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BUILD BIN report for SAIGEgds on merida1

This page was generated on 2021-05-06 12:36:38 -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: rm -rf SAIGEgds.buildbin-libdir && mkdir SAIGEgds.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh SAIGEgds_1.4.2.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R SAIGEgds.buildbin-libdir
StartedAt: 2021-05-06 09:54:15 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 09:55:16 -0400 (Thu, 06 May 2021)
EllapsedTime: 60.5 seconds
RetCode: 0
Status:   OK  
PackageFile: SAIGEgds_1.4.2.tgz
PackageFileSize: 1.998 MiB

Command output

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###
### Running command:
###
###   rm -rf SAIGEgds.buildbin-libdir && mkdir SAIGEgds.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh SAIGEgds_1.4.2.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R SAIGEgds.buildbin-libdir
###
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=SAIGEgds.buildbin-libdir SAIGEgds_1.4.2.tar.gz'
>>>>>>> 

* installing *source* package ‘SAIGEgds’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c SPATest.cpp -o SPATest.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c saige_fitnull.cpp -o saige_fitnull.o
In file included from saige_fitnull.cpp:27:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:34:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c saige_main.cpp -o saige_main.o
In file included from saige_main.cpp:29:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c vectorization.cpp -o vectorization.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o SAIGEgds.so SPATest.o saige_fitnull.o saige_main.o vectorization.o -lm -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.12-bioc/meat/SAIGEgds.buildbin-libdir/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)


>>>>>>> 
>>>>>>> FIXING LINKS FOR SAIGEgds.buildbin-libdir/SAIGEgds/libs/SAIGEgds.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgcc_s.1.dylib" "SAIGEgds.buildbin-libdir/SAIGEgds/libs/SAIGEgds.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgfortran.5.dylib" "SAIGEgds.buildbin-libdir/SAIGEgds/libs/SAIGEgds.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libquadmath.0.dylib" "SAIGEgds.buildbin-libdir/SAIGEgds/libs/SAIGEgds.so"
install_name_tool -change "/usr/local/gfortran/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgfortran.5.dylib" "SAIGEgds.buildbin-libdir/SAIGEgds/libs/SAIGEgds.so"
install_name_tool -change "/usr/local/gfortran/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libquadmath.0.dylib" "SAIGEgds.buildbin-libdir/SAIGEgds/libs/SAIGEgds.so"