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BUILD BIN report for cliqueMS on merida1

This page was generated on 2021-05-06 12:34:33 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the cliqueMS package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 313/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cliqueMS 1.4.0  (landing page)
Oriol Senan Campos
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/cliqueMS
Branch: RELEASE_3_12
Last Commit: 89665c6
Last Changed Date: 2020-10-27 11:51:40 -0400 (Tue, 27 Oct 2020)
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    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: cliqueMS
Version: 1.4.0
Command: rm -rf cliqueMS.buildbin-libdir && mkdir cliqueMS.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh cliqueMS_1.4.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R cliqueMS.buildbin-libdir
StartedAt: 2021-05-06 08:13:11 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 08:15:01 -0400 (Thu, 06 May 2021)
EllapsedTime: 110.4 seconds
RetCode: 0
Status:   OK  
PackageFile: cliqueMS_1.4.0.tgz
PackageFileSize: 1.008 MiB

Command output

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###
### Running command:
###
###   rm -rf cliqueMS.buildbin-libdir && mkdir cliqueMS.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh cliqueMS_1.4.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R cliqueMS.buildbin-libdir
###
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=cliqueMS.buildbin-libdir cliqueMS_1.4.0.tar.gz'
>>>>>>> 

* installing *source* package ‘cliqueMS’ ...
** 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/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
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/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c findAnnotationR.cpp -o findAnnotationR.o
In file included from findAnnotationR.cpp:1:
In file included from ./annotationCliqueMSR.h:16:
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__();
                 ^
In file included from findAnnotationR.cpp:1:
./annotationCliqueMSR.h:739:5: warning: variable 'completeroundscore' is uninitialized when used here [-Wuninitialized]
    completeroundscore += *ritv;
    ^~~~~~~~~~~~~~~~~~
./annotationCliqueMSR.h:733:28: note: initialize the variable 'completeroundscore' to silence this warning
  double completeroundscore,remainderroundscore = 0;
                           ^
                            = 0.0
2 warnings 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/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c findCliquesR.cpp -o findCliquesR.o
In file included from findCliquesR.cpp:2:
In file included from ./networkCliqueMSR.h:7:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include/RcppArmadilloExtensions/sample.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include/RcppArmadilloExtensions/fixprob.h:25:
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/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c findIsotopesR.cpp -o findIsotopesR.o
In file included from findIsotopesR.cpp:1:
In file included from ./isotopesanCliqueMSR.h:4:
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 -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 cliqueMS.so RcppExports.o findAnnotationR.o findCliquesR.o findIsotopesR.o -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/cliqueMS.buildbin-libdir/00LOCK-cliqueMS/00new/cliqueMS/libs
** R
** data
** 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 (cliqueMS)


>>>>>>> 
>>>>>>> FIXING LINKS FOR cliqueMS.buildbin-libdir/cliqueMS/libs/cliqueMS.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" "cliqueMS.buildbin-libdir/cliqueMS/libs/cliqueMS.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgfortran.5.dylib" "cliqueMS.buildbin-libdir/cliqueMS/libs/cliqueMS.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libquadmath.0.dylib" "cliqueMS.buildbin-libdir/cliqueMS/libs/cliqueMS.so"
install_name_tool -change "/usr/local/gfortran/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgfortran.5.dylib" "cliqueMS.buildbin-libdir/cliqueMS/libs/cliqueMS.so"
install_name_tool -change "/usr/local/gfortran/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libquadmath.0.dylib" "cliqueMS.buildbin-libdir/cliqueMS/libs/cliqueMS.so"