Multiple platform build/check report for BioC 3.20 - BUILD BIN results for DEGseq on kjohnson1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup"	4679
palomino4	Windows Server 2022 Datacenter	x64	4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"	4414
merida1	macOS 12.7.4 Monterey	x86_64	4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"	4441
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"	4394
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 DEGseq on kjohnson1

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

Version: 1.59.0

Command: rm -rf DEGseq.buildbin-libdir && mkdir DEGseq.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh DEGseq_1.59.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R DEGseq.buildbin-libdir

StartedAt: 2024-06-11 13:07:37 -0400 (Tue, 11 Jun 2024)

EndedAt: 2024-06-11 13:07:54 -0400 (Tue, 11 Jun 2024)

EllapsedTime: 17.2 seconds

RetCode: 0

Status: OK

PackageFile: DEGseq_1.59.0.tgz

PackageFileSize: 2.246 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf DEGseq.buildbin-libdir && mkdir DEGseq.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh DEGseq_1.59.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R DEGseq.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=DEGseq.buildbin-libdir DEGseq_1.59.0.tar.gz'
>>>>>>> 

* installing *source* package ‘DEGseq’ ...
** using staged installation
** libs
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   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c getGeneExp.cpp -o getGeneExp.o
getGeneExp.cpp:413:6: warning: variable 'isoforn_count' set but not used [-Wunused-but-set-variable]
        int isoforn_count=0;
            ^
getGeneExp.cpp:464:9: warning: variable 'count' set but not used [-Wunused-but-set-variable]
    int count=0;
        ^
getGeneExp.cpp:670:9: warning: variable 'total_reads' set but not used [-Wunused-but-set-variable]
    int total_reads = 0;
        ^
getGeneExp.cpp:697:9: warning: variable 'total_reads' set but not used [-Wunused-but-set-variable]
    int total_reads = 0;
        ^
4 warnings 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 DEGseq.so getGeneExp.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.20-bioc/meat/DEGseq.buildbin-libdir/00LOCK-DEGseq/00new/DEGseq/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 (DEGseq)


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

>>>>>>> Paths before fix:
DEGseq.buildbin-libdir/DEGseq/libs/DEGseq.so:
	DEGseq.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.0)
	/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/4.4-arm64/Resources/lib/libgcc_s.1.1.dylib" "DEGseq.buildbin-libdir/DEGseq/libs/DEGseq.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "DEGseq.buildbin-libdir/DEGseq/libs/DEGseq.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "DEGseq.buildbin-libdir/DEGseq/libs/DEGseq.so"

>>>>>>> Paths after fix:
DEGseq.buildbin-libdir/DEGseq/libs/DEGseq.so:
	DEGseq.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.0)
	/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)