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CHECK report for GOSemSim on tokay1

This page was generated on 2018-04-12 13:19:30 -0400 (Thu, 12 Apr 2018).

Package 600/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GOSemSim 2.4.1
Guangchuang Yu
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/GOSemSim
Branch: RELEASE_3_6
Last Commit: 0656e84
Last Changed Date: 2018-01-31 04:23:53 -0400 (Wed, 31 Jan 2018)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GOSemSim
Version: 2.4.1
Command: rm -rf GOSemSim.buildbin-libdir GOSemSim.Rcheck && mkdir GOSemSim.buildbin-libdir GOSemSim.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GOSemSim.buildbin-libdir GOSemSim_2.4.1.tar.gz >GOSemSim.Rcheck\00install.out 2>&1 && cp GOSemSim.Rcheck\00install.out GOSemSim-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=GOSemSim.buildbin-libdir --install="check:GOSemSim-install.out" --force-multiarch --no-vignettes --timings GOSemSim_2.4.1.tar.gz
StartedAt: 2018-04-12 00:28:47 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 00:32:01 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 193.7 seconds
RetCode: 0
Status:  OK  
CheckDir: GOSemSim.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf GOSemSim.buildbin-libdir GOSemSim.Rcheck && mkdir GOSemSim.buildbin-libdir GOSemSim.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GOSemSim.buildbin-libdir GOSemSim_2.4.1.tar.gz >GOSemSim.Rcheck\00install.out 2>&1 && cp GOSemSim.Rcheck\00install.out GOSemSim-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=GOSemSim.buildbin-libdir --install="check:GOSemSim-install.out" --force-multiarch --no-vignettes --timings GOSemSim_2.4.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/GOSemSim.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GOSemSim/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GOSemSim' version '2.4.1'
* package encoding: UTF-8
* 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 'GOSemSim' 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
* 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 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 ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.6-bioc/meat/GOSemSim.buildbin-libdir/GOSemSim/libs/i386/GOSemSim.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
clusterSim 4.94   0.08    5.01
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
clusterSim 5.53   0.41    5.94
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 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
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/GOSemSim.Rcheck/00check.log'
for details.

Installation output

GOSemSim.Rcheck/00install.out


install for i386

* installing *source* package 'GOSemSim' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -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:82:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (std::size_t i=0; i < ic_.size(); i++ ) {
                             ^
ICmethod.cpp:88:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (std::size_t i=0; i < ic_.size(); i++ ) {
                             ^
ICmethod.cpp:107:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (std::size_t i=0; i < anc_.size(); i++ ) {
                             ^
ICmethod.cpp:118:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( std::size_t i = 0; i < id1_.size(); i++ ) {
                              ^
ICmethod.cpp:125:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for ( std::size_t j = 0; j < id2_.size(); j++ ) {
                                  ^
ICmethod.cpp:152:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for ( std::size_t j = 0; j < id2_.size(); j++ ) {
                                  ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o GOSemSim.dll tmp.def ICmethod.o RcppExports.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/GOSemSim.buildbin-libdir/GOSemSim/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'GOSemSim'
    finding HTML links ... done
    GOSemSim-package                        html  
    GOSemSimDATA-class                      html  
    clusterSim                              html  
    combineScores                           html  
    geneSim                                 html  
    goSim                                   html  
    go_term_table                           html  
    godata                                  html  
    infoContentMethod                       html  
    load_OrgDb                              html  
    mclusterSim                             html  
    mgeneSim                                html  
    mgoSim                                  html  
    termSim                                 html  
    wangMethod_internal                     html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'GOSemSim' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -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:82:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (std::size_t i=0; i < ic_.size(); i++ ) {
                             ^
ICmethod.cpp:88:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (std::size_t i=0; i < ic_.size(); i++ ) {
                             ^
ICmethod.cpp:107:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (std::size_t i=0; i < anc_.size(); i++ ) {
                             ^
ICmethod.cpp:118:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( std::size_t i = 0; i < id1_.size(); i++ ) {
                              ^
ICmethod.cpp:125:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for ( std::size_t j = 0; j < id2_.size(); j++ ) {
                                  ^
ICmethod.cpp:152:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for ( std::size_t j = 0; j < id2_.size(); j++ ) {
                                  ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o GOSemSim.dll tmp.def ICmethod.o RcppExports.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/GOSemSim.buildbin-libdir/GOSemSim/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GOSemSim' as GOSemSim_2.4.1.zip
* DONE (GOSemSim)
In R CMD INSTALL
In R CMD INSTALL

Tests output

GOSemSim.Rcheck/tests_i386/testthat.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(GOSemSim)

GOSemSim v2.4.1  For help: https://guangchuangyu.github.io/GOSemSim

If you use GOSemSim in published research, please cite:
Guangchuang Yu, Fei Li, Yide Qin, Xiaochen Bo, Yibo Wu, Shengqi Wang. GOSemSim: an R package for measuring semantic similarity among GO terms and gene products Bioinformatics 2010, 26(7):976-978
> 
> test_check("GOSemSim")
== testthat results  ===========================================================
OK: 4 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   7.56    0.45    8.01

GOSemSim.Rcheck/tests_x64/testthat.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(GOSemSim)

GOSemSim v2.4.1  For help: https://guangchuangyu.github.io/GOSemSim

If you use GOSemSim in published research, please cite:
Guangchuang Yu, Fei Li, Yide Qin, Xiaochen Bo, Yibo Wu, Shengqi Wang. GOSemSim: an R package for measuring semantic similarity among GO terms and gene products Bioinformatics 2010, 26(7):976-978
> 
> test_check("GOSemSim")
== testthat results  ===========================================================
OK: 4 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   8.53    0.26    8.79

Example timings

GOSemSim.Rcheck/examples_i386/GOSemSim-Ex.timings

nameusersystemelapsed
clusterSim4.940.085.01
geneSim4.280.214.50
goSim3.300.173.47
mclusterSim3.500.223.72
mgeneSim3.710.143.85
mgoSim3.400.143.54

GOSemSim.Rcheck/examples_x64/GOSemSim-Ex.timings

nameusersystemelapsed
clusterSim5.530.415.94
geneSim3.690.193.88
goSim3.070.233.31
mclusterSim3.220.273.49
mgeneSim3.550.153.70
mgoSim3.890.324.21