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BioC 2.14: CHECK report for MLP on moscato2

This page was generated on 2014-10-08 08:53:39 -0700 (Wed, 08 Oct 2014).

Package 506/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MLP 1.12.0
Tobias Verbeke
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/MLP
Last Changed Rev: 88838 / Revision: 95116
Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ] OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: MLP
Version: 1.12.0
Command: rm -rf MLP.buildbin-libdir && mkdir MLP.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MLP.buildbin-libdir MLP_1.12.0.tar.gz >MLP-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=MLP.buildbin-libdir --install="check:MLP-install.out" --force-multiarch --no-vignettes --timings MLP_1.12.0.tar.gz
StartedAt: 2014-10-08 03:03:53 -0700 (Wed, 08 Oct 2014)
EndedAt: 2014-10-08 03:11:19 -0700 (Wed, 08 Oct 2014)
EllapsedTime: 446.5 seconds
RetCode: 0
Status:  OK  
CheckDir: MLP.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf MLP.buildbin-libdir && mkdir MLP.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MLP.buildbin-libdir MLP_1.12.0.tar.gz >MLP-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=MLP.buildbin-libdir --install="check:MLP-install.out" --force-multiarch --no-vignettes --timings MLP_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/MLP.Rcheck'
* using R version 3.1.1 (2014-07-10)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MLP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MLP' version '1.12.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'AnnotationDbi' 'affy' 'plotrix' 'gplots' 'gmodels' 'gdata' 'gtools'
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 'MLP' 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' calls to packages already attached by Depends:
  'gdata' 'gmodels' 'gplots' 'gtools'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'affy' 'gdata' 'gmodels' 'gplots' 'gtools' 'plotrix'
  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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [67s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
MLP         34.74   0.37   35.20
getGeneSets 18.96   0.55   20.65
** running examples for arch 'x64' ... [84s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
MLP         40.95   0.41   41.36
getGeneSets 26.89   0.56   27.46
plot.MLP     7.19   0.12    7.35
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test.MLP.R' [80s]
 [80s] OK
** running tests for arch 'x64' ...
  Running 'test.MLP.R' [80s]
 [80s] 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 2 notes.
See
  'E:/biocbld/bbs-2.14-bioc/meat/MLP.Rcheck/00check.log'
for details.

MLP.Rcheck/00install.out:


install for i386

* installing *source* package 'MLP' ...
** 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 'MLP' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MLP' as MLP_1.12.0.zip
* DONE (MLP)

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

nameusersystemelapsed
MLP34.74 0.3735.20
getGeneSets18.96 0.5520.65
mlpBarplot0.090.000.09
plot.MLP4.580.034.60
plotGOgraph0.840.030.87
plotGeneSetSignificance0.890.040.94

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

nameusersystemelapsed
MLP40.95 0.4141.36
getGeneSets26.89 0.5627.46
mlpBarplot0.110.000.11
plot.MLP7.190.127.35
plotGOgraph1.590.021.61
plotGeneSetSignificance1.320.031.44