Back to Multiple platform build/check report for BioC 3.20:   simplified   long
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (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

Package 392/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNORode 1.48.0  (landing page)
Attila Gabor
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/CNORode
git_branch: RELEASE_3_20
git_last_commit: b26387a
git_last_commit_date: 2024-10-29 09:43:02 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

BUILD BIN results for CNORode on merida1

To the developers/maintainers of the CNORode package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CNORode.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: CNORode
Version: 1.48.0
Command: rm -rf CNORode.buildbin-libdir && mkdir CNORode.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CNORode_1.48.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R CNORode.buildbin-libdir
StartedAt: 2024-12-20 12:08:21 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 12:09:02 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 40.2 seconds
RetCode: 0
Status:   OK  
PackageFile: CNORode_1.48.0.tgz
PackageFileSize: 451.8 KiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf CNORode.buildbin-libdir && mkdir CNORode.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CNORode_1.48.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R CNORode.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=CNORode.buildbin-libdir CNORode_1.48.0.tar.gz'
>>>>>>> 

* installing *source* package ‘CNORode’ ...
** 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   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c FG_transfer_function.c -o FG_transfer_function.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c cvodea_io.c -o cvodea_io.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c cvodes_band.c -o cvodes_band.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c cvodes_bandpre.c -o cvodes_bandpre.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c cvodes_bbdpre.c -o cvodes_bbdpre.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c cvodes_dense.c -o cvodes_dense.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c cvodes_diag.c -o cvodes_diag.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c cvodes_direct.c -o cvodes_direct.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c cvodes_io.c -o cvodes_io.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c cvodes_spbcgs.c -o cvodes_spbcgs.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c cvodes_spgmr.c -o cvodes_spgmr.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c cvodes_spils.c -o cvodes_spils.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c cvodes_sptfqmr.c -o cvodes_sptfqmr.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c decimal2binary.c -o decimal2binary.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c findStates.c -o findStates.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c fnvector_serial.c -o fnvector_serial.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c getAdjacencyMatrix.c -o getAdjacencyMatrix.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c getNumBits.c -o getNumBits.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c getNumInputs.c -o getNumInputs.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c getStateIndex.c -o getStateIndex.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c getTruthTables.c -o getTruthTables.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c get_count_bits.c -o get_count_bits.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c get_input_index.c -o get_input_index.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c get_support_truth_tables.c -o get_support_truth_tables.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c get_truth_tables_index.c -o get_truth_tables_index.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c hill_function.c -o hill_function.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c linear_transfer_function.c -o linear_transfer_function.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c normHill.c -o normHill.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c normHill_mod.c -o normHill_mod.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c nvector_serial.c -o nvector_serial.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c printAdjMat.c -o printAdjMat.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c printInterMat.c -o printInterMat.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c printNminiTerms.c -o printNminiTerms.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c printTruthTables.c -o printTruthTables.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c rhsODE.c -o rhsODE.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c sim_logic_ode.c -o sim_logic_ode.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c sundials_band.c -o sundials_band.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c sundials_dense.c -o sundials_dense.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c sundials_direct.c -o sundials_direct.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c sundials_iterative.c -o sundials_iterative.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c sundials_math.c -o sundials_math.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c sundials_nvector.c -o sundials_nvector.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c sundials_spbcgs.c -o sundials_spbcgs.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c sundials_spgmr.c -o sundials_spgmr.o
sundials_spgmr.c:439:29: warning: variable 'yg' set but not used [-Wunused-but-set-variable]
  realtype **Hes, *givens, *yg;
                            ^
sundials_spgmr.c:439:20: warning: variable 'givens' set but not used [-Wunused-but-set-variable]
  realtype **Hes, *givens, *yg;
                   ^
2 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c sundials_sptfqmr.c -o sundials_sptfqmr.o
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 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
installing to /Users/biocbuild/bbs-3.20-bioc/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 PATHS TO DYNAMIC LIBRARIES FOR CNORode.buildbin-libdir/CNORode/libs/CNORode.so
>>>>>>> 

>>>>>>> Paths before fix:
CNORode.buildbin-libdir/CNORode/libs/CNORode.so:
	CNORode.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 4.4.2)
	/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)

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

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