Multiple platform build/check report for BioC 3.8 - CHECK report for GOSemSim on malbec1

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:GOSemSim.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings GOSemSim_2.8.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/GOSemSim.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘2.8.0’
* 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 for sufficient/correct file permissions ... 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
* 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
clusterSim  7.280  0.184   7.920
mclusterSim 6.200  0.068   6.440
geneSim     6.036  0.108   6.527
mgoSim      5.916  0.136   6.107
goSim       5.868  0.124   6.149
mgeneSim    5.892  0.092   6.063
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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
  ‘/home/biocbuild/bbs-3.8-bioc/meat/GOSemSim.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL GOSemSim
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘GOSemSim’ ...
** libs
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/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:82:29: 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++ ) {
                                  ^
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o GOSemSim.so ICmethod.o RcppExports.o -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/library/GOSemSim/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GOSemSim)

Tests output


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 v2.8.0  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 
  9.888   0.384  10.399

CHECK report for GOSemSim on malbec1

Summary

Command output

Installation output

Tests output

Example timings

name	user	system	elapsed
clusterSim	7.280	0.184	7.920
geneSim	6.036	0.108	6.527
goSim	5.868	0.124	6.149
mclusterSim	6.200	0.068	6.440
mgeneSim	5.892	0.092	6.063
mgoSim	5.916	0.136	6.107