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BioC 2.12: CHECK report for GeneNetworkBuilder on petty

This page was generated on 2013-10-09 09:40:13 -0700 (Wed, 09 Oct 2013).

Package 257/671HostnameOS / ArchBUILDCHECKBUILD BIN
GeneNetworkBuilder 1.2.0
Jianhong Ou
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/GeneNetworkBuilder
Last Changed Rev: 75263 / Revision: 81334
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: GeneNetworkBuilder
Version: 1.2.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GeneNetworkBuilder_1.2.0.tar.gz
StartedAt: 2013-10-08 22:29:20 -0700 (Tue, 08 Oct 2013)
EndedAt: 2013-10-08 22:31:02 -0700 (Tue, 08 Oct 2013)
EllapsedTime: 101.8 seconds
RetCode: 0
Status:  OK 
CheckDir: GeneNetworkBuilder.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/GeneNetworkBuilder.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'GeneNetworkBuilder/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GeneNetworkBuilder' version '1.2.0'
* 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 for sufficient/correct file permissions ... OK
* checking whether package 'GeneNetworkBuilder' can be installed ... [14s/14s] OK
* checking installed package size ... OK
* checking package 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
* 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 for unstated 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [24s/24s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
polishNetwork 7.230  0.487   7.796
filterNetwork 5.343  0.269   5.658
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'runTests.R' [3s/3s]
 [3s/3s] OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: 'RBGL'
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/GeneNetworkBuilder.Rcheck/00check.log'
for details.

GeneNetworkBuilder.Rcheck/00install.out:

* installing *source* package 'GeneNetworkBuilder' ...
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2  -c geneTree.cpp -o geneTree.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2  -c nodefilter.cpp -o nodefilter.o
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o GeneNetworkBuilder.so geneTree.o nodefilter.o /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/lib/libRcpp.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/GeneNetworkBuilder.Rcheck/GeneNetworkBuilder/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GeneNetworkBuilder)

GeneNetworkBuilder.Rcheck/GeneNetworkBuilder-Ex.timings:

nameusersystemelapsed
buildNetwork1.5050.0981.617
ce.IDsMap1.3330.0471.411
ce.interactionmap0.0730.0230.097
ce.mapIDs0.7620.0450.814
ce.miRNA.map0.0140.0060.020
convertID1.4150.0571.485
example.data0.2390.0050.245
filterNetwork5.3430.2695.658
hs.IDsMap0.3820.0130.399
hs.interactionmap0.1400.0130.153
hs.mapIDs0.0950.0050.102
hs.miRNA.map0.0100.0070.016
polishNetwork7.2300.4877.796
uniqueExprsData0.9780.0721.063