Back to Mac ARM64 build report for BioC 3.17
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This page was generated on 2023-10-20 09:38:09 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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Package 1530/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
plier 1.70.0  (landing page)
Crispin Miller
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/plier
git_branch: RELEASE_3_17
git_last_commit: 48517ea
git_last_commit_date: 2023-04-25 09:41:29 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

BUILD BIN results for plier on kjohnson2


To the developers/maintainers of the plier package:
- 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: plier
Version: 1.70.0
Command: rm -rf plier.buildbin-libdir && mkdir plier.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh plier_1.70.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R plier.buildbin-libdir
StartedAt: 2023-10-19 15:54:01 -0400 (Thu, 19 Oct 2023)
EndedAt: 2023-10-19 15:54:15 -0400 (Thu, 19 Oct 2023)
EllapsedTime: 14.0 seconds
RetCode: 0
Status:   OK  
PackageFile: plier_1.70.0.tgz
PackageFileSize: 40.27 KiB

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf plier.buildbin-libdir && mkdir plier.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh plier_1.70.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R plier.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=plier.buildbin-libdir plier_1.70.0.tar.gz'
>>>>>>> 

* installing *source* package ‘plier’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c affyplier.cpp -o affyplier.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c plier_impl.cpp -o plier_impl.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c plieralg.cpp -o plieralg.o
plieralg.cpp:905:14: warning: variable 'icount' set but not used [-Wunused-but-set-variable]
        long count, icount;
                    ^
plieralg.cpp:49:12: warning: unused variable 'g_ErrorCode' [-Wunused-variable]
static int g_ErrorCode=NoError;
           ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c rwrapper.cpp -o rwrapper.o
rwrapper.cpp:192:5: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
    delete pm_ptr;  
    ^
          []
rwrapper.cpp:151:23: note: allocated with 'new[]' here
    double **pm_ptr = new double *[*num_exp];
                      ^
rwrapper.cpp:193:5: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
    delete mm_ptr;
    ^
          []
rwrapper.cpp:152:23: note: allocated with 'new[]' here
    double **mm_ptr = new double *[*num_exp];
                      ^
rwrapper.cpp:194:5: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
    delete rpct;
    ^
          []
rwrapper.cpp:159:21: note: allocated with 'new[]' here
    long    *rpct = new long [*num_exp]; /* the API expects a long array that it wants to delete itself (replicate). We have an int array that R owns so we need to create the long one here, but let the API handle the clean up. Which is nice. */
                    ^
3 warnings generated.
clang++ -arch arm64 -std=gnu++17 -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 plier.so affyplier.o plier_impl.o plieralg.o rwrapper.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/plier.buildbin-libdir/00LOCK-plier/00new/plier/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (plier)


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

>>>>>>> Paths before fix:
plier.buildbin-libdir/plier/libs/plier.so:
	plier.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)

>>>>>>> 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" "plier.buildbin-libdir/plier/libs/plier.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgfortran.5.dylib" "plier.buildbin-libdir/plier/libs/plier.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libquadmath.0.dylib" "plier.buildbin-libdir/plier/libs/plier.so"

>>>>>>> Paths after fix:

plier.buildbin-libdir/plier/libs/plier.so:
	plier.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)