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This page was generated on 2025-10-16 11:39 -0400 (Thu, 16 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.6 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.7.5 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4555
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4586
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 883/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GLAD 2.72.0  (landing page)
Philippe Hupe
Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025)
git_url: https://git.bioconductor.org/packages/GLAD
git_branch: RELEASE_3_21
git_last_commit: 3e7d1d1
git_last_commit_date: 2025-04-15 09:35:12 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
merida1macOS 12.7.6 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.7.5 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    WARNINGS  

BUILD BIN results for GLAD on merida1

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: 2.72.0
Command: rm -rf GLAD.buildbin-libdir && mkdir GLAD.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh GLAD_2.72.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R GLAD.buildbin-libdir
StartedAt: 2025-10-14 13:36:48 -0400 (Tue, 14 Oct 2025)
EndedAt: 2025-10-14 13:37:40 -0400 (Tue, 14 Oct 2025)
EllapsedTime: 52.1 seconds
RetCode: 0
Status:   OK  
PackageFile: GLAD_2.72.0.tgz
PackageFileSize: 1.458 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf GLAD.buildbin-libdir && mkdir GLAD.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh GLAD_2.72.0.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_2.72.0.tar.gz'
>>>>>>> 

* installing *source* package ‘GLAD’ ...
** this is package ‘GLAD’ version ‘2.72.0’
** using staged installation
checking for pkg-config... /usr/local/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/x86_64/lib -lgsl -lgslcblas -lm
PKG_CPPFLAGS = -DIS_MAC_OS

** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS  -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c BkpInfo.cpp -o BkpInfo.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS  -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS  -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c MoveBkp.cpp -o MoveBkp.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS  -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c OutliersGNL.cpp -o OutliersGNL.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS  -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c chrBreakpoints.cpp -o chrBreakpoints.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS  -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c cutree.cpp -o cutree.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS  -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c daglad.cpp -o daglad.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS  -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c distance.cpp -o distance.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS  -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c filterBkp.cpp -o filterBkp.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS  -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c findCluster.cpp -o findCluster.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS  -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS  -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c hclust.cpp -o hclust.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS  -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c laws.c -o laws.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS  -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c loopRemove.cpp -o loopRemove.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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/x86_64/lib -lgsl -lgslcblas -lm -F/Library/Frameworks/R.framework/.. -framework R
installing to /Users/biocbuild/bbs-3.21-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/4.5-x86_64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.1)
	/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/4.5-x86_64/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/4.5-x86_64/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/4.5-x86_64/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/4.5-x86_64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.1)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)