Tomoyuki Furuta
| Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/GBScleanR |
| git_branch: RELEASE_3_21 |
| git_last_commit: 8528fbe |
| git_last_commit_date: 2025-04-15 12:44:00 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-10-16 11:38 -0400 (Thu, 16 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 |
| 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 785/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GBScleanR 2.2.0 (landing page) Tomoyuki Furuta
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
|
To the developers/maintainers of the GBScleanR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GBScleanR.git to reflect on this report. See Troubleshooting Build Report for more information. - 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. |
| Package: GBScleanR |
| Version: 2.2.0 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL GBScleanR |
| StartedAt: 2025-10-15 15:31:12 -0400 (Wed, 15 Oct 2025) |
| EndedAt: 2025-10-15 15:31:58 -0400 (Wed, 15 Oct 2025) |
| EllapsedTime: 46.5 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL GBScleanR
###
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘GBScleanR’ ...
** this is package ‘GBScleanR’ version ‘2.2.0’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c gbsrCalcProb.cpp -o gbsrCalcProb.o
gbsrCalcProb.cpp: In function ‘std::vector<double> calcGenoprob(const double&, const double&, const double&, const double&, const double&, const bool&, const int&)’:
gbsrCalcProb.cpp:25:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
25 | for(int g = 0; g < prob.size(); ++g){
| ~~^~~~~~~~~~~~~
gbsrCalcProb.cpp:37:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
37 | for(int g = 0; g < prob.size(); ++g){
| ~~^~~~~~~~~~~~~
gbsrCalcProb.cpp: In function ‘void calcMissmap(std::vector<double>&, const double&, const double&, const bool&, const int&)’:
gbsrCalcProb.cpp:72:21: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
72 | } else if(g == ploidy){
| ~~^~~~~~~~~
gbsrCalcProb.cpp:74:22: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
74 | if(h == ploidy){
| ~~^~~~~~~~~
gbsrCalcProb.cpp:87:29: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
87 | } else if(h == ploidy){
| ~~^~~~~~~~~
gbsrCalcProb.cpp:127:29: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
127 | } else if(g == ploidy){
| ~~^~~~~~~~~
gbsrCalcProb.cpp: In function ‘void offsetProb(std::vector<double>&, const bool&, const int&)’:
gbsrCalcProb.cpp:170:28: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
170 | if(g == 0 && g == ploidy){
| ~~^~~~~~~~~
gbsrCalcProb.cpp:185:32: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
185 | if(g == 0 && g == ploidy){
| ~~^~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c gbsrFB.cpp -o gbsrFB.o
gbsrFB.cpp: In member function ‘virtual void ParFB::operator()(size_t, size_t)’:
gbsrFB.cpp:109:17: warning: ‘hap_offset_ij’ may be used uninitialized [-Wmaybe-uninitialized]
109 | int hap_offset_ij;
| ^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c gbsrIPO.cpp -o gbsrIPO.o
gbsrIPO.cpp: In member function ‘virtual void ParGenoProb::operator()(size_t, size_t)’:
gbsrIPO.cpp:57:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
57 | for(int g = 0; g < prob.size(); ++g){
| ~~^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c gbsrStats.cpp -o gbsrStats.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c gbsrViterbi.cpp -o gbsrViterbi.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c gbsrutil.cpp -o gbsrutil.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o GBScleanR.so RcppExports.o gbsrCalcProb.o gbsrFB.o gbsrIPO.o gbsrStats.o gbsrViterbi.o gbsrutil.o -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-GBScleanR/00new/GBScleanR/libs
** R
** 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 (GBScleanR)