Multiple platform build/check report for BioC 3.20 - BUILD BIN results for BUSseq on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4744
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4487
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4515
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (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*

BUILD BIN results for BUSseq on merida1

To the developers/maintainers of the BUSseq package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BUSseq.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: BUSseq

Version: 1.12.0

Command: rm -rf BUSseq.buildbin-libdir && mkdir BUSseq.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh BUSseq_1.12.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R BUSseq.buildbin-libdir

StartedAt: 2024-12-20 12:01:52 -0500 (Fri, 20 Dec 2024)

EndedAt: 2024-12-20 12:02:52 -0500 (Fri, 20 Dec 2024)

EllapsedTime: 59.9 seconds

RetCode: 0

Status: OK

PackageFile: BUSseq_1.12.0.tgz

PackageFileSize: 964.2 KiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf BUSseq.buildbin-libdir && mkdir BUSseq.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh BUSseq_1.12.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R BUSseq.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=BUSseq.buildbin-libdir BUSseq_1.12.0.tar.gz'
>>>>>>> 

* installing *source* package ‘BUSseq’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
/Library/Frameworks/R.framework/Resources/share/make/shlib.mk:10: warning: overriding commands for target `BUSseq.so'
Makevars:9: warning: ignoring old commands for target `BUSseq.so'
/Library/Frameworks/R.framework/Resources/share/make/shlib.mk:10: warning: overriding commands for target `BUSseq.so'
Makevars:9: warning: ignoring old commands for target `BUSseq.so'
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c BUSseq.cpp -o BUSseq.o
BUSseq.cpp:2674:7: warning: variable 'All_Drop' set but not used [-Wunused-but-set-variable]
        bool All_Drop = true;
             ^
BUSseq.cpp:3033:6: warning: variable 'count_gene' set but not used [-Wunused-but-set-variable]
        int count_gene = 0;
            ^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c rngstream.cpp -o rngstream.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 BUSseq.so BUSseq.o rngstream.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.20-bioc/meat/BUSseq.buildbin-libdir/00LOCK-BUSseq/00new/BUSseq/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (BUSseq)


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

>>>>>>> Paths before fix:
BUSseq.buildbin-libdir/BUSseq/libs/BUSseq.so:
	BUSseq.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRlapack.dylib (compatibility version 4.4.0, current version 4.4.2)
	/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0)
	/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0)
	/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0/libquadmath.0.dylib (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 4.4.2)
	/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)
	/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" "BUSseq.buildbin-libdir/BUSseq/libs/BUSseq.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" "BUSseq.buildbin-libdir/BUSseq/libs/BUSseq.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" "BUSseq.buildbin-libdir/BUSseq/libs/BUSseq.so"
install_name_tool -change "/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgfortran.5.dylib" "BUSseq.buildbin-libdir/BUSseq/libs/BUSseq.so"
install_name_tool -change "/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libquadmath.0.dylib" "BUSseq.buildbin-libdir/BUSseq/libs/BUSseq.so"

>>>>>>> Paths after fix:
BUSseq.buildbin-libdir/BUSseq/libs/BUSseq.so:
	BUSseq.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRlapack.dylib (compatibility version 4.4.0, current version 4.4.2)
	/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libquadmath.0.dylib (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 4.4.2)
	/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)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)