Guangchuang Yu
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/GOSemSim |
| Branch: RELEASE_3_10 |
| Last Commit: 35fce78 |
| Last Changed Date: 2020-03-18 23:12:50 -0400 (Wed, 18 Mar 2020) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:05:26 -0400 (Wed, 15 Apr 2020).
| Package 724/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| GOSemSim 2.12.1 Guangchuang Yu
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: GOSemSim |
| Version: 2.12.1 |
| Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:GOSemSim.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings GOSemSim_2.12.1.tar.gz |
| StartedAt: 2020-04-15 00:35:05 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 00:37:03 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 117.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GOSemSim.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:GOSemSim.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings GOSemSim_2.12.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/GOSemSim.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘2.12.1’
* 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 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 5.744 0.216 5.973
mclusterSim 5.412 0.076 5.500
mgoSim 5.264 0.068 5.343
geneSim 5.212 0.116 5.342
* 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-3.10-bioc/meat/GOSemSim.Rcheck/00check.log’
for details.
GOSemSim.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL GOSemSim
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘GOSemSim’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/lib -L/usr/local/lib -o GOSemSim.so ICmethod.o RcppExports.o -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.10-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)
GOSemSim.Rcheck/tests/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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 v2.12.1 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 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
9.512 0.332 9.859
GOSemSim.Rcheck/GOSemSim-Ex.timings
| name | user | system | elapsed | |
| clusterSim | 5.744 | 0.216 | 5.973 | |
| geneSim | 5.212 | 0.116 | 5.342 | |
| goSim | 4.844 | 0.108 | 4.971 | |
| mclusterSim | 5.412 | 0.076 | 5.500 | |
| mgeneSim | 4.544 | 0.036 | 4.597 | |
| mgoSim | 5.264 | 0.068 | 5.343 | |