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 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GLAD ### ############################################################################## ############################################################################## * 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’