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BioC 2.14: CHECK report for clipper on moscato2

This page was generated on 2014-10-08 08:55:16 -0700 (Wed, 08 Oct 2014).

Package 155/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
clipper 1.4.0
Paolo Martini
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/clipper
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: clipper
Version: 1.4.0
Command: rm -rf clipper.buildbin-libdir && mkdir clipper.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=clipper.buildbin-libdir clipper_1.4.0.tar.gz >clipper-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=clipper.buildbin-libdir --install="check:clipper-install.out" --force-multiarch --no-vignettes --timings clipper_1.4.0.tar.gz
StartedAt: 2014-10-07 23:55:01 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-08 00:01:12 -0700 (Wed, 08 Oct 2014)
EllapsedTime: 370.9 seconds
RetCode: 0
Status:  OK  
CheckDir: clipper.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf clipper.buildbin-libdir && mkdir clipper.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=clipper.buildbin-libdir clipper_1.4.0.tar.gz >clipper-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=clipper.buildbin-libdir --install="check:clipper-install.out" --force-multiarch --no-vignettes --timings clipper_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/clipper.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 'clipper/DESCRIPTION' ... OK
* this is package 'clipper' version '1.4.0'
* 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 'clipper' 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 ... OK
* 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' ... NOTE
The following files should probably not be installed:
  'Cytoscape.png'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [54s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
clipperAllRoots 12.48   0.05   12.53
pathwayTest      9.67   0.03    9.70
clipper          6.05   0.06    6.21
** running examples for arch 'x64' ... [58s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
clipperAllRoots 14.40   0.10   14.51
pathwayTest      9.00   0.04    9.04
clipper          6.55   0.03    6.63
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R' [12s]
 [13s] OK
** running tests for arch 'x64' ...
  Running 'runTests.R' [13s]
 [14s] 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 was 1 note.
See
  'E:/biocbld/bbs-2.14-bioc/meat/clipper.Rcheck/00check.log'
for details.

clipper.Rcheck/00install.out:


install for i386

* installing *source* package 'clipper' ...
** 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 'clipper' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'clipper' as clipper_1.4.0.zip
* DONE (clipper)

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

nameusersystemelapsed
clipper6.050.066.21
clipperAllRoots12.48 0.0512.53
cliqueMeanTest3.340.023.35
cliqueMixedTest3.200.003.19
cliquePairedTest3.140.053.37
cliqueVarianceTest3.200.013.21
deleteEdge0.230.020.25
easyClip2.950.002.95
getGraphEntryGenes0.280.000.28
getJunctionTreePaths0.260.000.26
nameCliques000
pathwayTest9.670.039.70
plotInCytoscape000
prunePaths000

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

nameusersystemelapsed
clipper6.550.036.63
clipperAllRoots14.40 0.1014.51
cliqueMeanTest3.640.033.67
cliqueMixedTest3.550.033.59
cliquePairedTest3.340.063.41
cliqueVarianceTest3.400.053.45
deleteEdge0.240.000.25
easyClip2.950.083.03
getGraphEntryGenes0.320.000.31
getJunctionTreePaths0.30.00.3
nameCliques000
pathwayTest9.000.049.04
plotInCytoscape000
prunePaths000