Multiple platform build/check report for BioC 3.23 - BUILD BIN results for motifmatchr on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.4 LTS)	x86_64	4.6.0 RC (2026-04-17 r89917) -- "Because it was There"	4988
kjohnson3	macOS 13.7.7 Ventura	arm64	4.6.0 Patched (2026-04-24 r89963) -- "Because it was There"	4718
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*
BUILD BIN results for motifmatchr on kjohnson3

To the developers/maintainers of the motifmatchr package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/motifmatchr.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
raw results
Summary

Package: motifmatchr
Version: 1.34.0
Command: rm -rf motifmatchr.buildbin-libdir && mkdir motifmatchr.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh motifmatchr_1.34.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R motifmatchr.buildbin-libdir
StartedAt: 2026-04-30 23:06:25 -0400 (Thu, 30 Apr 2026)
EndedAt: 2026-04-30 23:06:50 -0400 (Thu, 30 Apr 2026)
EllapsedTime: 25.4 seconds
RetCode: 0
Status: OK
PackageFile: motifmatchr_1.34.0.tgz
PackageFileSize: 183.6 KiB
Command output

##############################################################################
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###
### Running command:
###
###   rm -rf motifmatchr.buildbin-libdir && mkdir motifmatchr.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh motifmatchr_1.34.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R motifmatchr.buildbin-libdir
###
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##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=motifmatchr.buildbin-libdir motifmatchr_1.34.0.tar.gz'
>>>>>>> 

