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This page was generated on 2024-11-20 12:06 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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 895/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gpuMagic 1.22.0  (landing page)
Jiefei Wang
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/gpuMagic
git_branch: RELEASE_3_20
git_last_commit: cc5ec08
git_last_commit_date: 2024-10-29 10:37:03 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  ERROR    ERROR  skipped

BUILD BIN results for gpuMagic on lconway

To the developers/maintainers of the gpuMagic package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/gpuMagic.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: gpuMagic
Version: 1.22.0
Command: rm -rf gpuMagic.buildbin-libdir && mkdir gpuMagic.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh gpuMagic_1.22.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R gpuMagic.buildbin-libdir
StartedAt: 2024-11-20 04:30:08 -0500 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 04:30:43 -0500 (Wed, 20 Nov 2024)
EllapsedTime: 35.5 seconds
RetCode: 0
Status:   OK  
PackageFile: gpuMagic_1.22.0.tgz
PackageFileSize: 1.49 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf gpuMagic.buildbin-libdir && mkdir gpuMagic.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh gpuMagic_1.22.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R gpuMagic.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=gpuMagic.buildbin-libdir gpuMagic_1.22.0.tar.gz'
>>>>>>> 

* installing *source* package ‘gpuMagic’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Library/Frameworks/R.framework/Resources/include -I../inst/include/OpenCL_header -DCL_TARGET_OPENCL_VERSION=220 -DCL_USE_DEPRECATED_OPENCL_1_2_APIS  -DCL_SILENCE_DEPRECATION -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c C_Interface.cpp -o C_Interface.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Library/Frameworks/R.framework/Resources/include -I../inst/include/OpenCL_header -DCL_TARGET_OPENCL_VERSION=220 -DCL_USE_DEPRECATED_OPENCL_1_2_APIS  -DCL_SILENCE_DEPRECATION -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c R_functionRegistration.cpp -o R_functionRegistration.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Library/Frameworks/R.framework/Resources/include -I../inst/include/OpenCL_header -DCL_TARGET_OPENCL_VERSION=220 -DCL_USE_DEPRECATED_OPENCL_1_2_APIS  -DCL_SILENCE_DEPRECATION -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c Tools.cpp -o Tools.o
Tools.cpp:41:8: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
        error(errorInfo.c_str());
              ^~~~~~~~~~~~~~~~~
Tools.cpp:41:8: note: treat the string as an argument to avoid this
        error(errorInfo.c_str());
              ^
              "%s", 
Tools.cpp:51:10: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
        warning(warningInfo.c_str());
                ^~~~~~~~~~~~~~~~~~~
Tools.cpp:51:10: note: treat the string as an argument to avoid this
        warning(warningInfo.c_str());
                ^
                "%s", 
Tools.cpp:60:10: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
        Rprintf(msg.c_str());
                ^~~~~~~~~~~
Tools.cpp:60:10: note: treat the string as an argument to avoid this
        Rprintf(msg.c_str());
                ^
                "%s", 
3 warnings generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Library/Frameworks/R.framework/Resources/include -I../inst/include/OpenCL_header -DCL_TARGET_OPENCL_VERSION=220 -DCL_USE_DEPRECATED_OPENCL_1_2_APIS  -DCL_SILENCE_DEPRECATION -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c kernelManager.cpp -o kernelManager.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Library/Frameworks/R.framework/Resources/include -I../inst/include/OpenCL_header -DCL_TARGET_OPENCL_VERSION=220 -DCL_USE_DEPRECATED_OPENCL_1_2_APIS  -DCL_SILENCE_DEPRECATION -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c openArray.cpp -o openArray.o
clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o gpuMagic.so C_Interface.o R_functionRegistration.o Tools.o kernelManager.o openArray.o -framework OpenCL -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.20-bioc/meat/gpuMagic.buildbin-libdir/00LOCK-gpuMagic/00new/gpuMagic/libs
** R
** 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 (gpuMagic)


>>>>>>> 
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR gpuMagic.buildbin-libdir/gpuMagic/libs/gpuMagic.so
>>>>>>> 

>>>>>>> Paths before fix:
gpuMagic.buildbin-libdir/gpuMagic/libs/gpuMagic.so:
	gpuMagic.so (compatibility version 0.0.0, current version 0.0.0)
	/System/Library/Frameworks/OpenCL.framework/Versions/A/OpenCL (compatibility version 1.0.0, current version 1.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.1)
	/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)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)

>>>>>>> Fix with install_name_tool:
install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgcc_s.1.1.dylib" "gpuMagic.buildbin-libdir/gpuMagic/libs/gpuMagic.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgfortran.5.dylib" "gpuMagic.buildbin-libdir/gpuMagic/libs/gpuMagic.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libquadmath.0.dylib" "gpuMagic.buildbin-libdir/gpuMagic/libs/gpuMagic.so"

>>>>>>> Paths after fix:
gpuMagic.buildbin-libdir/gpuMagic/libs/gpuMagic.so:
	gpuMagic.so (compatibility version 0.0.0, current version 0.0.0)
	/System/Library/Frameworks/OpenCL.framework/Versions/A/OpenCL (compatibility version 1.0.0, current version 1.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.1)
	/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)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)