Xiuwen Zheng
| Snapshot Date: 2023-03-23 14:00:15 -0400 (Thu, 23 Mar 2023) |
| git_url: https://git.bioconductor.org/packages/SAIGEgds |
| git_branch: devel |
| git_last_commit: 20cf813 |
| git_last_commit_date: 2023-03-21 20:47:36 -0400 (Tue, 21 Mar 2023) |
| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-03-24 11:06:21 -0400 (Fri, 24 Mar 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | R Under development (unstable) (2023-03-16 r83996) -- "Unsuffered Consequences" | 4546 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2023-03-15 r83984 ucrt) -- "Unsuffered Consequences" | 4307 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2023-03-16 r83985) -- "Unsuffered Consequences" | 4299 |
| 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 | ||||
|
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 1775/2195 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SAIGEgds 1.99.1 (landing page) Xiuwen Zheng
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: SAIGEgds |
| Version: 1.99.1 |
| Command: rm -rf SAIGEgds.buildbin-libdir && mkdir SAIGEgds.buildbin-libdir && F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL --build --library=SAIGEgds.buildbin-libdir SAIGEgds_1.99.1.tar.gz |
| StartedAt: 2023-03-24 09:24:34 -0400 (Fri, 24 Mar 2023) |
| EndedAt: 2023-03-24 09:26:11 -0400 (Fri, 24 Mar 2023) |
| EllapsedTime: 96.2 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: SAIGEgds_1.99.1.zip |
| PackageFileSize: 2.551 MiB |
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### Running command:
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### rm -rf SAIGEgds.buildbin-libdir && mkdir SAIGEgds.buildbin-libdir && F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL --build --library=SAIGEgds.buildbin-libdir SAIGEgds_1.99.1.tar.gz
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* installing *source* package 'SAIGEgds' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
using C++11
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppParallel/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c SPATest.cpp -o SPATest.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppParallel/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c saige_fitnull.cpp -o saige_fitnull.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppParallel/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c saige_main.cpp -o saige_main.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppParallel/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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 long unsigned int'} [-Wsign-compare]
626 | if (SAIGE_NumThread > n_block) SAIGE_NumThread = n_block;
| ~~~~~~~~~~~~~~~~^~~~~~~~~
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppParallel/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c vec_ext_avx2.cpp -o vec_ext_avx2.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppParallel/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c vec_ext_avx512bw.cpp -o vec_ext_avx512bw.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppParallel/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c vec_ext_def.cpp -o vec_ext_def.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppParallel/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c vectorization.cpp -o vectorization.o
g++ -shared -s -static-libgcc -o SAIGEgds.dll tmp.def 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 -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lRlapack -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LF:/biocbuild/bbs-3.17-bioc/R/library/RcppParallel/lib/x64 -ltbb -ltbbmalloc -lgcc -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.17-bioc/meat/SAIGEgds.buildbin-libdir/00LOCK-SAIGEgds/00new/SAIGEgds/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* MD5 sums
packaged installation of 'SAIGEgds' as SAIGEgds_1.99.1.zip
* DONE (SAIGEgds)