BioC 2.11: CHECK report for GeneNetworkBuilder on lamb1

Package: GeneNetworkBuilder

Version: 1.0.1

Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings GeneNetworkBuilder_1.0.1.tar.gz

StartedAt: 2013-03-25 01:23:40 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 01:24:51 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 70.7 seconds

RetCode: 0

Status: OK

CheckDir: GeneNetworkBuilder.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/GeneNetworkBuilder.Rcheck’
* using R version 2.15.3 (2013-03-01)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneNetworkBuilder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GeneNetworkBuilder’ version ‘1.0.1’
* 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 whether package ‘GeneNetworkBuilder’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
polishNetwork 6.533  0.064   6.598
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’
 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
  ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/GeneNetworkBuilder.Rcheck/00check.log’
for details.

* installing *source* package ‘GeneNetworkBuilder’ ...
** libs
g++ -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c geneTree.cpp -o geneTree.o
geneTree.cpp: In member function ‘void GTree::ChangeTolerance(node*)’:
geneTree.cpp:112:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
geneTree.cpp: In member function ‘std::vector<node*> GTree::Travel()’:
geneTree.cpp:207:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
geneTree.cpp: In member function ‘void GTree::verifyFilter(int)’:
geneTree.cpp:275:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c nodefilter.cpp -o nodefilter.o
nodefilter.cpp: In function ‘SEXPREC* filterNodes(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
nodefilter.cpp:76:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
nodefilter.cpp:86:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
nodefilter.cpp:94:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -shared -L/usr/local/lib64 -o GeneNetworkBuilder.so geneTree.o nodefilter.o -L/loc/home/biocbuild/bbs-2.11-bioc/R/library/Rcpp/lib -lRcpp -Wl,-rpath,/loc/home/biocbuild/bbs-2.11-bioc/R/library/Rcpp/lib -L/home/biocbuild/bbs-2.11-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.11-bioc/meat/GeneNetworkBuilder.Rcheck/GeneNetworkBuilder/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘GeneNetworkBuilder.Rnw’ 
** testing if installed package can be loaded

* DONE (GeneNetworkBuilder)

name	user	system	elapsed
buildNetwork	1.304	0.044	1.415
ce.IDsMap	0.844	0.016	0.866
ce.interactionmap	0.040	0.000	0.041
ce.mapIDs	0.688	0.004	0.715
ce.miRNA.map	0.004	0.000	0.005
convertID	1.068	0.020	1.157
example.data	0.120	0.000	0.145
filterNetwork	4.844	0.032	4.893
hs.IDsMap	0.184	0.000	0.183
hs.interactionmap	0.040	0.004	0.065
hs.mapIDs	0.052	0.000	0.060
hs.miRNA.map	0.004	0.000	0.005
polishNetwork	6.533	0.064	6.598
uniqueExprsData	0.776	0.008	0.786

Summary

Command output