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INSTALL report for SAIGEgds on tokay1

This page was generated on 2021-05-06 12:33:25 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the SAIGEgds package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1612/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SAIGEgds 1.4.2  (landing page)
Xiuwen Zheng
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/SAIGEgds
Branch: RELEASE_3_12
Last Commit: 631315f
Last Changed Date: 2021-04-30 22:15:37 -0400 (Fri, 30 Apr 2021)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    ERROR  skippedskipped
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: SAIGEgds
Version: 1.4.2
Command: C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/SAIGEgds_1.4.2.tar.gz && rm -rf SAIGEgds.buildbin-libdir && mkdir SAIGEgds.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SAIGEgds.buildbin-libdir SAIGEgds_1.4.2.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL SAIGEgds_1.4.2.zip && rm SAIGEgds_1.4.2.tar.gz SAIGEgds_1.4.2.zip
StartedAt: 2021-05-05 17:05:40 -0400 (Wed, 05 May 2021)
EndedAt: 2021-05-05 17:07:23 -0400 (Wed, 05 May 2021)
EllapsedTime: 102.4 seconds
RetCode: 0
Status:   OK   

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/SAIGEgds_1.4.2.tar.gz && rm -rf SAIGEgds.buildbin-libdir && mkdir SAIGEgds.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SAIGEgds.buildbin-libdir SAIGEgds_1.4.2.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL SAIGEgds_1.4.2.zip && rm SAIGEgds_1.4.2.tar.gz SAIGEgds_1.4.2.zip
###
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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-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"  -DRCPP_PARALLEL_USE_TBB=1   -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-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"  -DRCPP_PARALLEL_USE_TBB=1   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c saige_fitnull.cpp -o saige_fitnull.o
saige_fitnull.cpp: In function 'SEXPREC* saige_get_sparse(SEXP)':
saige_fitnull.cpp:250:10: 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))
      ~~~~^~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"  -DRCPP_PARALLEL_USE_TBB=1   -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-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"  -DRCPP_PARALLEL_USE_TBB=1   -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-3~1.12-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/Users/biocbuild/bbs-3.12-bioc/R/library/RcppParallel/lib/i386 -ltbb -ltbbmalloc -lgcc -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-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  
    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-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"  -DRCPP_PARALLEL_USE_TBB=1   -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-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"  -DRCPP_PARALLEL_USE_TBB=1   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c saige_fitnull.cpp -o saige_fitnull.o
saige_fitnull.cpp: In function 'SEXPREC* saige_get_sparse(SEXP)':
saige_fitnull.cpp:250:10: 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))
      ~~~~^~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"  -DRCPP_PARALLEL_USE_TBB=1   -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-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"  -DRCPP_PARALLEL_USE_TBB=1   -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-3~1.12-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/Users/biocbuild/bbs-3.12-bioc/R/library/RcppParallel/lib/x64 -ltbb -ltbbmalloc -lgcc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/SAIGEgds.buildbin-libdir/SAIGEgds/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SAIGEgds' as SAIGEgds_1.4.2.zip
* DONE (SAIGEgds)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'SAIGEgds' successfully unpacked and MD5 sums checked