Xiuwen Zheng
| Snapshot Date: 2024-04-15 14:05:01 -0400 (Mon, 15 Apr 2024) |
| git_url: https://git.bioconductor.org/packages/SAIGEgds |
| git_branch: RELEASE_3_18 |
| git_last_commit: 511d2b8 |
| git_last_commit_date: 2024-01-27 01:17:00 -0400 (Sat, 27 Jan 2024) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-04-17 11:36:20 -0400 (Wed, 17 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4676 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4414 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4437 |
| 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 1835/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SAIGEgds 2.2.1 (landing page) Xiuwen Zheng
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the SAIGEgds package: - 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 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: SAIGEgds |
| Version: 2.2.1 |
| Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL SAIGEgds |
| StartedAt: 2024-04-15 15:11:24 -0400 (Mon, 15 Apr 2024) |
| EndedAt: 2024-04-15 15:12:32 -0400 (Mon, 15 Apr 2024) |
| EllapsedTime: 67.8 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL SAIGEgds
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* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘SAIGEgds’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-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-3.18-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c saige_fitnull.cpp -o saige_fitnull.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-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-3.18-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c saige_misc.cpp -o saige_misc.o
saige_misc.cpp: In function ‘SEXPREC* saige_grm_sp_calc_ijx(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
saige_misc.cpp:626:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
626 | if (SAIGE_NumThread > n_block) SAIGE_NumThread = n_block;
| ~~~~~~~~~~~~~~~~^~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c vec_ext_avx2.cpp -o vec_ext_avx2.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c vec_ext_avx512bw.cpp -o vec_ext_avx512bw.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c vec_ext_def.cpp -o vec_ext_def.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-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-3.18-bioc/R/lib -L/usr/local/lib -o SAIGEgds.so SPATest.o saige_fitnull.o saige_main.o saige_misc.o vec_ext_avx2.o vec_ext_avx512bw.o vec_ext_def.o vectorization.o -lm -llapack -L/home/biocbuild/bbs-3.18-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -lgcc -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.18-bioc/R/site-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)