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BioC 3.2: CHECK report for clipper on moscato1

This page was generated on 2016-04-23 10:19:02 -0700 (Sat, 23 Apr 2016).

Package 181/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
clipper 1.10.0
Paolo Martini
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/clipper
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: clipper
Version: 1.10.0
Command: rm -rf clipper.buildbin-libdir clipper.Rcheck && mkdir clipper.buildbin-libdir clipper.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=clipper.buildbin-libdir clipper_1.10.0.tar.gz >clipper.Rcheck\00install.out 2>&1 && cp clipper.Rcheck\00install.out clipper-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=clipper.buildbin-libdir --install="check:clipper-install.out" --force-multiarch --no-vignettes --timings clipper_1.10.0.tar.gz
StartedAt: 2016-04-23 00:44:43 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 00:54:31 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 587.9 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: clipper.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf clipper.buildbin-libdir clipper.Rcheck && mkdir clipper.buildbin-libdir clipper.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=clipper.buildbin-libdir clipper_1.10.0.tar.gz >clipper.Rcheck\00install.out 2>&1 && cp clipper.Rcheck\00install.out clipper-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=clipper.buildbin-libdir --install="check:clipper-install.out" --force-multiarch --no-vignettes --timings clipper_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/clipper.Rcheck'
* using R version 3.2.4 (2016-03-10)
* 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 '1.10.0'
* 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 ... WARNING
Found the following significant warnings:
  Warning: package 'Matrix' was built under R version 3.2.5
See 'D:/biocbld/bbs-3.2-bioc/meat/clipper.Rcheck/00install.out' for details.
* 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' ... [75s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
clipperAllRoots 15.56   0.04   15.62
pathwayTest     12.70   0.07   12.76
clipper          7.99   0.08    9.45
** running examples for arch 'x64' ... [76s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
clipperAllRoots  18.05   0.05   18.09
pathwayTest      12.56   0.05   12.61
clipper           7.63   0.17    8.05
cliquePairedTest  5.01   0.07    5.07
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R' [18s]
 [19s] OK
** running tests for arch 'x64' ...
  Running 'runTests.R' [22s]
 [23s] 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 WARNING
See
  'D:/biocbld/bbs-3.2-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
Warning: package 'Matrix' was built under R version 3.2.5
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: package 'Matrix' was built under R version 3.2.5

install for x64

* installing *source* package 'clipper' ...
** testing if installed package can be loaded
Warning: package 'Matrix' was built under R version 3.2.5
* MD5 sums
packaged installation of 'clipper' as clipper_1.10.0.zip
* DONE (clipper)

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

nameusersystemelapsed
clipper7.990.089.45
clipperAllRoots15.56 0.0415.62
cliqueMeanTest4.040.024.05
cliqueMixedTest4.090.054.13
cliquePairedTest4.680.014.70
cliqueVarianceTest3.500.033.53
deleteEdge0.250.020.26
easyClip4.320.084.48
getGraphEntryGenes0.480.000.49
getJunctionTreePaths0.450.040.50
nameCliques000
pathwayTest12.70 0.0712.76
plotInCytoscape000
prunePaths0.010.000.01

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

nameusersystemelapsed
clipper7.630.178.05
clipperAllRoots18.05 0.0518.09
cliqueMeanTest3.900.033.93
cliqueMixedTest4.330.044.38
cliquePairedTest5.010.075.07
cliqueVarianceTest4.070.064.14
deleteEdge0.270.030.30
easyClip4.340.024.35
getGraphEntryGenes0.390.000.39
getJunctionTreePaths0.530.010.55
nameCliques000
pathwayTest12.56 0.0512.61
plotInCytoscape000
prunePaths0.010.000.02