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###
### Running command:
###
### rm -rf garfield.buildbin-libdir && mkdir garfield.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh garfield_1.39.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R garfield.buildbin-libdir
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=garfield.buildbin-libdir garfield_1.39.0.tar.gz'
>>>>>>>
* installing *source* package ‘garfield’ ...
** this is package ‘garfield’ version ‘1.39.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
using C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
using SDK: ‘MacOSX26.2.sdk’
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c garfield_init.c -o garfield_init.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c garfield_perm.cpp -o garfield_perm.o
garfield_perm.cpp:144:14: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
144 | int randnap[nperm], rdd, ind=0;
| ^~~~~
garfield_perm.cpp:144:14: note: function parameter 'nperm' with unknown value cannot be used in a constant expression
garfield_perm.cpp:141:45: note: declared here
141 | double ep(vector< vector<double> > vd, long nperm, long nbins, int nap, int optim_mode, double thresh, int minit){
| ^
garfield_perm.cpp:306:74: warning: format specifies type 'char *' but the argument has type 'long' [-Wformat]
306 | Rprintf("\r%s/%s\t\t%s\%\t\t%s annotations/s\t\t Time remaining: %s s",j+1,nannot, 100.0 * (j+1) / nannot, nannot,1.0 * (nannot - (j+1)) / perms_per_sec );
| ~~ ^~~
| %ld
garfield_perm.cpp:306:78: warning: format specifies type 'char *' but the argument has type 'int' [-Wformat]
306 | Rprintf("\r%s/%s\t\t%s\%\t\t%s annotations/s\t\t Time remaining: %s s",j+1,nannot, 100.0 * (j+1) / nannot, nannot,1.0 * (nannot - (j+1)) / perms_per_sec );
| ~~ ^~~~~~
| %d
garfield_perm.cpp:306:86: warning: format specifies type 'char *' but the argument has type 'double' [-Wformat]
306 | Rprintf("\r%s/%s\t\t%s\%\t\t%s annotations/s\t\t Time remaining: %s s",j+1,nannot, 100.0 * (j+1) / nannot, nannot,1.0 * (nannot - (j+1)) / perms_per_sec );
| ~~ ^~~~~~~~~~~~~~~~~~~~~~
| %f
garfield_perm.cpp:306:27: warning: invalid conversion specifier '\x09' [-Wformat-invalid-specifier]
306 | Rprintf("\r%s/%s\t\t%s\%\t\t%s annotations/s\t\t Time remaining: %s s",j+1,nannot, 100.0 * (j+1) / nannot, nannot,1.0 * (nannot - (j+1)) / perms_per_sec );
| ~~^
garfield_perm.cpp:306:110: warning: format specifies type 'char *' but the argument has type 'int' [-Wformat]
306 | Rprintf("\r%s/%s\t\t%s\%\t\t%s annotations/s\t\t Time remaining: %s s",j+1,nannot, 100.0 * (j+1) / nannot, nannot,1.0 * (nannot - (j+1)) / perms_per_sec );
| ~~ ^~~~~~
| %d
garfield_perm.cpp:306:117: warning: format specifies type 'char *' but the argument has type 'double' [-Wformat]
306 | Rprintf("\r%s/%s\t\t%s\%\t\t%s annotations/s\t\t Time remaining: %s s",j+1,nannot, 100.0 * (j+1) / nannot, nannot,1.0 * (nannot - (j+1)) / perms_per_sec );
| ~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| %f
garfield_perm.cpp:356:16: warning: format specifies type 'char *' but the argument has type 'int' [-Wformat]
356 | Rprintf("%s",nannot);
| ~~ ^~~~~~
| %d
8 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c garfield_prep.cpp -o garfield_prep.o
garfield_prep.cpp:225:37: warning: 'iterator<std::output_iterator_tag, void, void, void, void>' is deprecated [-Wdeprecated-declarations]
225 | struct TagsOutputIterator1 : public iterator<output_iterator_tag,void,void,void,void> {
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<std::output_iterator_tag, void, void, void, void>' has been explicitly marked deprecated here
23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__config:737:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
737 | # define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__config:710:49: note: expanded from macro '_LIBCPP_DEPRECATED'
710 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
| ^
garfield_prep.cpp:234:37: warning: 'iterator<std::output_iterator_tag, void, void, void, void>' is deprecated [-Wdeprecated-declarations]
234 | struct TagsOutputIterator2 : public iterator<output_iterator_tag,void,void,void,void> {
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<std::output_iterator_tag, void, void, void, void>' has been explicitly marked deprecated here
23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__config:737:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
