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### Running command:
###
### rm -rf BiocSingular.buildbin-libdir && mkdir BiocSingular.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh BiocSingular_1.16.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R BiocSingular.buildbin-libdir
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=BiocSingular.buildbin-libdir BiocSingular_1.16.0.tar.gz'
>>>>>>>
* installing *source* package ‘BiocSingular’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c compute_scale.cpp -o compute_scale.o
In file included from compute_scale.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/beachmat3/beachmat.h:24:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/beachmat3/read_lin_block.h:11:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:218:43: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual]
virtual sparse_index<const int*, int> get_row(size_t r, int* work_x, int* work_i, size_t first, size_t last) = 0;
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5)
virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0;
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5)
virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0;
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:236:43: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual]
virtual sparse_index<const int*, int> get_col(size_t c, int* work_x, int* work_i, size_t first, size_t last) = 0;
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5)
virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0;
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5)
virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0;
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:254:46: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual]
virtual sparse_index<const double*, int> get_row(size_t r, double* work_x, int* work_i, size_t first, size_t last) = 0;
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5)
virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0;
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5)
virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0;
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:272:46: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual]
virtual sparse_index<const double*, int> get_col(size_t c, double* work_x, int* work_i, size_t first, size_t last) = 0;
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5)
virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0;
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5)
virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0;
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:287:35: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual]
sparse_index<const int*, int> get_col(size_t c, int* work_x, int* work_i) {
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3)
virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0;
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3)
virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0;
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:304:35: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual]
sparse_index<const int*, int> get_row(size_t r, int* work_x, int* work_i) {
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3)
virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0;
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3)
virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0;
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:321:38: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual]
sparse_index<const double*, int> get_col(size_t c, double* work_x, int* work_i) {
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3)
virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0;
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3)
virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0;
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:338:38: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual]
sparse_index<const double*, int> get_row(size_t r, double* work_x, int* work_i) {
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3)
virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0;
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3)
virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0;
^
8 warnings generated.
clang++ -arch arm64 -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/opt/R/arm64/lib -o BiocSingular.so RcppExports.o compute_scale.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/BiocSingular.buildbin-libdir/00LOCK-BiocSingular/00new/BiocSingular/libs
** R
** 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 (BiocSingular)
>>>>>>>
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR BiocSingular.buildbin-libdir/BiocSingular/libs/BiocSingular.so
>>>>>>>
>>>>>>> Paths before fix:
BiocSingular.buildbin-libdir/BiocSingular/libs/BiocSingular.so:
BiocSingular.so (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1)
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
/usr/lib/libobjc.A.dylib (compatibility version 1.0.0, current version 228.0.0)
>>>>>>> Fix with install_name_tool:
install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgcc_s.1.1.dylib" "BiocSingular.buildbin-libdir/BiocSingular/libs/BiocSingular.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgfortran.5.dylib" "BiocSingular.buildbin-libdir/BiocSingular/libs/BiocSingular.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libquadmath.0.dylib" "BiocSingular.buildbin-libdir/BiocSingular/libs/BiocSingular.so"
>>>>>>> Paths after fix:
BiocSingular.buildbin-libdir/BiocSingular/libs/BiocSingular.so:
BiocSingular.so (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1)
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
/usr/lib/libobjc.A.dylib (compatibility version 1.0.0, current version 228.0.0)
