Back to Using R 4.1.3 to BUILD/CHECK a small subset of 3.18 packages

This page was generated on 2024-03-08 16:41:48 -0500 (Fri, 08 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 655
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

Package 61/118HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GOSemSim 2.28.1  (landing page)
Guangchuang Yu
Snapshot Date: 2024-03-08 15:25:35 -0500 (Fri, 08 Mar 2024)
git_url: https://git.bioconductor.org/packages/GOSemSim
git_branch: RELEASE_3_18
git_last_commit: 84618af
git_last_commit_date: 2024-01-16 19:48:46 -0500 (Tue, 16 Jan 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  ERROR    ERROR  skipped

INSTALL results for GOSemSim on nebbiolo2


To the developers/maintainers of the GOSemSim package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: GOSemSim
Version: 2.28.1
Command: /home/hpages/bbs-3.18-bioc-R41/R/bin/R CMD INSTALL GOSemSim
StartedAt: 2024-03-08 15:31:23 -0500 (Fri, 08 Mar 2024)
EndedAt: 2024-03-08 15:31:34 -0500 (Fri, 08 Mar 2024)
EllapsedTime: 10.4 seconds
RetCode: 1
Status:   ERROR  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/hpages/bbs-3.18-bioc-R41/R/bin/R CMD INSTALL GOSemSim
###
##############################################################################
##############################################################################


* installing to library ‘/home/hpages/bbs-3.18-bioc-R41/R/site-library’
* installing *source* package ‘GOSemSim’ ...
** using staged installation
** libs
g++ -std=gnu++14 -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG  -I'/home/hpages/bbs-3.18-bioc-R41/R/site-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 of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   82 |     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 unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   88 |     for (std::size_t i=0; i < ic_.size(); i++ ) {
      |                           ~~^~~~~~~~~~~~
ICmethod.cpp:118:29: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
  118 |     for (std::size_t i=0; i < anc_.size(); i++ ) {
      |                           ~~^~~~~~~~~~~~~
ICmethod.cpp:131:30: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
  131 |   for ( std::size_t i = 0; i < id1_.size(); i++ ) {
      |                            ~~^~~~~~~~~~~~~
ICmethod.cpp:138:34: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
  138 |       for ( std::size_t j = 0; j < id2_.size(); j++ ) {
      |                                ~~^~~~~~~~~~~~~
ICmethod.cpp:165:34: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
  165 |       for ( std::size_t j = 0; j < id2_.size(); j++ ) {
      |                                ~~^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG  -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++14 -shared -L/home/hpages/bbs-3.18-bioc-R41/R/lib -L/usr/local/lib -o GOSemSim.so ICmethod.o RcppExports.o -L/home/hpages/bbs-3.18-bioc-R41/R/lib -lR
installing to /home/hpages/bbs-3.18-bioc-R41/R/site-library/00LOCK-GOSemSim/00new/GOSemSim/libs
** R
Error in parse(outFile) : 
  /home/hpages/bbs-3.18-bioc-R41/meat/GOSemSim/R/buildGOmap.R:33:35: unexpected input
32:         return(d)
33:     }) |> do.call('rbind', args = _
                                      ^
ERROR: unable to collate and parse R files for package ‘GOSemSim’
* removing ‘/home/hpages/bbs-3.18-bioc-R41/R/site-library/GOSemSim’