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BioC 2.13: CHECK report for pcaGoPromoter on moscato1

This page was generated on 2014-04-05 09:50:38 -0700 (Sat, 05 Apr 2014).

Package 516/750HostnameOS / ArchBUILDCHECKBUILD BIN
pcaGoPromoter 1.6.0
Morten Hansen
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/pcaGoPromoter
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: pcaGoPromoter
Version: 1.6.0
Command: rm -rf pcaGoPromoter.buildbin-libdir && mkdir pcaGoPromoter.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=pcaGoPromoter.buildbin-libdir pcaGoPromoter_1.6.0.tar.gz >pcaGoPromoter-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=pcaGoPromoter.buildbin-libdir --install="check:pcaGoPromoter-install.out" --force-multiarch --no-vignettes --timings pcaGoPromoter_1.6.0.tar.gz && mv pcaGoPromoter.buildbin-libdir/* pcaGoPromoter.Rcheck/ && rmdir pcaGoPromoter.buildbin-libdir
StartedAt: 2014-04-05 05:43:55 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 05:51:37 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 461.4 seconds
RetCode: 0
Status:  OK  
CheckDir: pcaGoPromoter.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/pcaGoPromoter.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 'pcaGoPromoter/DESCRIPTION' ... OK
* this is package 'pcaGoPromoter' version '1.6.0'
* 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 'pcaGoPromoter' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' 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 dependencies in R code ... NOTE
'library' or 'require' call to 'ellipse' which was already attached by Depends.
  Please remove these calls from your code.
Namespace in Imports field not imported from: 'Biobase'
  All declared Imports should be used.
Package in Depends field not imported from: 'ellipse'
  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 ... NOTE
primoData.getPromoters: no visible global function definition for
  'readFASTA'
* 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 installed files from 'inst/doc' ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'pcaGoPromoter.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [177s] OK
Examples with CPU or elapsed time > 5s
        user system elapsed
GOtree 95.32   2.06  105.84
primo  58.49   0.49   63.44
** running examples for arch 'x64' ... [167s] OK
Examples with CPU or elapsed time > 5s
        user system elapsed
GOtree 98.47   1.70  100.17
primo  57.64   0.51   58.16
pca     4.73   0.02    5.59
* 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/pcaGoPromoter.Rcheck/00check.log'
for details.

pcaGoPromoter.Rcheck/00install.out:


install for i386

* installing *source* package 'pcaGoPromoter' ...
** R
** 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 'pcaGoPromoter' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'pcaGoPromoter' as pcaGoPromoter_1.6.0.zip
* DONE (pcaGoPromoter)

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

nameusersystemelapsed
GOtree 95.32 2.06105.84
pca3.620.063.68
pcaGoPromoter-package000
primo58.49 0.4963.44
primoData000

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

nameusersystemelapsed
GOtree 98.47 1.70100.17
pca4.730.025.59
pcaGoPromoter-package000
primo57.64 0.5158.16
primoData000