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BioC 3.3: BUILD BIN report for DESeq2 on oaxaca

This page was generated on 2016-10-13 12:58:57 -0700 (Thu, 13 Oct 2016).

Package 295/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DESeq2 1.12.4
Michael Love
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/DESeq2
Last Changed Rev: 119935 / Revision: 122332
Last Changed Date: 2016-08-07 07:08:50 -0700 (Sun, 07 Aug 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: DESeq2
Version: 1.12.4
Command: rm -rf DESeq2.buildbin-libdir && mkdir DESeq2.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh DESeq2_1.12.4.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R DESeq2.buildbin-libdir
StartedAt: 2016-10-13 07:31:50 -0700 (Thu, 13 Oct 2016)
EndedAt: 2016-10-13 07:32:21 -0700 (Thu, 13 Oct 2016)
EllapsedTime: 31.5 seconds
RetCode: 0
Status:  OK 
PackageFile: DESeq2_1.12.4.tgz
PackageFileSize: 1.59 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf DESeq2.buildbin-libdir && mkdir DESeq2.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh DESeq2_1.12.4.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R DESeq2.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=DESeq2.buildbin-libdir DESeq2_1.12.4.tar.gz'
>>>>>>> 

* installing *source* package ‘DESeq2’ ...
** libs
clang++ -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/RcppArmadillo/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c DESeq2.cpp -o DESeq2.o
DESeq2.cpp:59:37: warning: 'i' is deprecated [-Wdeprecated-declarations]
  double ddetb = ( det(b) * trace(b.i(true) * db) );
                                    ^
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppArmadillo/include/armadillo_bits/Base_bones.hpp:21:51: note: 'i' has been explicitly marked deprecated here
  arma_deprecated inline const Op<derived,op_inv> i(const bool ) const;   //!< kept only for compatibility with old user code
                                                  ^
DESeq2.cpp:87:21: warning: 'i' is deprecated [-Wdeprecated-declarations]
  arma::mat b_i = b.i(true);
                    ^
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppArmadillo/include/armadillo_bits/Base_bones.hpp:21:51: note: 'i' has been explicitly marked deprecated here
  arma_deprecated inline const Op<derived,op_inv> i(const bool ) const;   //!< kept only for compatibility with old user code
                                                  ^
DESeq2.cpp:90:37: warning: 'i' is deprecated [-Wdeprecated-declarations]
  double ddetb = ( det(b) * trace(b.i(true) * db) );
                                    ^
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppArmadillo/include/armadillo_bits/Base_bones.hpp:21:51: note: 'i' has been explicitly marked deprecated here
  arma_deprecated inline const Op<derived,op_inv> i(const bool ) const;   //!< kept only for compatibility with old user code
                                                  ^
DESeq2.cpp:348:56: warning: 'i' is deprecated [-Wdeprecated-declarations]
    hat_matrix = sqrt(w) * x * (x.t() * w * x + ridge).i(true) * x.t() * sqrt(w);
                                                       ^
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppArmadillo/include/armadillo_bits/Base_bones.hpp:21:51: note: 'i' has been explicitly marked deprecated here
  arma_deprecated inline const Op<derived,op_inv> i(const bool ) const;   //!< kept only for compatibility with old user code
                                                  ^
DESeq2.cpp:351:37: warning: 'i' is deprecated [-Wdeprecated-declarations]
    sigma = (x.t() * w * x + ridge).i(true) * x.t() * w * x * (x.t() * w * x + ridge).i(true);
                                    ^
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppArmadillo/include/armadillo_bits/Base_bones.hpp:21:51: note: 'i' has been explicitly marked deprecated here
  arma_deprecated inline const Op<derived,op_inv> i(const bool ) const;   //!< kept only for compatibility with old user code
                                                  ^
DESeq2.cpp:351:87: warning: 'i' is deprecated [-Wdeprecated-declarations]
    sigma = (x.t() * w * x + ridge).i(true) * x.t() * w * x * (x.t() * w * x + ridge).i(true);
                                                                                      ^
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppArmadillo/include/armadillo_bits/Base_bones.hpp:21:51: note: 'i' has been explicitly marked deprecated here
  arma_deprecated inline const Op<derived,op_inv> i(const bool ) const;   //!< kept only for compatibility with old user code
                                                  ^
6 warnings generated.
clang++ -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/RcppArmadillo/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -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 DESeq2.so DESeq2.o RcppExports.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.3-bioc/meat/DESeq2.buildbin-libdir/DESeq2/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DESeq2)


>>>>>>> 
>>>>>>> FIXING LINKS FOR DESeq2.buildbin-libdir/DESeq2/libs//DESeq2.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" "DESeq2.buildbin-libdir/DESeq2/libs//DESeq2.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libgfortran.3.dylib" "DESeq2.buildbin-libdir/DESeq2/libs//DESeq2.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" "DESeq2.buildbin-libdir/DESeq2/libs//DESeq2.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libreadline.dylib" "DESeq2.buildbin-libdir/DESeq2/libs//DESeq2.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libquadmath.0.dylib" "DESeq2.buildbin-libdir/DESeq2/libs//DESeq2.so"