BioC 3.2: CHECK report for GOSemSim on zin1

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings GOSemSim_1.27.4.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/GOSemSim.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GOSemSim/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GOSemSim’ version ‘1.27.4’
* 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 ... NOTE
Found the following hidden files and directories:
  .svnignore
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘GOSemSim’ can be installed ... [13s/13s] 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
* 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 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 compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [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
  ‘/home/biocbuild/bbs-3.2-bioc/meat/GOSemSim.Rcheck/00check.log’
for details.

* installing *source* package ‘GOSemSim’ ...
** libs
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c ICmethod.cpp -o ICmethod.o
ICmethod.cpp: In function ‘Rcpp::NumericMatrix infoContentMethod_cpp(Rcpp::StringVector&, Rcpp::StringVector&, Rcpp::List&, Rcpp::NumericVector&, const string&, const string&)’:
ICmethod.cpp:82:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (std::size_t i=0; i < ic_.size(); i++ ) {
                                        ^
ICmethod.cpp:88:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (std::size_t i=0; i < ic_.size(); i++ ) {
                                        ^
ICmethod.cpp:107:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (std::size_t i=0; i < anc_.size(); i++ ) {
                                         ^
ICmethod.cpp:118:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( std::size_t i = 0; i < id1_.size(); i++ ) {
                                          ^
ICmethod.cpp:125:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for ( std::size_t j = 0; j < id2_.size(); j++ ) {
                                              ^
ICmethod.cpp:152:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for ( std::size_t j = 0; j < id2_.size(); j++ ) {
                                              ^
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -shared -L/home/biocbuild/bbs-3.2-bioc/R/lib -L/usr/local/lib -o GOSemSim.so ICmethod.o RcppExports.o -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-bioc/meat/GOSemSim.Rcheck/GOSemSim/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 (GOSemSim)

name	user	system	elapsed
clusterSim	0.000	0.000	0.001
geneSim	0.847	0.020	0.885
goSim	0.228	0.000	0.228
mclusterSim	0.000	0.000	0.001
mgeneSim	1.848	0.020	1.883
mgoSim	0.784	0.000	0.783

BioC 3.2: CHECK report for GOSemSim on zin1

Summary

Command output