Multiple platform build/check report for BioC 3.21 - BUILD BIN results for marr on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"	4831
palomino7	Windows Server 2022 Datacenter	x64	4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six"	4573
lconway	macOS 12.7.1 Monterey	x86_64	4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"	4599
kjohnson3	macOS 13.7.1 Ventura	arm64	4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"	4553
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4570
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 marr on lconway

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

Version: 1.18.0

Command: rm -rf marr.buildbin-libdir && mkdir marr.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh marr_1.18.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R marr.buildbin-libdir

StartedAt: 2025-04-22 00:52:56 -0400 (Tue, 22 Apr 2025)

EndedAt: 2025-04-22 00:53:44 -0400 (Tue, 22 Apr 2025)

EllapsedTime: 47.7 seconds

RetCode: 0

Status: OK

PackageFile: marr_1.18.0.tgz

PackageFileSize: 808.3 KiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf marr.buildbin-libdir && mkdir marr.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh marr_1.18.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R marr.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=marr.buildbin-libdir marr_1.18.0.tar.gz'
>>>>>>> 

* installing *source* package ‘marr’ ...
** this is package ‘marr’ version ‘1.18.0’
** using staged installation
** libs
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  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c marrUtility.cpp -o marrUtility.o
marrUtility.cpp:75:7: warning: variable 'i' set but not used [-Wunused-but-set-variable]
  int i=0;
      ^
1 warning generated.
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 marr.so RcppExports.o marrUtility.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Users/biocbuild/bbs-3.21-bioc/meat/marr.buildbin-libdir/00LOCK-marr/00new/marr/libs
** R
** data
** 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 (marr)


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

>>>>>>> Paths before fix:
marr.buildbin-libdir/marr/libs/marr.so:
	marr.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0)
	/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-x86_64/Resources/lib/libgcc_s.1.1.dylib" "marr.buildbin-libdir/marr/libs/marr.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" "marr.buildbin-libdir/marr/libs/marr.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" "marr.buildbin-libdir/marr/libs/marr.so"

>>>>>>> Paths after fix:
marr.buildbin-libdir/marr/libs/marr.so:
	marr.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0)
	/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)