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BioC 3.1: CHECK report for MergeMaid on moscato2

This page was generated on 2015-10-09 09:27:17 -0700 (Fri, 09 Oct 2015).

Package 572/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MergeMaid 2.40.0
Xiaogang Zhong
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/MergeMaid
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  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: MergeMaid
Version: 2.40.0
Command: rm -rf MergeMaid.buildbin-libdir MergeMaid.Rcheck && mkdir MergeMaid.buildbin-libdir MergeMaid.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MergeMaid.buildbin-libdir MergeMaid_2.40.0.tar.gz >MergeMaid.Rcheck\00install.out 2>&1 && cp MergeMaid.Rcheck\00install.out MergeMaid-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=MergeMaid.buildbin-libdir --install="check:MergeMaid-install.out" --force-multiarch --no-vignettes --timings MergeMaid_2.40.0.tar.gz
StartedAt: 2015-10-09 03:32:46 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 03:35:33 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 167.0 seconds
RetCode: 0
Status:  OK  
CheckDir: MergeMaid.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf MergeMaid.buildbin-libdir MergeMaid.Rcheck && mkdir MergeMaid.buildbin-libdir MergeMaid.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MergeMaid.buildbin-libdir MergeMaid_2.40.0.tar.gz >MergeMaid.Rcheck\00install.out 2>&1 && cp MergeMaid.Rcheck\00install.out MergeMaid-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=MergeMaid.buildbin-libdir --install="check:MergeMaid-install.out" --force-multiarch --no-vignettes --timings MergeMaid_2.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/MergeMaid.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 'MergeMaid/DESCRIPTION' ... OK
* this is package 'MergeMaid' version '2.40.0'
* 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 'MergeMaid' 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
Packages in Depends field not imported from:
  'MASS' 'methods' 'survival'
  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
.fdr.mergeCor: no visible global function definition for '.getnull'
.mergemodel: no visible global function definition for 'coxph'
maxintcor: no visible global function definition for 'ginv'
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [54s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
intcorDens               27.25   0.04   27.47
class.mergeExpressionSet  9.75   0.00    9.75
intCor                    5.37   0.02    5.38
** running examples for arch 'x64' ... [64s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
intcorDens               31.44   0.04   31.48
class.mergeExpressionSet 12.57   0.00   12.57
intCor                    6.22   0.00    6.22
* 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: 2 NOTEs
See
  'E:/biocbld/bbs-3.1-bioc/meat/MergeMaid.Rcheck/00check.log'
for details.


MergeMaid.Rcheck/00install.out:


install for i386

* installing *source* package 'MergeMaid' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'plot' from package 'graphics' in package 'MergeMaid'
Creating a generic function for 'hist' from package 'graphics' in package 'MergeMaid'
Creating a generic function for 'summary' from package 'base' in package 'MergeMaid'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'MergeMaid' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MergeMaid' as MergeMaid_2.40.0.zip
* DONE (MergeMaid)

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

nameusersystemelapsed
class.mergeCoeff1.340.031.38
class.mergeCor3.490.013.51
class.mergeExpressionSet9.750.009.75
intCor5.370.025.38
intcorDens27.25 0.0427.47
intersection0.180.000.17
mergeExprs3.610.043.65
modelOutcome1.610.001.64

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

nameusersystemelapsed
class.mergeCoeff1.460.001.47
class.mergeCor4.080.014.09
class.mergeExpressionSet12.57 0.0012.57
intCor6.220.006.22
intcorDens31.44 0.0431.48
intersection0.260.000.27
mergeExprs4.560.004.55
modelOutcome2.330.002.32