Xiuwen Zheng
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/SAIGEgds |
| git_branch: RELEASE_3_13 |
| git_last_commit: bbfe3bd |
| git_last_commit_date: 2021-05-19 12:46:49 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:21 -0400 (Fri, 15 Oct 2021).
|
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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1664/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SAIGEgds 1.6.0 (landing page) Xiuwen Zheng
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | ERROR | skipped | skipped | |||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: SAIGEgds |
| Version: 1.6.0 |
| Command: C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/SAIGEgds_1.6.0.tar.gz && rm -rf SAIGEgds.buildbin-libdir && mkdir SAIGEgds.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SAIGEgds.buildbin-libdir SAIGEgds_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL SAIGEgds_1.6.0.zip && rm SAIGEgds_1.6.0.tar.gz SAIGEgds_1.6.0.zip |
| StartedAt: 2021-10-14 07:49:08 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 07:50:54 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 106.6 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/SAIGEgds_1.6.0.tar.gz && rm -rf SAIGEgds.buildbin-libdir && mkdir SAIGEgds.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SAIGEgds.buildbin-libdir SAIGEgds_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL SAIGEgds_1.6.0.zip && rm SAIGEgds_1.6.0.tar.gz SAIGEgds_1.6.0.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
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install for i386
* installing *source* package 'SAIGEgds' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include' -I"c:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=0 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c SPATest.cpp -o SPATest.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include' -I"c:/extsoft/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]
const int th_idx = 0; \
^~~~~~
saige_fitnull.cpp:71:13: note: in definition of macro 'PARALLEL_FOR'
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 unsigned int'} and 'R_len_t' {aka 'int'} [-Wsign-compare]
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]
const int th_idx = 0; \
^~~~~~
saige_fitnull.cpp:71:13: note: in definition of macro 'PARALLEL_FOR'
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]
const int th_idx = 0; \
^~~~~~
saige_fitnull.cpp:75:13: note: in definition of macro 'PARALLEL_RANGE'
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]
const int th_idx = 0; \
^~~~~~
saige_fitnull.cpp:75:13: note: in definition of macro 'PARALLEL_RANGE'
const int th_idx = 0; \
^~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include' -I"c:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=0 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c saige_main.cpp -o saige_main.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include' -I"c:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=0 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c vectorization.cpp -o vectorization.o
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o SAIGEgds.dll tmp.def SPATest.o saige_fitnull.o saige_main.o vectorization.o -lm -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/lib/i386 -ltbb -ltbbmalloc -lgcc -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/SAIGEgds.buildbin-libdir/00LOCK-SAIGEgds/00new/SAIGEgds/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'SAIGEgds'
finding HTML links ... done
SAIGEgds-package html
glmmHeritability html
pACAT html
seqAssocGLMM_SPA html
finding level-2 HTML links ... done
seqAssocGLMM_spaACAT_O html
seqAssocGLMM_spaACAT_V html
seqAssocGLMM_spaBurden html
seqFitNullGLMM_SPA html
seqGLMM_GxG_spa html
seqSAIGE_LoadPval html
** 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
install for x64
* installing *source* package 'SAIGEgds' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=0 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c SPATest.cpp -o SPATest.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include' -I"C:/extsoft/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]
const int th_idx = 0; \
^~~~~~
saige_fitnull.cpp:71:13: note: in definition of macro 'PARALLEL_FOR'
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]
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]
const int th_idx = 0; \
^~~~~~
saige_fitnull.cpp:71:13: note: in definition of macro 'PARALLEL_FOR'
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]
const int th_idx = 0; \
^~~~~~
saige_fitnull.cpp:75:13: note: in definition of macro 'PARALLEL_RANGE'
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]
const int th_idx = 0; \
^~~~~~
saige_fitnull.cpp:75:13: note: in definition of macro 'PARALLEL_RANGE'
const int th_idx = 0; \
^~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=0 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c saige_main.cpp -o saige_main.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=0 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c vectorization.cpp -o vectorization.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o SAIGEgds.dll tmp.def SPATest.o saige_fitnull.o saige_main.o vectorization.o -lm -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/lib/x64 -ltbb -ltbbmalloc -lgcc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/SAIGEgds.buildbin-libdir/SAIGEgds/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SAIGEgds' as SAIGEgds_1.6.0.zip
* DONE (SAIGEgds)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'SAIGEgds' successfully unpacked and MD5 sums checked