Multiple platform build/check report for BioC 3.22 - BUILD BIN results for COSNet on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4753
palomino8	Windows Server 2022 Datacenter	x64	4.5.0 (2025-04-11 ucrt) -- "How About a Twenty-Six"	4528
lconway	macOS 12.7.1 Monterey	x86_64	4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six"	4553
kjohnson3	macOS 13.7.1 Ventura	arm64	4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six"	4493
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4460
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 COSNet on lconway

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

Version: 1.43.0

Command: rm -rf COSNet.buildbin-libdir && mkdir COSNet.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh COSNet_1.43.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R COSNet.buildbin-libdir

StartedAt: 2025-05-23 00:25:30 -0400 (Fri, 23 May 2025)

EndedAt: 2025-05-23 00:25:36 -0400 (Fri, 23 May 2025)

EllapsedTime: 5.8 seconds

RetCode: 0

Status: OK

PackageFile: COSNet_1.43.0.tgz

PackageFileSize: 560.2 KiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf COSNet.buildbin-libdir && mkdir COSNet.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh COSNet_1.43.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R COSNet.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=COSNet.buildbin-libdir COSNet_1.43.0.tar.gz'
>>>>>>> 

* installing *source* package ‘COSNet’ ...
** this is package ‘COSNet’ version ‘1.43.0’
** 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 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c COSNet.c -o COSNet.o
COSNet.c:403:61: warning: variable 'tn_o' set but not used [-Wunused-but-set-variable]
        int N_pos = 0, pos_halfplane = 0, N_neg, tp_o, fn_o, fp_o, tn_o, tp_u, fn_u, fp_u, tn_u, 
                                                                   ^
1 warning generated.
clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o COSNet.so COSNet.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Users/biocbuild/bbs-3.22-bioc/meat/COSNet.buildbin-libdir/00LOCK-COSNet/00new/COSNet/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
COSNet: Cost-Sensitive algorithm for binary classification in graphs.
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
COSNet: Cost-Sensitive algorithm for binary classification in graphs.
** testing if installed package keeps a record of temporary installation path
* DONE (COSNet)


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

>>>>>>> Paths before fix:
COSNet.buildbin-libdir/COSNet/libs/COSNet.so:
	COSNet.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/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" "COSNet.buildbin-libdir/COSNet/libs/COSNet.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" "COSNet.buildbin-libdir/COSNet/libs/COSNet.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" "COSNet.buildbin-libdir/COSNet/libs/COSNet.so"

>>>>>>> Paths after fix:
COSNet.buildbin-libdir/COSNet/libs/COSNet.so:
	COSNet.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/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)