Xiuwen Zheng
| Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022) |
| git_url: https://git.bioconductor.org/packages/SAIGEgds |
| git_branch: RELEASE_3_15 |
| git_last_commit: 9c55c6f |
| git_last_commit_date: 2022-04-26 11:59:57 -0400 (Tue, 26 Apr 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-10-19 13:22:13 -0400 (Wed, 19 Oct 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4386 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" | 4138 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4205 |
| 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 1735/2140 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SAIGEgds 1.10.0 (landing page) Xiuwen Zheng
| nebbiolo1 | Linux (Ubuntu 20.04.5 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: 1.10.0 |
| Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL SAIGEgds |
| StartedAt: 2022-10-18 15:52:58 -0400 (Tue, 18 Oct 2022) |
| EndedAt: 2022-10-18 15:53:59 -0400 (Tue, 18 Oct 2022) |
| EllapsedTime: 61.0 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL SAIGEgds
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* installing to library 'F:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'SAIGEgds' ...
** using staged installation
** libs
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/RcppParallel/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=0 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c SPATest.cpp -o SPATest.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/RcppParallel/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=0 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c saige_fitnull.cpp -o saige_fitnull.o
saige_fitnull.cpp: In function 'SEXPREC* saige_store_2b_geno(SEXP, SEXP, SEXP, SEXP, SEXP)':
saige_fitnull.cpp:71:13: warning: unused variable 'th_idx' [-Wunused-variable]
71 | const int th_idx = 0; \
| ^~~~~~
saige_fitnull.cpp:71:13: note: in definition of macro 'PARALLEL_FOR'
71 | const int th_idx = 0; \
| ^~~~~~
saige_fitnull.cpp: In function 'SEXPREC* saige_get_sparse(SEXP)':
saige_fitnull.cpp:249:10: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const long long unsigned int'} and 'R_len_t' {aka 'int'} [-Wsign-compare]
249 | if (num > Rf_length(geno))
| ~~~~^~~~~~~~~~~~~~~~~
saige_fitnull.cpp: In function 'SEXPREC* saige_store_sp_geno(SEXP, SEXP, SEXP, SEXP, SEXP)':
saige_fitnull.cpp:71:13: warning: unused variable 'th_idx' [-Wunused-variable]
71 | const int th_idx = 0; \
| ^~~~~~
saige_fitnull.cpp:71:13: note: in definition of macro 'PARALLEL_FOR'
71 | const int th_idx = 0; \
| ^~~~~~
saige_fitnull.cpp: In function 'void get_crossprod_b_grm(const dcolvec&, arma::dvec&)':
saige_fitnull.cpp:75:13: warning: unused variable 'th_idx' [-Wunused-variable]
75 | const int th_idx = 0; \
| ^~~~~~
saige_fitnull.cpp:75:13: note: in definition of macro 'PARALLEL_RANGE'
75 | const int th_idx = 0; \
| ^~~~~~
saige_fitnull.cpp: In function 'void get_diag_sigma(const dvec&, const dvec&, arma::dvec&)':
saige_fitnull.cpp:75:13: warning: unused variable 'th_idx' [-Wunused-variable]
75 | const int th_idx = 0; \
| ^~~~~~
saige_fitnull.cpp:75:13: note: in definition of macro 'PARALLEL_RANGE'
75 | const int th_idx = 0; \
| ^~~~~~
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/RcppParallel/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=0 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c saige_main.cpp -o saige_main.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/RcppParallel/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=0 -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 vectorization.o -lm -LF:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lRlapack -LF:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LF:/biocbuild/bbs-3.15-bioc/R/library/RcppParallel/lib/x64 -ltbb -ltbbmalloc -lgcc -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.15-bioc/R/library/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
* DONE (SAIGEgds)