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BioC 3.4: BUILD BIN report for dada2 on morelia

This page was generated on 2016-09-21 03:55:38 -0700 (Wed, 21 Sep 2016).

Package 285/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dada2 1.1.5
Benjamin Callahan
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/dada2
Last Changed Rev: 119878 / Revision: 121152
Last Changed Date: 2016-08-03 17:28:37 -0700 (Wed, 03 Aug 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: dada2
Version: 1.1.5
Command: rm -rf dada2.buildbin-libdir && mkdir dada2.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh dada2_1.1.5.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R dada2.buildbin-libdir
StartedAt: 2016-09-20 14:48:23 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 14:49:18 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 54.6 seconds
RetCode: 0
Status:  OK 
PackageFile: dada2_1.1.5.tgz
PackageFileSize: 1.421 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf dada2.buildbin-libdir && mkdir dada2.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh dada2_1.1.5.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R dada2.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=dada2.buildbin-libdir dada2_1.1.5.tar.gz'
>>>>>>> 

* installing *source* package ‘dada2’ ...
** libs
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppParallel/include"   -fPIC  -Wall -mtune=core2 -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=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppParallel/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c Rmain.cpp -o Rmain.o
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppParallel/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c chimera.cpp -o chimera.o
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppParallel/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c cluster.cpp -o cluster.o
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppParallel/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c error.cpp -o error.o
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppParallel/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c evaluate.cpp -o evaluate.o
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppParallel/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c filter.cpp -o filter.o
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppParallel/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c misc.cpp -o misc.o
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppParallel/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c nwalign_endsfree.cpp -o nwalign_endsfree.o
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppParallel/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c nwalign_vectorized.cpp -o nwalign_vectorized.o
nwalign_vectorized.cpp:79:43: warning: unused variable 'ptr_index' [-Wunused-variable]
  int16_t *ptr_left, *ptr_diag, *ptr_up, *ptr_index, *ptr_d, *ptr_p;
                                          ^
1 warning generated.
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppParallel/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c pval.cpp -o pval.o
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppParallel/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c strmap.cpp -o strmap.o
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppParallel/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c taxonomy.cpp -o taxonomy.o
clang++ -std=c++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 error.o evaluate.o filter.o misc.o nwalign_endsfree.o nwalign_vectorized.o pval.o strmap.o taxonomy.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.4-bioc/meat/dada2.buildbin-libdir/dada2/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing 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/3.3/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/3.3/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/3.3/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/3.3/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/3.3/Resources/lib/libquadmath.0.dylib" "dada2.buildbin-libdir/dada2/libs//dada2.so"