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BioC 3.1: CHECK report for pwOmics on moscato2

This page was generated on 2015-10-09 09:32:23 -0700 (Fri, 09 Oct 2015).

Package 760/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pwOmics 1.0.2
Astrid Wachter
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/pwOmics
Last Changed Rev: 107705 / Revision: 109384
Last Changed Date: 2015-08-24 00:29:04 -0700 (Mon, 24 Aug 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK NO, built version is LOWER than in internal repository!!!
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK NO, built version is LOWER than in internal repository!!!
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK NO, built version is LOWER than in internal repository!!!

Summary

Package: pwOmics
Version: 1.0.2
Command: rm -rf pwOmics.buildbin-libdir pwOmics.Rcheck && mkdir pwOmics.buildbin-libdir pwOmics.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=pwOmics.buildbin-libdir pwOmics_1.0.2.tar.gz >pwOmics.Rcheck\00install.out 2>&1 && cp pwOmics.Rcheck\00install.out pwOmics-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=pwOmics.buildbin-libdir --install="check:pwOmics-install.out" --force-multiarch --no-vignettes --timings pwOmics_1.0.2.tar.gz
StartedAt: 2015-10-09 05:06:34 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 05:10:33 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 238.5 seconds
RetCode: 0
Status:  OK  
CheckDir: pwOmics.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf pwOmics.buildbin-libdir pwOmics.Rcheck && mkdir pwOmics.buildbin-libdir pwOmics.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=pwOmics.buildbin-libdir pwOmics_1.0.2.tar.gz >pwOmics.Rcheck\00install.out 2>&1 && cp pwOmics.Rcheck\00install.out pwOmics-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=pwOmics.buildbin-libdir --install="check:pwOmics-install.out" --force-multiarch --no-vignettes --timings pwOmics_1.0.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/pwOmics.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 'pwOmics/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'pwOmics' version '1.0.2'
* 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 'pwOmics' 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 ... NOTE
SteinerTree_cons: no visible binding for global variable 'igraph'
* 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' ... [29s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
readTFdata 19.07    0.7    20.9
** running examples for arch 'x64' ... [23s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
readTFdata 13.79   0.62      15
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R' [5s]
 [5s] OK
** running tests for arch 'x64' ...
  Running 'runTests.R' [6s]
 [6s] 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
  'E:/biocbld/bbs-3.1-bioc/meat/pwOmics.Rcheck/00check.log'
for details.


pwOmics.Rcheck/00install.out:


install for i386

* installing *source* package 'pwOmics' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'

install for x64

* installing *source* package 'pwOmics' ...
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* MD5 sums
packaged installation of 'pwOmics' as pwOmics_1.0.2.zip
* DONE (pwOmics)

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

nameusersystemelapsed
clusterTimeProfiles0.110.000.11
dynamicConsensusNet0.090.000.10
enrichPWs0.090.000.09
enrichTFs0.100.000.09
getBiopaxModel0.080.000.08
getDS_PWs0.060.000.06
getDS_TFs0.060.000.07
getDS_TGs0.050.010.06
getGenesIntersection0.040.020.06
getOmicsDataset0.130.010.14
getOmicsTimepoints0.060.000.06
getOmicsallGeneIDs0.440.050.49
getOmicsallProteinIDs0.080.000.08
getProteinIntersection0.060.000.06
getTFIntersection0.060.000.06
getUS_PWs0.060.000.06
getUS_TFs0.070.000.07
getUS_regulators0.040.020.06
gettpIntersection0.080.000.08
identifyPWTFTGs0.060.000.06
identifyPWs0.070.000.06
identifyRsofTFs0.060.000.06
identifyTFs0.060.000.07
plotConsensusGraph0.060.000.06
plotTimeProfileClusters0.070.000.06
plotdynConsensusNet0.060.000.06
readOmics0.060.000.07
readPWdata0.060.000.06
readTFdata19.07 0.7020.90
staticConsensusNet0.090.000.10

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

nameusersystemelapsed
clusterTimeProfiles0.070.000.06
dynamicConsensusNet0.060.000.06
enrichPWs0.040.010.04
enrichTFs0.060.000.07
getBiopaxModel0.060.000.06
getDS_PWs0.050.000.04
getDS_TFs0.060.000.07
getDS_TGs0.060.000.06
getGenesIntersection0.050.000.05
getOmicsDataset0.090.030.12
getOmicsTimepoints0.070.000.06
getOmicsallGeneIDs0.260.070.35
getOmicsallProteinIDs0.300.000.29
getProteinIntersection0.060.000.07
getTFIntersection0.050.000.04
getUS_PWs0.060.000.06
getUS_TFs0.090.000.10
getUS_regulators0.080.000.08
gettpIntersection0.070.000.08
identifyPWTFTGs0.080.000.08
identifyPWs0.080.000.08
identifyRsofTFs0.050.000.04
identifyTFs0.040.010.07
plotConsensusGraph0.070.000.06
plotTimeProfileClusters0.040.000.04
plotdynConsensusNet0.050.020.07
readOmics0.060.000.06
readPWdata0.050.000.05
readTFdata13.79 0.6215.00
staticConsensusNet0.060.000.07