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BioC 3.1: CHECK report for motifRG on moscato2

This page was generated on 2015-10-09 09:29:45 -0700 (Fri, 09 Oct 2015).

Package 623/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
motifRG 1.12.0
Zizhen Yao
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/motifRG
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: motifRG
Version: 1.12.0
Command: rm -rf motifRG.buildbin-libdir motifRG.Rcheck && mkdir motifRG.buildbin-libdir motifRG.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=motifRG.buildbin-libdir motifRG_1.12.0.tar.gz >motifRG.Rcheck\00install.out 2>&1 && cp motifRG.Rcheck\00install.out motifRG-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=motifRG.buildbin-libdir --install="check:motifRG-install.out" --force-multiarch --no-vignettes --timings motifRG_1.12.0.tar.gz
StartedAt: 2015-10-09 04:04:12 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 04:10:34 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 381.8 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 && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=motifRG.buildbin-libdir motifRG_1.12.0.tar.gz >motifRG.Rcheck\00install.out 2>&1 && cp motifRG.Rcheck\00install.out motifRG-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=motifRG.buildbin-libdir --install="check:motifRG-install.out" --force-multiarch --no-vignettes --timings motifRG_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/motifRG.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 'motifRG/DESCRIPTION' ... OK
* this is package 'motifRG' version '1.12.0'
* 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
Malformed Description field: should contain one or more complete sentences.
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'
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' ... [64s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
findMotif 52.76   0.06   53.51
** running examples for arch 'x64' ... [72s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
findMotif 60.17   0.06   60.99
* 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: 5 NOTEs
See
  'E:/biocbld/bbs-3.1-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
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'

install for x64

* installing *source* package 'motifRG' ...
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* MD5 sums
packaged installation of 'motifRG' as motifRG_1.12.0.zip
* DONE (motifRG)

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

nameusersystemelapsed
findMotif52.76 0.0653.51
motifLatexTable0.330.000.36
plotMotif0.060.000.06
refinePWMMotif3.310.143.54
summaryMotif0.050.000.05

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

nameusersystemelapsed
findMotif60.17 0.0660.99
motifLatexTable0.370.000.38
plotMotif0.100.000.09
refinePWMMotif3.540.083.62
summaryMotif0.050.000.05