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BUILD BIN report for dada2 on merida2

This page was generated on 2019-04-09 13:32:49 -0400 (Tue, 09 Apr 2019).

Package 378/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dada2 1.11.3
Benjamin Callahan
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/dada2
Branch: master
Last Commit: 57f82f4
Last Changed Date: 2019-03-25 16:31:01 -0400 (Mon, 25 Mar 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK [ OK ]

Summary

Package: dada2
Version: 1.11.3
Command: rm -rf dada2.buildbin-libdir && mkdir dada2.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh dada2_1.11.3.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R dada2.buildbin-libdir
StartedAt: 2019-04-09 05:06:54 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 05:09:28 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 153.8 seconds
RetCode: 0
Status:  OK 
PackageFile: dada2_1.11.3.tgz
PackageFileSize: 2.436 MiB

Command output

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###
### Running command:
###
###   rm -rf dada2.buildbin-libdir && mkdir dada2.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh dada2_1.11.3.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R dada2.buildbin-libdir
###
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=dada2.buildbin-libdir dada2_1.11.3.tar.gz'
>>>>>>> 

* installing *source* package ‘dada2’ ...
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppParallel/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 ./../inst/include/dada2.h:7:
./../inst/include/dada2_RcppExports.h:14:14: warning: unused function 'validateSignature' [-Wunused-function]
        void validateSignature(const char* sig) {
             ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppParallel/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c Rmain.cpp -o Rmain.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppParallel/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c chimera.cpp -o chimera.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppParallel/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c cluster.cpp -o cluster.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppParallel/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c containers.cpp -o containers.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppParallel/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c error.cpp -o error.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppParallel/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c evaluate.cpp -o evaluate.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppParallel/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c filter.cpp -o filter.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppParallel/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c kmers.cpp -o kmers.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppParallel/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c misc.cpp -o misc.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppParallel/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c nwalign_endsfree.cpp -o nwalign_endsfree.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppParallel/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c nwalign_vectorized.cpp -o nwalign_vectorized.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppParallel/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c pval.cpp -o pval.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppParallel/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c taxonomy.cpp -o taxonomy.o
clang++ -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 dada2.so RcppExports.o Rmain.o chimera.o cluster.o containers.o error.o evaluate.o filter.o kmers.o misc.o nwalign_endsfree.o nwalign_vectorized.o pval.o taxonomy.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.9-bioc/meat/dada2.buildbin-libdir/dada2/libs
** R
** data
*** moving datasets to lazyload DB
** 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
* DONE (dada2)


>>>>>>> 
>>>>>>> FIXING LINKS FOR dada2.buildbin-libdir/dada2/libs//dada2.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgcc_s.1.dylib" "dada2.buildbin-libdir/dada2/libs//dada2.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgfortran.3.dylib" "dada2.buildbin-libdir/dada2/libs//dada2.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.5.2.dylib" "dada2.buildbin-libdir/dada2/libs//dada2.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.dylib" "dada2.buildbin-libdir/dada2/libs//dada2.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libquadmath.0.dylib" "dada2.buildbin-libdir/dada2/libs//dada2.so"