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This page was generated on 2024-11-27 11:44 -0500 (Wed, 27 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4748
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4459
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4396
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4110
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 2021/2272HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SpliceWiz 1.9.0  (landing page)
Alex Chit Hei Wong
Snapshot Date: 2024-11-26 13:40 -0500 (Tue, 26 Nov 2024)
git_url: https://git.bioconductor.org/packages/SpliceWiz
git_branch: devel
git_last_commit: 8784449
git_last_commit_date: 2024-10-29 11:12:40 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  NO, package depends on 'rtracklayer' which is only available as a source package that needs compilation
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  NO, package depends on 'rtracklayer' which is only available as a source package that needs compilation

BUILD BIN results for SpliceWiz on kjohnson3

To the developers/maintainers of the SpliceWiz package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SpliceWiz.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: SpliceWiz
Version: 1.9.0
Command: rm -rf SpliceWiz.buildbin-libdir && mkdir SpliceWiz.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh SpliceWiz_1.9.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R SpliceWiz.buildbin-libdir
StartedAt: 2024-11-27 07:41:02 -0500 (Wed, 27 Nov 2024)
EndedAt: 2024-11-27 07:41:43 -0500 (Wed, 27 Nov 2024)
EllapsedTime: 40.7 seconds
RetCode: 0
Status:   OK  
PackageFile: SpliceWiz_1.9.0.tgz
PackageFileSize: 5.825 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf SpliceWiz.buildbin-libdir && mkdir SpliceWiz.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh SpliceWiz_1.9.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R SpliceWiz.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=SpliceWiz.buildbin-libdir SpliceWiz_1.9.0.tar.gz'
>>>>>>> 

* installing *source* package ‘SpliceWiz’ ...
** using staged installation
Configuring without OpenMP for MacOS
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include    -DSPLICEWIZ -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c BAM2blocks.cpp -o BAM2blocks.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include    -DSPLICEWIZ -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c FastaReader.cpp -o FastaReader.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include    -DSPLICEWIZ -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c FragmentBlocks.cpp -o FragmentBlocks.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include    -DSPLICEWIZ -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c GZTools.cpp -o GZTools.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include    -DSPLICEWIZ -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include    -DSPLICEWIZ -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c ReadBlockProcessor.cpp -o ReadBlockProcessor.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include    -DSPLICEWIZ -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c ReadBlockProcessor_CoverageBlocks.cpp -o ReadBlockProcessor_CoverageBlocks.o
ReadBlockProcessor_CoverageBlocks.cpp:251:16: warning: variable 'len' set but not used [-Wunused-but-set-variable]
                unsigned int len=0;
                             ^
1 warning generated.
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include    -DSPLICEWIZ -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c ReadBlockProcessor_FragmentsMap.cpp -o ReadBlockProcessor_FragmentsMap.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include    -DSPLICEWIZ -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c ReadBlockProcessor_TandemJunctions.cpp -o ReadBlockProcessor_TandemJunctions.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include    -DSPLICEWIZ -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c covTools.cpp -o covTools.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include    -DSPLICEWIZ -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c main.cpp -o main.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include    -DSPLICEWIZ -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c swEngine.cpp -o swEngine.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include    -DSPLICEWIZ -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c synthReadGenerator.cpp -o synthReadGenerator.o
clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o SpliceWiz.so BAM2blocks.o FastaReader.o FragmentBlocks.o GZTools.o RcppExports.o ReadBlockProcessor.o ReadBlockProcessor_CoverageBlocks.o ReadBlockProcessor_FragmentsMap.o ReadBlockProcessor_TandemJunctions.o covTools.o main.o swEngine.o synthReadGenerator.o -DSPLICEWIZ -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.21-bioc/meat/SpliceWiz.buildbin-libdir/00LOCK-SpliceWiz/00new/SpliceWiz/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 (SpliceWiz)


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

>>>>>>> Paths before fix:
SpliceWiz.buildbin-libdir/SpliceWiz/libs/SpliceWiz.so:
	SpliceWiz.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0)
	/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/4.5-arm64/Resources/lib/libgcc_s.1.1.dylib" "SpliceWiz.buildbin-libdir/SpliceWiz/libs/SpliceWiz.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libgfortran.5.dylib" "SpliceWiz.buildbin-libdir/SpliceWiz/libs/SpliceWiz.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libquadmath.0.dylib" "SpliceWiz.buildbin-libdir/SpliceWiz/libs/SpliceWiz.so"

>>>>>>> Paths after fix:
SpliceWiz.buildbin-libdir/SpliceWiz/libs/SpliceWiz.so:
	SpliceWiz.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0)
	/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)