Attila Gabor
| Snapshot Date: 2023-04-12 13:00:02 -0400 (Wed, 12 Apr 2023) |
| git_url: https://git.bioconductor.org/packages/CNORode |
| git_branch: RELEASE_3_16 |
| git_last_commit: 8eb16ff |
| git_last_commit_date: 2022-11-01 11:07:28 -0400 (Tue, 01 Nov 2022) |
| Back to Mac ARM64 build report for BioC 3.16 |
|
This page was generated on 2023-04-19 11:01:53 -0400 (Wed, 19 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson | macOS 13.0 Ventura | arm64 | 4.2.2 (2022-10-31) -- "Innocent and Trusting" | 4256 |
| 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 | ||||
|
To the developers/maintainers of the CNORode package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 365/2183 | Hostname | OS / Arch | INSTALL | BUILD | BUILD BIN | ||||||||
| CNORode 1.40.0 (landing page) Attila Gabor
| kjohnson | macOS 13.0 Ventura / arm64 | OK | OK | OK | | |||||||
| Package: CNORode |
| Version: 1.40.0 |
| Command: rm -rf CNORode.buildbin-libdir && mkdir CNORode.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CNORode_1.40.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R CNORode.buildbin-libdir |
| StartedAt: 2023-04-18 14:37:58 -0400 (Tue, 18 Apr 2023) |
| EndedAt: 2023-04-18 14:38:48 -0400 (Tue, 18 Apr 2023) |
| EllapsedTime: 50.4 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: CNORode_1.40.0.tgz |
| PackageFileSize: 641.3 KiB |
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###
### Running command:
###
### rm -rf CNORode.buildbin-libdir && mkdir CNORode.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CNORode_1.40.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R CNORode.buildbin-libdir
###
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=CNORode.buildbin-libdir CNORode_1.40.0.tar.gz'
>>>>>>>
* installing *source* package ‘CNORode’ ...
** using staged installation
** libs
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c FG_transfer_function.c -o FG_transfer_function.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c cvodea.c -o cvodea.o
cvodea.c:2445:11: warning: variable 'retval' set but not used [-Wunused-but-set-variable]
int is, retval;
^
cvodea.c:2941:7: warning: variable 'flag' set but not used [-Wunused-but-set-variable]
int flag, retval;
^
2 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c cvodea_io.c -o cvodea_io.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c cvodes.c -o cvodes.o
cvodes.c:8834:20: warning: variable 'rDeltap' set but not used [-Wunused-but-set-variable]
realtype Deltap, rDeltap;
^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c cvodes_band.c -o cvodes_band.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c cvodes_bandpre.c -o cvodes_bandpre.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c cvodes_bbdpre.c -o cvodes_bbdpre.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c cvodes_dense.c -o cvodes_dense.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c cvodes_diag.c -o cvodes_diag.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c cvodes_direct.c -o cvodes_direct.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c cvodes_io.c -o cvodes_io.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c cvodes_spbcgs.c -o cvodes_spbcgs.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c cvodes_spgmr.c -o cvodes_spgmr.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c cvodes_spils.c -o cvodes_spils.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c cvodes_sptfqmr.c -o cvodes_sptfqmr.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c decimal2binary.c -o decimal2binary.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c findStates.c -o findStates.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c fnvector_serial.c -o fnvector_serial.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c getAdjacencyMatrix.c -o getAdjacencyMatrix.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c getNumBits.c -o getNumBits.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c getNumInputs.c -o getNumInputs.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c getStateIndex.c -o getStateIndex.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c getTruthTables.c -o getTruthTables.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c get_count_bits.c -o get_count_bits.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c get_input_index.c -o get_input_index.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c get_support_truth_tables.c -o get_support_truth_tables.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c get_truth_tables_index.c -o get_truth_tables_index.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c hill_function.c -o hill_function.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c linear_transfer_function.c -o linear_transfer_function.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c normHill.c -o normHill.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c normHill_mod.c -o normHill_mod.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c nvector_serial.c -o nvector_serial.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c printAdjMat.c -o printAdjMat.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c printInterMat.c -o printInterMat.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c printNminiTerms.c -o printNminiTerms.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c printTruthTables.c -o printTruthTables.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c rhsODE.c -o rhsODE.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c sim_logic_ode.c -o sim_logic_ode.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c simulateODE.c -o simulateODE.o
simulateODE.c:37:14: warning: variable 'counter' set but not used [-Wunused-but-set-variable]
int i,j,neq,counter,flag;
^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c sundials_band.c -o sundials_band.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c sundials_dense.c -o sundials_dense.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c sundials_direct.c -o sundials_direct.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c sundials_iterative.c -o sundials_iterative.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c sundials_math.c -o sundials_math.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c sundials_nvector.c -o sundials_nvector.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c sundials_spbcgs.c -o sundials_spbcgs.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c sundials_spgmr.c -o sundials_spgmr.o
sundials_spgmr.c:439:20: warning: variable 'givens' set but not used [-Wunused-but-set-variable]
realtype **Hes, *givens, *yg;
^
sundials_spgmr.c:439:29: warning: variable 'yg' set but not used [-Wunused-but-set-variable]
realtype **Hes, *givens, *yg;
^
2 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I./include -fPIC -falign-functions=64 -Wall -g -O2 -c sundials_sptfqmr.c -o sundials_sptfqmr.o
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o CNORode.so FG_transfer_function.o cvodea.o cvodea_io.o cvodes.o cvodes_band.o cvodes_bandpre.o cvodes_bbdpre.o cvodes_dense.o cvodes_diag.o cvodes_direct.o cvodes_io.o cvodes_spbcgs.o cvodes_spgmr.o cvodes_spils.o cvodes_sptfqmr.o decimal2binary.o findStates.o fnvector_serial.o getAdjacencyMatrix.o getNumBits.o getNumInputs.o getStateIndex.o getTruthTables.o get_count_bits.o get_input_index.o get_support_truth_tables.o get_truth_tables_index.o hill_function.o linear_transfer_function.o normHill.o normHill_mod.o nvector_serial.o printAdjMat.o printInterMat.o printNminiTerms.o printTruthTables.o rhsODE.o sim_logic_ode.o simulateODE.o sundials_band.o sundials_dense.o sundials_direct.o sundials_iterative.o sundials_math.o sundials_nvector.o sundials_spbcgs.o sundials_spgmr.o sundials_sptfqmr.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: -undefined dynamic_lookup may not work with chained fixups
installing to /Volumes/External/bbs-3.16-bioc-m1/meat/CNORode.buildbin-libdir/00LOCK-CNORode/00new/CNORode/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 (CNORode)
>>>>>>>
>>>>>>> FIXING LINKS FOR CNORode.buildbin-libdir/CNORode/libs/CNORode.so
>>>>>>>
install_name_tool -change "/opt/R/arm64/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libgcc_s.1.1.dylib" "CNORode.buildbin-libdir/CNORode/libs/CNORode.so"
install_name_tool -change "/opt/R/arm64/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libgfortran.5.dylib" "CNORode.buildbin-libdir/CNORode/libs/CNORode.so"
install_name_tool -change "/opt/R/arm64/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libquadmath.0.dylib" "CNORode.buildbin-libdir/CNORode/libs/CNORode.so"