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BioC 2.14: CHECK report for MergeMaid on moscato2

This page was generated on 2014-10-08 08:50:52 -0700 (Wed, 08 Oct 2014).

Package 476/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MergeMaid 2.36.0
Xiaogang Zhong
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/MergeMaid
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: MergeMaid
Version: 2.36.0
Command: rm -rf MergeMaid.buildbin-libdir && mkdir MergeMaid.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MergeMaid.buildbin-libdir MergeMaid_2.36.0.tar.gz >MergeMaid-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=MergeMaid.buildbin-libdir --install="check:MergeMaid-install.out" --force-multiarch --no-vignettes --timings MergeMaid_2.36.0.tar.gz
StartedAt: 2014-10-08 02:40:50 -0700 (Wed, 08 Oct 2014)
EndedAt: 2014-10-08 02:43:23 -0700 (Wed, 08 Oct 2014)
EllapsedTime: 152.1 seconds
RetCode: 0
Status:  OK  
CheckDir: MergeMaid.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf MergeMaid.buildbin-libdir && mkdir MergeMaid.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MergeMaid.buildbin-libdir MergeMaid_2.36.0.tar.gz >MergeMaid-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=MergeMaid.buildbin-libdir --install="check:MergeMaid-install.out" --force-multiarch --no-vignettes --timings MergeMaid_2.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/MergeMaid.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 'MergeMaid/DESCRIPTION' ... OK
* this is package 'MergeMaid' version '2.36.0'
* 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.
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
.fdr.mergeCor: no visible global function definition for '.getnull'
* 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' ... [47s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
intcorDens               22.48   0.04   22.51
class.mergeExpressionSet  9.03   0.00    9.03
** running examples for arch 'x64' ... [56s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
intcorDens               26.16   0.07   26.23
class.mergeExpressionSet 11.39   0.01   11.40
intCor                    5.18   0.00    5.18
* 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/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_2.36.0.zip
* DONE (MergeMaid)

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

nameusersystemelapsed
class.mergeCoeff1.390.001.39
class.mergeCor3.250.003.24
class.mergeExpressionSet9.030.009.03
intCor4.380.004.39
intcorDens22.48 0.0422.51
intersection0.210.000.20
mergeExprs3.550.003.56
modelOutcome1.920.001.92

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

nameusersystemelapsed
class.mergeCoeff1.610.001.61
class.mergeCor4.110.004.17
class.mergeExpressionSet11.39 0.0111.40
intCor5.180.005.18
intcorDens26.16 0.0726.23
intersection0.20.00.2
mergeExprs3.970.003.96
modelOutcome2.060.002.06