Warning: SystemRequirements specified C++11: support has been removed
* installing *source* package ‘motifmatchr’ ...
** this is package ‘motifmatchr’ version ‘1.34.0’
** using staged installation
** libs
specified C++11
using C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
using SDK: ‘MacOSX26.2.sdk’
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c r_interface.cpp -o r_interface.o
In file included from r_interface.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:26:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include/RcppCommon.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include/Rcpp/r/headers.h:67:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:39:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/unordered_map:595:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__hash_table:29:
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__memory/unique_ptr.h:78:5: warning: delete called on 'MOODS::scan::Motif' that is abstract but has non-virtual destructor [-Wdelete-abstract-non-virtual-dtor]
   78 |     delete __ptr;
      |     ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__memory/unique_ptr.h:300:7: note: in instantiation of member function 'std::default_delete<MOODS::scan::Motif>::operator()' requested here
  300 |       __deleter_(__tmp);
      |       ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__memory/unique_ptr.h:269:71: note: in instantiation of member function 'std::unique_ptr<MOODS::scan::Motif>::reset' requested here
  269 |   _LIBCPP_HIDE_FROM_ABI _LIBCPP_CONSTEXPR_SINCE_CXX23 ~unique_ptr() { reset(); }
      |                                                                       ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__memory/construct_at.h:66:11: note: in instantiation of member function 'std::unique_ptr<MOODS::scan::Motif>::~unique_ptr' requested here
   66 |   __loc->~_Tp();
      |           ^
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c MOODS/scanner.cpp -o MOODS/scanner.o
In file included from MOODS/scanner.cpp:12:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/memory:947:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__memory/inout_ptr.h:16:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__memory/shared_ptr.h:35:
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__memory/unique_ptr.h:78:5: warning: delete called on 'MOODS::scan::Motif' that is abstract but has non-virtual destructor [-Wdelete-abstract-non-virtual-dtor]
   78 |     delete __ptr;
      |     ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__memory/unique_ptr.h:300:7: note: in instantiation of member function 'std::default_delete<MOODS::scan::Motif>::operator()' requested here
  300 |       __deleter_(__tmp);
      |       ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__memory/unique_ptr.h:269:71: note: in instantiation of member function 'std::unique_ptr<MOODS::scan::Motif>::reset' requested here
  269 |   _LIBCPP_HIDE_FROM_ABI _LIBCPP_CONSTEXPR_SINCE_CXX23 ~unique_ptr() { reset(); }
      |                                                                       ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__memory/construct_at.h:66:11: note: in instantiation of member function 'std::unique_ptr<MOODS::scan::Motif>::~unique_ptr' requested here
   66 |   __loc->~_Tp();
      |           ^
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c MOODS/motif_h.cpp -o MOODS/motif_h.o
MOODS/motif_h.cpp:256:25: warning: '&' within '^' [-Wbitwise-op-parentheses]
  256 |             CODE = MASK & (CODE << SHIFT) ^ alphabet_map[s[ii + i + q - 1]];
      |                    ~~~~~^~~~~~~~~~~~~~~~~ ~
MOODS/motif_h.cpp:256:25: note: place parentheses around the '&' expression to silence this warning
  256 |             CODE = MASK & (CODE << SHIFT) ^ alphabet_map[s[ii + i + q - 1]];
      |                         ^
      |                    (                     )
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c MOODS/motif_0.cpp -o MOODS/motif_0.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c MOODS/moods_tools.cpp -o MOODS/moods_tools.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c MOODS/moods_scan.cpp -o MOODS/moods_scan.o
MOODS/moods_scan.cpp:97:14: warning: unused variable 'done' [-Wunused-variable]
   97 |         bool done = 0;
      |              ^~~~
MOODS/moods_scan.cpp:252:33: warning: '&' within '|' [-Wbitwise-op-parentheses]
  252 |                     CODE = MASK & (CODE << SHIFT) | alphabet_map[seq[i+j+q-1]];
      |                            ~~~~~^~~~~~~~~~~~~~~~~ ~
MOODS/moods_scan.cpp:252:33: note: place parentheses around the '&' expression to silence this warning
  252 |                     CODE = MASK & (CODE << SHIFT) | alphabet_map[seq[i+j+q-1]];
      |                                 ^
      |                            (                     )
In file included from MOODS/moods_scan.cpp:3:
In file included from MOODS/moods.h:5:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/vector:352:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/algorithm:1854:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__algorithm/for_each.h:16:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__ranges/movable_box.h:21:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/optional:1302:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/memory:947:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__memory/inout_ptr.h:16:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__memory/shared_ptr.h:35:
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__memory/unique_ptr.h:78:5: warning: delete called on 'MOODS::scan::Motif' that is abstract but has non-virtual destructor [-Wdelete-abstract-non-virtual-dtor]
   78 |     delete __ptr;
      |     ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__memory/unique_ptr.h:300:7: note: in instantiation of member function 'std::default_delete<MOODS::scan::Motif>::operator()' requested here
  300 |       __deleter_(__tmp);
      |       ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__memory/unique_ptr.h:269:71: note: in instantiation of member function 'std::unique_ptr<MOODS::scan::Motif>::reset' requested here
  269 |   _LIBCPP_HIDE_FROM_ABI _LIBCPP_CONSTEXPR_SINCE_CXX23 ~unique_ptr() { reset(); }
      |                                                                       ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__memory/construct_at.h:66:11: note: in instantiation of member function 'std::unique_ptr<MOODS::scan::Motif>::~unique_ptr' requested here
   66 |   __loc->~_Tp();
      |           ^
3 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c MOODS/moods_parsers.cpp -o MOODS/moods_parsers.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c MOODS/moods_misc.cpp -o MOODS/moods_misc.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c MOODS/match_types.cpp -o MOODS/match_types.o
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 motifmatchr.so ./RcppExports.o ./r_interface.o ./MOODS/scanner.o ./MOODS/motif_h.o ./MOODS/motif_0.o ./MOODS/moods_tools.o ./MOODS/moods_scan.o ./MOODS/moods_parsers.o ./MOODS/moods_misc.o ./MOODS/match_types.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Users/biocbuild/bbs-3.23-bioc/meat/motifmatchr.buildbin-libdir/00LOCK-motifmatchr/00new/motifmatchr/libs
** R
** data
** 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 (motifmatchr)


>>>>>>> 
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR motifmatchr.buildbin-libdir/motifmatchr/libs/motifmatchr.so
>>>>>>> 

>>>>>>> Paths before fix:
motifmatchr.buildbin-libdir/motifmatchr/libs/motifmatchr.so:
	motifmatchr.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:
install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libgcc_s.1.1.dylib" "motifmatchr.buildbin-libdir/motifmatchr/libs/motifmatchr.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libgfortran.5.dylib" "motifmatchr.buildbin-libdir/motifmatchr/libs/motifmatchr.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libquadmath.0.dylib" "motifmatchr.buildbin-libdir/motifmatchr/libs/motifmatchr.so"

>>>>>>> Paths after fix:
motifmatchr.buildbin-libdir/motifmatchr/libs/motifmatchr.so:
	motifmatchr.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)