737 | # define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__config:710:49: note: expanded from macro '_LIBCPP_DEPRECATED'
710 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
| ^
garfield_prep.cpp:144:28: warning: 'iterator<std::input_iterator_tag, snpid_pval>' is deprecated [-Wdeprecated-declarations]
144 | struct Enumerator : public iterator<input_iterator_tag, typename Iterator::value_type> {
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__type_traits/is_assignable.h:34:114: note: in instantiation of template class 'Enumerator<std::__wrap_iter<snpid_pval *>>' requested here
34 | __is_assignable(__add_lvalue_reference_t<_Tp>, __add_lvalue_reference_t<const _Tp>)> {};
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__utility/pair.h:226:29: note: in instantiation of template class 'std::is_copy_assignable<const Enumerator<std::__wrap_iter<snpid_pval *>> &>' requested here
226 | operator=(__conditional_t<is_copy_assignable<first_type>::value && is_copy_assignable<second_type>::value,
| ^
garfield_prep.cpp:238:9: note: in instantiation of template class 'std::pair<const Enumerator<std::__wrap_iter<snpid_pval *>> &, const std::istream_iterator<snpid_tags> &>' requested here
238 | {(*v)[a.first.i] = a.second->tags(); return *this;}
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<std::input_iterator_tag, snpid_pval>' has been explicitly marked deprecated here
23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__config:737:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
737 | # define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__config:710:49: note: expanded from macro '_LIBCPP_DEPRECATED'
710 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
| ^
garfield_prep.cpp:245:38: warning: 'iterator<std::output_iterator_tag, void, void, void, void>' is deprecated [-Wdeprecated-declarations]
245 | struct TagRefOutputIterator : public iterator<output_iterator_tag,void,void,void,void> {
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<std::output_iterator_tag, void, void, void, void>' has been explicitly marked deprecated here
23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__config:737:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
737 | # define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__config:710:49: note: expanded from macro '_LIBCPP_DEPRECATED'
710 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
| ^
garfield_prep.cpp:262:17: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
262 | annot1[i] = annot1[i] | annot2[i];
| ^~~~~~~~~~~~~~~~~~~~~
| ||
garfield_prep.cpp:262:17: note: cast one or both operands to int to silence this warning
garfield_prep.cpp:273:37: warning: 'iterator<std::output_iterator_tag, void, void, void, void>' is deprecated [-Wdeprecated-declarations]
273 | struct PrintOutputIterator : public iterator<output_iterator_tag,void,void,void,void> {
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__iterator/iterator.h:23:29: note: 'iterator<std::output_iterator_tag, void, void, void, void>' has been explicitly marked deprecated here
23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator {
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__config:737:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
737 | # define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__config:710:49: note: expanded from macro '_LIBCPP_DEPRECATED'
710 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
| ^
6 warnings generated.
clang++ -arch arm64 -std=gnu++20 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o garfield.so garfield_init.o garfield_perm.o garfield_prep.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Users/biocbuild/bbs-3.23-bioc/meat/garfield.buildbin-libdir/00LOCK-garfield/00new/garfield/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 (garfield)
>>>>>>>
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR garfield.buildbin-libdir/garfield/libs/garfield.so
>>>>>>>
>>>>>>> Paths before fix:
garfield.buildbin-libdir/garfield/libs/garfield.so:
garfield.so (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib (compatibility version 4.6.0, current version 4.6.0)
/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 2000.67.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1356.0.0)
>>>>>>> Fix with install_name_tool:
ERROR: R installation problem: File /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/lib/libR.dylib not found!
