| Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-01 07:38:50 -0000 (Wed, 01 Mar 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4266 |
| 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 | ||||
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To the developers/maintainers of the SAIGEgds package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SAIGEgds.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1752/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SAIGEgds 1.13.2 (landing page) Xiuwen Zheng
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: SAIGEgds |
| Version: 1.13.2 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL SAIGEgds |
| StartedAt: 2023-02-27 09:41:42 -0000 (Mon, 27 Feb 2023) |
| EndedAt: 2023-02-27 09:42:44 -0000 (Mon, 27 Feb 2023) |
| EllapsedTime: 62.0 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL SAIGEgds
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘SAIGEgds’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppParallel/include' -I/usr/local/include -fPIC -g -O2 -Wall -c SPATest.cpp -o SPATest.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppParallel/include' -I/usr/local/include -fPIC -g -O2 -Wall -c saige_fitnull.cpp -o saige_fitnull.o
saige_fitnull.cpp: In function ‘SEXPREC* saige_get_sparse(SEXP)’:
saige_fitnull.cpp:256:17: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_len_t’ {aka ‘int’} [-Wsign-compare]
256 | if (num > Rf_length(geno))
| ~~~~^~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppParallel/include' -I/usr/local/include -fPIC -g -O2 -Wall -c saige_main.cpp -o saige_main.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppParallel/include' -I/usr/local/include -fPIC -g -O2 -Wall -c vectorization.cpp -o vectorization.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o SAIGEgds.so SPATest.o saige_fitnull.o saige_main.o vectorization.o -lm -llapack -L/home/biocbuild/bbs-3.17-bioc/R/lib -lRblas -lgfortran -lm -lgcc -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-SAIGEgds/00new/SAIGEgds/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 (SAIGEgds)