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

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"	4748
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"	4459
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4398
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 HEM on lconway

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

Version: 1.79.0

Command: rm -rf HEM.buildbin-libdir && mkdir HEM.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh HEM_1.79.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R HEM.buildbin-libdir

StartedAt: 2024-11-28 04:04:44 -0500 (Thu, 28 Nov 2024)

EndedAt: 2024-11-28 04:04:57 -0500 (Thu, 28 Nov 2024)

EllapsedTime: 12.5 seconds

RetCode: 0

Status: OK

PackageFile: HEM_1.79.0.tgz

PackageFileSize: 717.3 KiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf HEM.buildbin-libdir && mkdir HEM.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh HEM_1.79.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R HEM.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=HEM.buildbin-libdir HEM_1.79.0.tar.gz'
>>>>>>> 

* installing *source* package ‘HEM’ ...
** 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 hem.c -o hem.o
hem.c:1390:12: warning: variable 'k' set but not used [-Wunused-but-set-variable]
        int i, j, k, m, n;
                  ^
hem.c:1593:16: warning: variable 'l' set but not used [-Wunused-but-set-variable]
  int i, j, k, l;
               ^
2 warnings 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 HEM.so hem.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.21-bioc/meat/HEM.buildbin-libdir/00LOCK-HEM/00new/HEM/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 (HEM)


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

>>>>>>> Paths before fix:
HEM.buildbin-libdir/HEM/libs/HEM.so:
	HEM.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)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
	/usr/lib/libobjc.A.dylib (compatibility version 1.0.0, current version 228.0.0)

>>>>>>> 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" "HEM.buildbin-libdir/HEM/libs/HEM.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" "HEM.buildbin-libdir/HEM/libs/HEM.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" "HEM.buildbin-libdir/HEM/libs/HEM.so"

>>>>>>> Paths after fix:
HEM.buildbin-libdir/HEM/libs/HEM.so:
	HEM.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)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
	/usr/lib/libobjc.A.dylib (compatibility version 1.0.0, current version 228.0.0)