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

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.3 (2025-02-28) -- "Trophy Case"	4764
palomino8	Windows Server 2022 Datacenter	x64	4.4.3 (2025-02-28 ucrt) -- "Trophy Case"	4495
merida1	macOS 12.7.5 Monterey	x86_64	4.4.3 (2025-02-28) -- "Trophy Case"	4522
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.3 (2025-02-28) -- "Trophy Case"	4449
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.4.3 (2025-02-28) -- "Trophy Case"	4426
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 Harman on merida1

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

Version: 1.34.0

Command: rm -rf Harman.buildbin-libdir && mkdir Harman.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Harman_1.34.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R Harman.buildbin-libdir

StartedAt: 2025-04-01 12:01:48 -0400 (Tue, 01 Apr 2025)

EndedAt: 2025-04-01 12:02:11 -0400 (Tue, 01 Apr 2025)

EllapsedTime: 23.7 seconds

RetCode: 0

Status: OK

PackageFile: Harman_1.34.0.tgz

PackageFileSize: 2.175 MiB

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf Harman.buildbin-libdir && mkdir Harman.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Harman_1.34.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R Harman.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=Harman.buildbin-libdir Harman_1.34.0.tar.gz'
>>>>>>> 

* installing *source* package ‘Harman’ ...
** 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 -D_ARRAYALIGNEMT=4 -D_USE_RCPP=1 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include   `/Library/Frameworks/R.framework/Resources/bin/Rscript -e "Rcpp:::CxxFlags()"` -I.  -fPIC  -falign-functions=64 -Wall -g -O2   -c Harman.cpp -o Harman.o
In file included from Harman.cpp:182:
./CSelectRandom.h:283:11: warning: variable 'seed' set but not used [-Wunused-but-set-variable]
                        size_t seed ;
                               ^
./CSelectRandom.h:394:40: warning: unused variable 'it2' [-Wunused-variable]
                        std::vector<double>::iterator  it1, it2 ;
                                                            ^
./CSelectRandom.h:392:11: warning: unused variable 'currindex' [-Wunused-variable]
                 size_t currindex ;
                        ^
./CSelectRandom.h:372:11: warning: variable 'seed' set but not used [-Wunused-but-set-variable]
                        size_t seed ;
                               ^
./CSelectRandom.h:394:35: warning: unused variable 'it1' [-Wunused-variable]
                        std::vector<double>::iterator  it1, it2 ;
                                                       ^
./CSelectRandom.h:639:11: warning: unused variable 'time1' [-Wunused-variable]
                        double time1, time2 ;
                               ^
./CSelectRandom.h:638:20: warning: unused variable 'ts1' [-Wunused-variable]
                        struct timespec ts1, ts2 ;
                                        ^
./CSelectRandom.h:639:18: warning: unused variable 'time2' [-Wunused-variable]
                        double time1, time2 ;
                                      ^
./CSelectRandom.h:638:25: warning: unused variable 'ts2' [-Wunused-variable]
                        struct timespec ts1, ts2 ;
                                             ^
./CSelectRandom.h:1019:23: warning: unused variable 'randData2' [-Wunused-variable]
                                size_t randData1, randData2  ;
                                                  ^
10 warnings 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 Harman.so Harman.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.20-bioc/meat/Harman.buildbin-libdir/00LOCK-Harman/00new/Harman/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 (Harman)


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

>>>>>>> Paths before fix:
Harman.buildbin-libdir/Harman/libs/Harman.so:
	Harman.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.3)
	/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" "Harman.buildbin-libdir/Harman/libs/Harman.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" "Harman.buildbin-libdir/Harman/libs/Harman.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" "Harman.buildbin-libdir/Harman/libs/Harman.so"

>>>>>>> Paths after fix:
Harman.buildbin-libdir/Harman/libs/Harman.so:
	Harman.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.3)
	/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)