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This page was generated on 2022-01-26 13:06:40 -0500 (Wed, 26 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for GOSemSim on tokay2


To the developers/maintainers of the GOSemSim package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GOSemSim.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 802/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GOSemSim 2.20.0  (landing page)
Guangchuang Yu
Snapshot Date: 2022-01-25 01:55:07 -0500 (Tue, 25 Jan 2022)
git_url: https://git.bioconductor.org/packages/GOSemSim
git_branch: RELEASE_3_14
git_last_commit: fa82442
git_last_commit_date: 2021-10-26 11:53:22 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: GOSemSim
Version: 2.20.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GOSemSim.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings GOSemSim_2.20.0.tar.gz
StartedAt: 2022-01-25 20:41:20 -0500 (Tue, 25 Jan 2022)
EndedAt: 2022-01-25 20:45:04 -0500 (Tue, 25 Jan 2022)
EllapsedTime: 224.3 seconds
RetCode: 0
Status:   OK  
CheckDir: GOSemSim.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GOSemSim.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings GOSemSim_2.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/GOSemSim.Rcheck'
* using R version 4.1.2 (2021-11-01)
* 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 '2.20.0'
* 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 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-3.14-bioc/R/library/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)
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/GOSemSim/libs/x64/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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
goSim       4.81   0.50    5.31
geneSim     4.99   0.24    5.22
clusterSim  4.86   0.23    5.10
mclusterSim 4.89   0.19    5.08
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
clusterSim  5.5   0.36    5.86
* 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-3.14-bioc/meat/GOSemSim.Rcheck/00check.log'
for details.



Installation output

GOSemSim.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/GOSemSim_2.20.0.tar.gz && rm -rf GOSemSim.buildbin-libdir && mkdir GOSemSim.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GOSemSim.buildbin-libdir GOSemSim_2.20.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL GOSemSim_2.20.0.zip && rm GOSemSim_2.20.0.tar.gz GOSemSim_2.20.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  550k  100  550k    0     0  1653k      0 --:--:-- --:--:-- --:--:-- 1656k

install for i386

* installing *source* package 'GOSemSim' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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 of integer expressions of different signedness: 'std::size_t' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
     for (std::size_t i=0; i < ic_.size(); i++ ) {
                           ~~^~~~~~~~~~~~
ICmethod.cpp:88:29: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
     for (std::size_t i=0; i < ic_.size(); i++ ) {
                           ~~^~~~~~~~~~~~
ICmethod.cpp:116:29: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
     for (std::size_t i=0; i < anc_.size(); i++ ) {
                           ~~^~~~~~~~~~~~~
ICmethod.cpp:129:30: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
   for ( std::size_t i = 0; i < id1_.size(); i++ ) {
                            ~~^~~~~~~~~~~~~
ICmethod.cpp:136:34: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
       for ( std::size_t j = 0; j < id2_.size(); j++ ) {
                                ~~^~~~~~~~~~~~~
ICmethod.cpp:163:34: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
       for ( std::size_t j = 0; j < id2_.size(); j++ ) {
                                ~~^~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o GOSemSim.dll tmp.def ICmethod.o RcppExports.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/GOSemSim.buildbin-libdir/00LOCK-GOSemSim/00new/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  
    tcss_cutoff                             html  
    termSim                                 html  
    wangMethod_internal                     html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'GOSemSim' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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 of integer expressions of different signedness: 'std::size_t' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
     for (std::size_t i=0; i < ic_.size(); i++ ) {
                           ~~^~~~~~~~~~~~
ICmethod.cpp:88:29: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
     for (std::size_t i=0; i < ic_.size(); i++ ) {
                           ~~^~~~~~~~~~~~
ICmethod.cpp:116:29: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
     for (std::size_t i=0; i < anc_.size(); i++ ) {
                           ~~^~~~~~~~~~~~~
ICmethod.cpp:129:30: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
   for ( std::size_t i = 0; i < id1_.size(); i++ ) {
                            ~~^~~~~~~~~~~~~
ICmethod.cpp:136:34: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
       for ( std::size_t j = 0; j < id2_.size(); j++ ) {
                                ~~^~~~~~~~~~~~~
ICmethod.cpp:163:34: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
       for ( std::size_t j = 0; j < id2_.size(); j++ ) {
                                ~~^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o GOSemSim.dll tmp.def ICmethod.o RcppExports.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/GOSemSim.buildbin-libdir/GOSemSim/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GOSemSim' as GOSemSim_2.20.0.zip
* DONE (GOSemSim)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'GOSemSim' successfully unpacked and MD5 sums checked

Tests output

GOSemSim.Rcheck/tests_i386/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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 v2.20.0  For help: https://yulab-smu.top/biomedical-knowledge-mining-book/

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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
   9.90    0.59   10.46 

GOSemSim.Rcheck/tests_x64/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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 v2.20.0  For help: https://yulab-smu.top/biomedical-knowledge-mining-book/

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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
  10.53    0.56   11.07 

Example timings

GOSemSim.Rcheck/examples_i386/GOSemSim-Ex.timings

nameusersystemelapsed
clusterSim4.860.235.10
geneSim4.990.245.22
goSim4.810.505.31
mclusterSim4.890.195.08
mgeneSim4.390.174.56
mgoSim4.130.254.37
tcss_cutoff000

GOSemSim.Rcheck/examples_x64/GOSemSim-Ex.timings

nameusersystemelapsed
clusterSim5.500.365.86
geneSim4.400.234.64
goSim3.780.053.83
mclusterSim3.890.194.08
mgeneSim4.410.204.61
mgoSim4.030.224.25
tcss_cutoff000