rcheck\00install.out 2>&1 && cp motifRG.Rcheck\00install.out motifRG-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=motifRG.buildbin-libdir --install="check:motifRG-install.out" --force-multiarch --no-vignettes --timings motifRG_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/motifRG.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'motifRG/DESCRIPTION' ... OK
* this is package 'motifRG' version '1.10.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'Biostrings' 'IRanges' 'seqLogo' 'parallel' 'grid' 'BSgenome'
  'XVector' 'BSgenome.Hsapiens.UCSC.hg19'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'motifRG' 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' 'IRanges' 'seqLogo' 'parallel' 'methods' 'grid' 'graphics' 'XVector'
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
** 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 ... NOTE
'library' or 'require' call to 'parallel' which was already attached by Depends.
  Please remove these calls from your code.
Namespaces in Imports field not imported from:
  'graphics' 'methods'
  All declared Imports should be used.
Packages in Depends field not imported from:
  'BSgenome.Hsapiens.UCSC.hg19' 'methods'
  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
bestPWMMatch: no visible global function definition for 'Rle'
getSequence: no visible global function definition for 'strand'
matchPWMCoor: no visible global function definition for 'GRanges'
my.pvec: no visible global function definition for 'mc.reset.stream'
my.pvec : <anonymous>: no visible global function definition for
  'mcparallel'
my.pvec: no visible global function definition for 'mccollect'
* checking Rd files ... NOTE
prepare_Rd: YY1.control.Rd:8-9: Dropping empty section \details
prepare_Rd: YY1.peak.Rd:8-9: Dropping empty section \details
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [80s] OK
Examples with CPU or elapsed time > 5s
          user system elapsed
findMotif 62.9   0.09   65.08
** running examples for arch 'x64' ... [82s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
findMotif 61.51   0.11   61.98
* 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

NOTE: There were 5 notes.
See
  'D:/biocbld/bbs-3.0-bioc/meat/motifRG.Rcheck/00check.log'
for details.

motifRG.Rcheck/00install.out:


install for i386

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

install for x64

* installing *source* package 'motifRG' ...
** testing if installed package can be loaded
Warning: replacing previous import by 'graphics::plot' when loading 'seqLogo'
* MD5 sums
packaged installation of 'motifRG' as motifRG_1.10.0.zip
* DONE (motifRG)

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

nameusersystemelapsed
findMotif62.90 0.0965.08
motifLatexTable0.450.020.72
plotMotif0.100.000.09
refinePWMMotif4.080.184.28
summaryMotif0.050.000.04

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

nameusersystemelapsed
findMotif61.51 0.1161.98
motifLatexTable0.390.020.42
plotMotif0.090.000.10
refinePWMMotif4.060.114.16
summaryMotif0.090.000.09