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

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4744
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4487
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4515
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4467
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 ternarynet on kjohnson1

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

Version: 1.50.0

Command: rm -rf ternarynet.buildbin-libdir && mkdir ternarynet.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh ternarynet_1.50.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R ternarynet.buildbin-libdir

StartedAt: 2024-12-21 16:57:16 -0500 (Sat, 21 Dec 2024)

EndedAt: 2024-12-21 16:57:28 -0500 (Sat, 21 Dec 2024)

EllapsedTime: 12.5 seconds

RetCode: 0

Status: OK

PackageFile: ternarynet_1.50.0.tgz

PackageFileSize: 568.1 KiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf ternarynet.buildbin-libdir && mkdir ternarynet.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh ternarynet_1.50.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R ternarynet.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=ternarynet.buildbin-libdir ternarynet_1.50.0.tar.gz'
>>>>>>> 

* installing *source* package ‘ternarynet’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c array.c -o array.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c gn.c -o gn.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c gn_Rwrap.c -o gn_Rwrap.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c init.c -o init.o
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 tnetfit.cc -o tnetfit.o
tnetfit.cc:24:9: warning: variable 'perturbationType' set but not used [-Wunused-but-set-variable]
    int perturbationType, scoreType, backupStage, maxStage, maxTransition;
        ^
tnetfit.cc:24:27: warning: variable 'scoreType' set but not used [-Wunused-but-set-variable]
    int perturbationType, scoreType, backupStage, maxStage, maxTransition;
                          ^
tnetfit.cc:24:38: warning: variable 'backupStage' set but not used [-Wunused-but-set-variable]
    int perturbationType, scoreType, backupStage, maxStage, maxTransition;
                                     ^
tnetfit.cc:73:39: warning: unused variable 'tempi' [-Wunused-variable]
    int nOutcomes=3, l0, stage_count, tempi, jtrans, nTransition;
                                      ^
tnetfit.cc:99:9: warning: variable 'acceptCount' set but not used [-Wunused-but-set-variable]
    int acceptCount;
        ^
5 warnings generated.
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 tnetfuncs.cc -o tnetfuncs.o
tnetfuncs.cc:427:5: warning: unused variable 'tableWidth' [-Wunused-variable]
int tableWidth = powi(nOutcomes,maxDegree);
    ^
tnetfuncs.cc:435:5: warning: unused variable 'ipause' [-Wunused-variable]
int ipause;
    ^
tnetfuncs.cc:517:6: warning: unused variable 'ipause' [-Wunused-variable]
        int ipause; 
            ^
tnetfuncs.cc:521:16: warning: unused variable 'i' [-Wunused-variable]
        int m1, m2, i;
                    ^
4 warnings generated.
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 tnetpost.cc -o tnetpost.o
tnetpost.cc:25:9: warning: unused variable 'ipause' [-Wunused-variable]
    int ipause;
        ^
tnetpost.cc:27:9: warning: unused variable 'm0fit' [-Wunused-variable]
    int m0fit;
        ^
tnetpost.cc:28:32: warning: variable 'minScore' set but not used [-Wunused-but-set-variable]
    double newScore, oldScore, minScore, finalScore;
                               ^
tnetpost.cc:28:42: warning: unused variable 'finalScore' [-Wunused-variable]
    double newScore, oldScore, minScore, finalScore;
                                         ^
tnetpost.cc:30:9: warning: unused variable 'l0' [-Wunused-variable]
    int l0, stage_count, tempi, jtrans, nTransition;
        ^
tnetpost.cc:30:13: warning: unused variable 'stage_count' [-Wunused-variable]
    int l0, stage_count, tempi, jtrans, nTransition;
            ^
tnetpost.cc:30:26: warning: unused variable 'tempi' [-Wunused-variable]
    int l0, stage_count, tempi, jtrans, nTransition;
                         ^
tnetpost.cc:30:33: warning: unused variable 'jtrans' [-Wunused-variable]
    int l0, stage_count, tempi, jtrans, nTransition;
                                ^
tnetpost.cc:30:41: warning: unused variable 'nTransition' [-Wunused-variable]
    int l0, stage_count, tempi, jtrans, nTransition;
                                        ^
tnetpost.cc:33:9: warning: variable 'acceptCount' set but not used [-Wunused-but-set-variable]
    int acceptCount;
        ^
tnetpost.cc:36:21: warning: variable 'xSeedFit' set but not used [-Wunused-but-set-variable]
    int m0, mdelta, xSeedFit;
                    ^
tnetpost.cc:38:9: warning: variable 'perturbationType' set but not used [-Wunused-but-set-variable]
    int perturbationType, scoreType, backupStage;
        ^
tnetpost.cc:38:27: warning: variable 'scoreType' set but not used [-Wunused-but-set-variable]
    int perturbationType, scoreType, backupStage;
                          ^
tnetpost.cc:38:38: warning: variable 'backupStage' set but not used [-Wunused-but-set-variable]
    int perturbationType, scoreType, backupStage;
                                     ^
tnetpost.cc:39:9: warning: variable 'maxStage' set but not used [-Wunused-but-set-variable]
    int maxStage, maxTransition;
        ^
tnetpost.cc:39:19: warning: variable 'maxTransition' set but not used [-Wunused-but-set-variable]
    int maxStage, maxTransition;
                  ^
tnetpost.cc:40:12: warning: variable 'epsilon' set but not used [-Wunused-but-set-variable]
    double epsilon, chi0, delta, rho; 
           ^
tnetpost.cc:40:21: warning: variable 'chi0' set but not used [-Wunused-but-set-variable]
    double epsilon, chi0, delta, rho; 
                    ^
tnetpost.cc:40:27: warning: variable 'delta' set but not used [-Wunused-but-set-variable]
    double epsilon, chi0, delta, rho; 
                          ^
tnetpost.cc:40:34: warning: variable 'rho' set but not used [-Wunused-but-set-variable]
    double epsilon, chi0, delta, rho; 
                                 ^
tnetpost.cc:44:9: warning: variable 'ne' set but not used [-Wunused-but-set-variable]
    int ne, maxDegree;
        ^
tnetpost.cc:150:10: warning: variable 'minDump' set but not used [-Wunused-but-set-variable]
    bool minDump = true;
         ^
tnetpost.cc:41:9: warning: variable 'Rf_beta' set but not used [-Wunused-but-set-variable]
    int beta;
        ^
/Library/Frameworks/R.framework/Resources/include/Rmath.h:210:15: note: expanded from macro 'beta'
#define beta            Rf_beta
                        ^
23 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c util.c -o util.o
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 ternarynet.so array.o gn.o gn_Rwrap.o init.o tnetfit.o tnetfuncs.o tnetpost.o util.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.20-bioc/meat/ternarynet.buildbin-libdir/00LOCK-ternarynet/00new/ternarynet/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 (ternarynet)


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

>>>>>>> Paths before fix:
ternarynet.buildbin-libdir/ternarynet/libs/ternarynet.so:
	ternarynet.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 4.4.2)
	/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" "ternarynet.buildbin-libdir/ternarynet/libs/ternarynet.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "ternarynet.buildbin-libdir/ternarynet/libs/ternarynet.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "ternarynet.buildbin-libdir/ternarynet/libs/ternarynet.so"

>>>>>>> Paths after fix:
ternarynet.buildbin-libdir/ternarynet/libs/ternarynet.so:
	ternarynet.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 4.4.2)
	/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)