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This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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

Package 867/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GLAD 2.70.0  (landing page)
Philippe Hupe
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/GLAD
git_branch: RELEASE_3_20
git_last_commit: 955d7f2
git_last_commit_date: 2024-10-29 09:23:29 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

BUILD BIN results for GLAD on kjohnson1

To the developers/maintainers of the GLAD package:
- 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 Troubleshooting Build Report for more information.
- 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: GLAD
Version: 2.70.0
Command: rm -rf GLAD.buildbin-libdir && mkdir GLAD.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh GLAD_2.70.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R GLAD.buildbin-libdir
StartedAt: 2024-12-21 15:05:10 -0500 (Sat, 21 Dec 2024)
EndedAt: 2024-12-21 15:05:30 -0500 (Sat, 21 Dec 2024)
EllapsedTime: 20.1 seconds
RetCode: 0
Status:   OK  
PackageFile: GLAD_2.70.0.tgz
PackageFileSize: 1.451 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf GLAD.buildbin-libdir && mkdir GLAD.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh GLAD_2.70.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R GLAD.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=GLAD.buildbin-libdir GLAD_2.70.0.tar.gz'
>>>>>>> 

* installing *source* package ‘GLAD’ ...
** using staged installation
checking for pkg-config... /opt/R/arm64/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/opt/R/arm64/lib -lgsl -lgslcblas -lm
PKG_CPPFLAGS = -DIS_MAC_OS

** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -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++17 -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++17 -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++17 -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++17 -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++17 -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++17 -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++17 -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++17 -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++17 -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++17 -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++17 -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++17 -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
loopRemove.cpp:38:9: warning: variable 'nb_loop' set but not used [-Wunused-but-set-variable]
    int nb_loop = 0;
        ^
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -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/opt/R/arm64/lib -lgsl -lgslcblas -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.20-bioc/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 PATHS TO DYNAMIC LIBRARIES FOR GLAD.buildbin-libdir/GLAD/libs/GLAD.so
>>>>>>> 

>>>>>>> Paths before fix:
GLAD.buildbin-libdir/GLAD/libs/GLAD.so:
	GLAD.so (compatibility version 0.0.0, current version 0.0.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
	/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.2)
	/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)

>>>>>>> Fix with install_name_tool:
install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgcc_s.1.1.dylib" "GLAD.buildbin-libdir/GLAD/libs/GLAD.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "GLAD.buildbin-libdir/GLAD/libs/GLAD.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "GLAD.buildbin-libdir/GLAD/libs/GLAD.so"

>>>>>>> Paths after fix:
GLAD.buildbin-libdir/GLAD/libs/GLAD.so:
	GLAD.so (compatibility version 0.0.0, current version 0.0.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
	/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.2)
	/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)