| Back to Multiple platform build/check report for BioC 3.16 |
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This page was generated on 2022-07-11 11:06:47 -0400 (Mon, 11 Jul 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4148 |
| lconway | macOS 12.2.1 Monterey | x86_64 | 4.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" | 4168 |
| kjohnson | macOS 12.4 Monterey | arm64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 3545 |
| 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: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GLAD.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 802/2130 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GLAD 2.61.0 (landing page) Philippe Hupe
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
| lconway | macOS 12.2.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
| kjohnson | macOS 12.4 Monterey / arm64 | ERROR | NA | NA | NA | |||||||||
| Package: GLAD |
| Version: 2.61.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GLAD |
| StartedAt: 2022-07-10 15:09:53 -0400 (Sun, 10 Jul 2022) |
| EndedAt: 2022-07-10 15:10:19 -0400 (Sun, 10 Jul 2022) |
| EllapsedTime: 26.2 seconds |
| RetCode: 1 |
| Status: ERROR |
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GLAD
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library’
* 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: ignoring file /usr/local/lib/libgslcblas.a, building for macOS-arm64 but attempting to link with file built for macOS-x86_64
ld: warning: ignoring file /usr/local/lib/libgsl.a, building for macOS-arm64 but attempting to link with file built for macOS-x86_64
installing to /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/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
Error: package or namespace load failed for ‘GLAD’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/00LOCK-GLAD/00new/GLAD/libs/GLAD.so':
dlopen(/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/00LOCK-GLAD/00new/GLAD/libs/GLAD.so, 0x0006): symbol not found in flat namespace '_gsl_cdf_gaussian_P'
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/GLAD’