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BUILD BIN report for scater on merida2

This page was generated on 2018-10-17 08:56:00 -0400 (Wed, 17 Oct 2018).

Package 1320/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scater 1.8.4
Davis McCarthy
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/scater
Branch: RELEASE_3_7
Last Commit: d560a9a
Last Changed Date: 2018-08-13 06:13:02 -0400 (Mon, 13 Aug 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: scater
Version: 1.8.4
Command: rm -rf scater.buildbin-libdir && mkdir scater.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh scater_1.8.4.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R scater.buildbin-libdir
StartedAt: 2018-10-17 02:06:20 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 02:07:45 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 84.8 seconds
RetCode: 0
Status:  OK 
PackageFile: scater_1.8.4.tgz
PackageFileSize: 9.121 MiB

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf scater.buildbin-libdir && mkdir scater.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh scater_1.8.4.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R scater.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=scater.buildbin-libdir scater_1.8.4.tar.gz'
>>>>>>> 

* installing *source* package ‘scater’ ...
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c calc_exprs.cpp -o calc_exprs.o
In file included from calc_exprs.cpp:1:
In file included from ./scater.h:5:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:106:13: warning: 'H5::Attribute::iterateAttrs' hides overloaded virtual function [-Woverloaded-virtual]
        int iterateAttrs() { return 0; }
            ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:82:21: note: hidden overloaded virtual function 'H5::H5Location::iterateAttrs' declared here: different number of parameters (3 vs 0)
        virtual int iterateAttrs(attr_operator_t user_op, unsigned* idx = NULL, void* op_data = NULL);
                    ^
In file included from calc_exprs.cpp:1:
In file included from ./scater.h:5:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:109:14: warning: 'H5::Attribute::renameAttr' hides overloaded virtual functions [-Woverloaded-virtual]
        void renameAttr() {}
             ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:89:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
        virtual void renameAttr(const char* oldname, const char* newname) const;
                     ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:90:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
        virtual void renameAttr(const H5std_string& oldname, const H5std_string& newname) const;
                     ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c calc_top_features.cpp -o calc_top_features.o
In file included from calc_top_features.cpp:1:
In file included from ./scater.h:5:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:106:13: warning: 'H5::Attribute::iterateAttrs' hides overloaded virtual function [-Woverloaded-virtual]
        int iterateAttrs() { return 0; }
            ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:82:21: note: hidden overloaded virtual function 'H5::H5Location::iterateAttrs' declared here: different number of parameters (3 vs 0)
        virtual int iterateAttrs(attr_operator_t user_op, unsigned* idx = NULL, void* op_data = NULL);
                    ^
In file included from calc_top_features.cpp:1:
In file included from ./scater.h:5:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:109:14: warning: 'H5::Attribute::renameAttr' hides overloaded virtual functions [-Woverloaded-virtual]
        void renameAttr() {}
             ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:89:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
        virtual void renameAttr(const char* oldname, const char* newname) const;
                     ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:90:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
        virtual void renameAttr(const H5std_string& oldname, const H5std_string& newname) const;
                     ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c init.cpp -o init.o
In file included from init.cpp:1:
In file included from ./scater.h:5:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:106:13: warning: 'H5::Attribute::iterateAttrs' hides overloaded virtual function [-Woverloaded-virtual]
        int iterateAttrs() { return 0; }
            ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:82:21: note: hidden overloaded virtual function 'H5::H5Location::iterateAttrs' declared here: different number of parameters (3 vs 0)
        virtual int iterateAttrs(attr_operator_t user_op, unsigned* idx = NULL, void* op_data = NULL);
                    ^
In file included from init.cpp:1:
In file included from ./scater.h:5:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:109:14: warning: 'H5::Attribute::renameAttr' hides overloaded virtual functions [-Woverloaded-virtual]
        void renameAttr() {}
             ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:89:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
        virtual void renameAttr(const char* oldname, const char* newname) const;
                     ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:90:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
        virtual void renameAttr(const H5std_string& oldname, const H5std_string& newname) const;
                     ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c matrix_stats.cpp -o matrix_stats.o
In file included from matrix_stats.cpp:1:
In file included from ./scater.h:5:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:106:13: warning: 'H5::Attribute::iterateAttrs' hides overloaded virtual function [-Woverloaded-virtual]
        int iterateAttrs() { return 0; }
            ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:82:21: note: hidden overloaded virtual function 'H5::H5Location::iterateAttrs' declared here: different number of parameters (3 vs 0)
        virtual int iterateAttrs(attr_operator_t user_op, unsigned* idx = NULL, void* op_data = NULL);
                    ^
In file included from matrix_stats.cpp:1:
In file included from ./scater.h:5:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:109:14: warning: 'H5::Attribute::renameAttr' hides overloaded virtual functions [-Woverloaded-virtual]
        void renameAttr() {}
             ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:89:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
        virtual void renameAttr(const char* oldname, const char* newname) const;
                     ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:90:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
        virtual void renameAttr(const H5std_string& oldname, const H5std_string& newname) const;
                     ^
2 warnings generated.
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 scater.so calc_exprs.o calc_top_features.o init.o matrix_stats.o /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/lib/libbeachmat.a /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/lib/libhdf5_cpp.a /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/lib/libhdf5.a /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/lib/libsz.a -lz -pthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
clang-4.0: warning: argument unused during compilation: '-pthread' [-Wunused-command-line-argument]
installing to /Users/biocbuild/bbs-3.7-bioc/meat/scater.buildbin-libdir/scater/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘mutate’ in package ‘scater’
Creating a new generic function for ‘filter’ in package ‘scater’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (scater)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgcc_s.1.dylib" "scater.buildbin-libdir/scater/libs//scater.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgfortran.3.dylib" "scater.buildbin-libdir/scater/libs//scater.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libreadline.5.2.dylib" "scater.buildbin-libdir/scater/libs//scater.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libreadline.dylib" "scater.buildbin-libdir/scater/libs//scater.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libquadmath.0.dylib" "scater.buildbin-libdir/scater/libs//scater.so"