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BioC 3.5: CHECK report for clipper on tokay2

This page was generated on 2017-10-18 14:22:19 -0400 (Wed, 18 Oct 2017).

Package 228/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
clipper 1.16.0
Paolo Martini
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/clipper
Branch: RELEASE_3_5
Last Commit: 8cf42f9
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: clipper
Version: 1.16.0
Command: rm -rf clipper.buildbin-libdir clipper.Rcheck && mkdir clipper.buildbin-libdir clipper.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=clipper.buildbin-libdir clipper_1.16.0.tar.gz >clipper.Rcheck\00install.out 2>&1 && cp clipper.Rcheck\00install.out clipper-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=clipper.buildbin-libdir --install="check:clipper-install.out" --force-multiarch --no-vignettes --timings clipper_1.16.0.tar.gz
StartedAt: 2017-10-17 22:46:28 -0400 (Tue, 17 Oct 2017)
EndedAt: 2017-10-17 22:53:26 -0400 (Tue, 17 Oct 2017)
EllapsedTime: 417.1 seconds
RetCode: 0
Status:  OK  
CheckDir: clipper.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf clipper.buildbin-libdir clipper.Rcheck && mkdir clipper.buildbin-libdir clipper.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=clipper.buildbin-libdir clipper_1.16.0.tar.gz >clipper.Rcheck\00install.out 2>&1 && cp clipper.Rcheck\00install.out clipper-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=clipper.buildbin-libdir --install="check:clipper-install.out" --force-multiarch --no-vignettes --timings clipper_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/clipper.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'clipper/DESCRIPTION' ... OK
* this is package 'clipper' version '1.16.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'RCytoscape'
* 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' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
clipperAllRoots 9.31   0.06    9.37
pathwayTest     7.75   0.05    7.80
clipper         4.96   0.24    6.18
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
clipperAllRoots 9.11   0.06    9.17
pathwayTest     8.10   0.07    8.16
clipper         5.91   0.10    6.08
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.R'
 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
* DONE

Status: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.5-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_1.16.0.zip
* DONE (clipper)

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

nameusersystemelapsed
clipper4.960.246.18
clipperAllRoots9.310.069.37
cliqueMeanTest2.900.032.93
cliqueMixedTest3.560.083.65
cliquePairedTest3.080.083.15
cliqueVarianceTest2.670.062.73
deleteEdge0.090.010.11
easyClip3.130.023.22
getGraphEntryGenes0.170.000.17
getJunctionTreePaths0.130.000.13
nameCliques0.010.000.01
pathwayTest7.750.057.80
plotInCytoscape000
prunePaths0.020.000.02

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

nameusersystemelapsed
clipper5.910.106.08
clipperAllRoots9.110.069.17
cliqueMeanTest2.660.032.68
cliqueMixedTest3.640.033.68
cliquePairedTest3.470.033.50
cliqueVarianceTest3.000.143.14
deleteEdge0.100.000.09
easyClip2.990.053.03
getGraphEntryGenes0.220.010.23
getJunctionTreePaths0.120.020.14
nameCliques000
pathwayTest8.100.078.16
plotInCytoscape000
prunePaths0.040.000.04