Philippe Hupe
| Snapshot Date: 2023-04-12 13:00:02 -0400 (Wed, 12 Apr 2023) |
| git_url: https://git.bioconductor.org/packages/GLAD |
| git_branch: RELEASE_3_16 |
| git_last_commit: 48f2c31 |
| git_last_commit_date: 2022-11-01 10:37:56 -0400 (Tue, 01 Nov 2022) |
| Back to Mac ARM64 build report for BioC 3.16 |
|
This page was generated on 2023-04-19 11:01:55 -0400 (Wed, 19 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson | macOS 13.0 Ventura | arm64 | 4.2.2 (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 | ||||
|
To the developers/maintainers of the GLAD package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 822/2183 | Hostname | OS / Arch | INSTALL | BUILD | BUILD BIN | ||||||||
| GLAD 2.62.0 (landing page) Philippe Hupe
| kjohnson | macOS 13.0 Ventura / arm64 | OK | OK | OK | | |||||||
| Package: GLAD |
| Version: 2.62.0 |
| Command: rm -rf GLAD.buildbin-libdir && mkdir GLAD.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh GLAD_2.62.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R GLAD.buildbin-libdir |
| StartedAt: 2023-04-18 16:11:18 -0400 (Tue, 18 Apr 2023) |
| EndedAt: 2023-04-18 16:12:05 -0400 (Tue, 18 Apr 2023) |
| EllapsedTime: 47.0 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: GLAD_2.62.0.tgz |
| PackageFileSize: 1.451 MiB |
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### Running command:
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### rm -rf GLAD.buildbin-libdir && mkdir GLAD.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh GLAD_2.62.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R GLAD.buildbin-libdir
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=GLAD.buildbin-libdir GLAD_2.62.0.tar.gz'
>>>>>>>
* installing *source* package ‘GLAD’ ...
** using staged installation
checking for pkg-config... /opt/homebrew/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for GSL... yes
GSL has been found on the operating system
operating system: Darwin
configure: creating ./config.status
config.status: creating src/Makevars
src/Makevars file
PKG_LIBS = -L/usr/local/lib -lgsl -lgslcblas
PKG_CPPFLAGS = -DIS_MAC_OS
** libs
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c BkpInfo.cpp -o BkpInfo.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c HaarSeg.cpp -o HaarSeg.o
HaarSeg.cpp:50:12: warning: variable 'lowSquareSum' set but not used [-Wunused-but-set-variable]
double lowSquareSum = 0;
^
1 warning generated.
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c MoveBkp.cpp -o MoveBkp.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c OutliersGNL.cpp -o OutliersGNL.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c chrBreakpoints.cpp -o chrBreakpoints.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c cutree.cpp -o cutree.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c daglad.cpp -o daglad.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c distance.cpp -o distance.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c filterBkp.cpp -o filterBkp.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c findCluster.cpp -o findCluster.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c glad-utils.cpp -o glad-utils.o
glad-utils.cpp:862:27: warning: unused variable 'it_new_end_NormalCluster' [-Wunused-variable]
vector<int>::iterator it_new_end_NormalCluster;
^
1 warning generated.
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c hclust.cpp -o hclust.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c laws.c -o laws.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c loopRemove.cpp -o loopRemove.o
clang++ -arch arm64 -std=gnu++14 -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 GLAD.so BkpInfo.o HaarSeg.o MoveBkp.o OutliersGNL.o chrBreakpoints.o cutree.o daglad.o distance.o filterBkp.o findCluster.o glad-utils.o hclust.o laws.o loopRemove.o -L/usr/local/lib -lgsl -lgslcblas -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/GLAD.buildbin-libdir/00LOCK-GLAD/00new/GLAD/libs
** R
** data
** demo
** 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 (GLAD)
>>>>>>>
>>>>>>> FIXING LINKS FOR GLAD.buildbin-libdir/GLAD/libs/GLAD.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" "GLAD.buildbin-libdir/GLAD/libs/GLAD.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" "GLAD.buildbin-libdir/GLAD/libs/GLAD.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" "GLAD.buildbin-libdir/GLAD/libs/GLAD.so"