Back to Mac ARM64 build report for BioC 3.16
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This page was generated on 2023-04-19 11:01:55 -0400 (Wed, 19 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnsonmacOS 13.0 Venturaarm644.2.2 (2022-10-31) -- "Innocent and Trusting" 4256
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 HMMcopy on kjohnson


To the developers/maintainers of the HMMcopy package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 921/2183HostnameOS / ArchINSTALLBUILDBUILD BIN
HMMcopy 1.40.0  (landing page)
Daniel Lai
Snapshot Date: 2023-04-12 13:00:02 -0400 (Wed, 12 Apr 2023)
git_url: https://git.bioconductor.org/packages/HMMcopy
git_branch: RELEASE_3_16
git_last_commit: 47a99fe
git_last_commit_date: 2022-11-01 11:07:29 -0400 (Tue, 01 Nov 2022)
kjohnsonmacOS 13.0 Ventura / arm64  OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: HMMcopy
Version: 1.40.0
Command: rm -rf HMMcopy.buildbin-libdir && mkdir HMMcopy.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh HMMcopy_1.40.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R HMMcopy.buildbin-libdir
StartedAt: 2023-04-18 16:27:50 -0400 (Tue, 18 Apr 2023)
EndedAt: 2023-04-18 16:28:04 -0400 (Tue, 18 Apr 2023)
EllapsedTime: 14.3 seconds
RetCode: 0
Status:   OK  
PackageFile: HMMcopy_1.40.0.tgz
PackageFileSize: 1.891 MiB

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf HMMcopy.buildbin-libdir && mkdir HMMcopy.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh HMMcopy_1.40.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R HMMcopy.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=HMMcopy.buildbin-libdir HMMcopy_1.40.0.tar.gz'
>>>>>>> 

* installing *source* package ‘HMMcopy’ ...
** using staged installation
** libs
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c forward_backward.c -o forward_backward.o
forward_backward.c:28:13: warning: unused variable 'tmp' [-Wunused-variable]
  int K, T, tmp;
            ^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c register.c -o register.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c viterbi.c -o viterbi.o
viterbi.c:21:13: warning: unused variable 'tmp' [-Wunused-variable]
  int K, T, tmp;
            ^
1 warning generated.
clang -arch arm64 -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 HMMcopy.so forward_backward.o register.o viterbi.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: -undefined dynamic_lookup may not work with chained fixups
installing to /Volumes/External/bbs-3.16-bioc-m1/meat/HMMcopy.buildbin-libdir/00LOCK-HMMcopy/00new/HMMcopy/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 (HMMcopy)


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

install_name_tool -change "/opt/R/arm64/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libgcc_s.1.1.dylib" "HMMcopy.buildbin-libdir/HMMcopy/libs/HMMcopy.so"
install_name_tool -change "/opt/R/arm64/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libgfortran.5.dylib" "HMMcopy.buildbin-libdir/HMMcopy/libs/HMMcopy.so"
install_name_tool -change "/opt/R/arm64/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libquadmath.0.dylib" "HMMcopy.buildbin-libdir/HMMcopy/libs/HMMcopy.so"