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CHECK report for GOSemSim on malbec2

This page was generated on 2020-10-17 11:54:53 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE GOSemSim PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 754/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GOSemSim 2.14.2
Guangchuang Yu
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/GOSemSim
Branch: RELEASE_3_11
Last Commit: 15b32bb
Last Changed Date: 2020-09-04 06:14:40 -0400 (Fri, 04 Sep 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GOSemSim
Version: 2.14.2
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:GOSemSim.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings GOSemSim_2.14.2.tar.gz
StartedAt: 2020-10-17 01:53:37 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 01:55:38 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 120.6 seconds
RetCode: 0
Status:  OK 
CheckDir: GOSemSim.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:GOSemSim.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings GOSemSim_2.14.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/GOSemSim.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘2.14.2’
* 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 (user + system) or elapsed time > 5s
             user system elapsed
mclusterSim 5.996  0.116   6.113
mgoSim      5.286  0.113   5.398
geneSim     4.965  0.108   5.072
* 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-3.11-bioc/meat/GOSemSim.Rcheck/00check.log’
for details.



Installation output

GOSemSim.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL GOSemSim
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘GOSemSim’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-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:120:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( std::size_t i = 0; i < id1_.size(); i++ ) {
                            ~~^~~~~~~~~~~~~
ICmethod.cpp:127:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for ( std::size_t j = 0; j < id2_.size(); j++ ) {
                                ~~^~~~~~~~~~~~~
ICmethod.cpp:154:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for ( std::size_t j = 0; j < id2_.size(); j++ ) {
                                ~~^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.11-bioc/R/lib -L/usr/local/lib -o GOSemSim.so ICmethod.o RcppExports.o -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.11-bioc/R/library/00LOCK-GOSemSim/00new/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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GOSemSim)

Tests output

GOSemSim.Rcheck/tests/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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 v2.14.2  For help: https://guangchuangyu.github.io/GOSemSim

If you use GOSemSim in published research, please cite:
- Guangchuang Yu. Gene Ontology Semantic Similarity Analysis Using GOSemSim. In: Kidder B. (eds) Stem Cell Transcriptional Networks. Methods in Molecular Biology, 2020, 2117:207-215. Humana, New York, NY. doi:10.1007/978-1-0716-0301-7_11
- 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. doi:10.1093/bioinformatics/btq064


> 
> test_check("GOSemSim")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 4 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 11.627   0.284  11.962 

Example timings

GOSemSim.Rcheck/GOSemSim-Ex.timings

nameusersystemelapsed
clusterSim4.5690.1604.729
geneSim4.9650.1085.072
goSim3.9360.0563.993
mclusterSim5.9960.1166.113
mgeneSim4.7450.0574.804
mgoSim5.2860.1135.398