'non-zero exit status' upon installing in R studio Mac

[Calvin2077]

Hello and good day,

I am trying to install Cobrar into my R studio on My Mac M1 using

install.packages("remotes")
library(remotes)
remotes::install_github("Waschina/cobrar")

However I am getting a massive error message which despite me trying I cannot solve thus if I can have some help it would mean a lot!

Downloading GitHub repo Waschina/cobrar@HEAD
── R CMD build ──────────────────────────────────────────────────────────────────────────────────────────────────────
✔  checking for file ‘/private/var/folders/bj/gpwqmjsj6c1bwfknb93mxtf00000gn/T/RtmpHmALia/remotes8d43263d1ee1/Waschina-cobrar-2b0becf/DESCRIPTION’ ...
─  preparing ‘cobrar’:
✔  checking DESCRIPTION meta-information ...
─  cleaning src
─  running ‘cleanup’
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘cobrar_0.1.1.tar.gz’
   
* installing *source* package ‘cobrar’ ...
** using staged installation
checking for pkg-config... /opt/homebrew/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for gcc... clang -arch arm64
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether clang -arch arm64 accepts -g... yes
checking for clang -arch arm64 option to accept ISO C89... none needed
checking for LIBSBML... yes
checking for glp_version in -lglpk... no
checking for __gmpz_init in -lgmp... no
libsbml found: -I/usr/local/Cellar/libsbml/5.20.4/include -L/usr/local/Cellar/libsbml/5.20.4/lib -lsbml
glpk found: -I/opt/homebrew/Cellar/GLPK/5.0/include -L/opt/homebrew/Cellar/glpk/5.0/lib -lglpk
gmp found: -I/opt/homebrew/Cellar/GMP/6.2.1_1/include -L/opt/homebrew/Cellar/gmp/6.2.1_1/lib -lgmp
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.3.9.4)’
using SDK: ‘MacOSX14.4.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include    -I/usr/local/Cellar/libsbml/5.20.4/include -I/opt/homebrew/Cellar/GLPK/5.0/include -I/opt/homebrew/Cellar/GMP/6.2.1_1/include -fPIC  -falign-functions=64 -Wall -g -O2   -c GLPK.cpp -o GLPK.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include    -I/usr/local/Cellar/libsbml/5.20.4/include -I/opt/homebrew/Cellar/GLPK/5.0/include -I/opt/homebrew/Cellar/GMP/6.2.1_1/include -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include    -I/usr/local/Cellar/libsbml/5.20.4/include -I/opt/homebrew/Cellar/GLPK/5.0/include -I/opt/homebrew/Cellar/GMP/6.2.1_1/include -fPIC  -falign-functions=64 -Wall -g -O2   -c SBML.cpp -o SBML.o
In file included from SBML.cpp:5:
In file included from /usr/local/Cellar/libsbml/5.20.4/include/sbml/SBMLTypes.h:48:
In file included from /usr/local/Cellar/libsbml/5.20.4/include/sbml/SBMLDocument.h:305:
/usr/local/Cellar/libsbml/5.20.4/include/sbml/SBMLErrorLog.h:298:8: warning: 'SBMLErrorLog::add' hides overloaded virtual functions [-Woverloaded-virtual]
  void add (const SBMLError& error);
       ^
/usr/local/Cellar/libsbml/5.20.4/include/sbml/xml/XMLErrorLog.h:200:16: note: hidden overloaded virtual function 'XMLErrorLog::add' declared here: type mismatch at 1st parameter ('const std::list<XMLError> &' vs 'const SBMLError &')
  virtual void add (const std::list<XMLError>& errors);
               ^
/usr/local/Cellar/libsbml/5.20.4/include/sbml/xml/XMLErrorLog.h:211:16: note: hidden overloaded virtual function 'XMLErrorLog::add' declared here: type mismatch at 1st parameter ('const std::vector<XMLError *> &' vs 'const SBMLError &')
  virtual void add (const std::vector<XMLError*>& errors);
               ^
In file included from SBML.cpp:5:
In file included from /usr/local/Cellar/libsbml/5.20.4/include/sbml/SBMLTypes.h:48:
In file included from /usr/local/Cellar/libsbml/5.20.4/include/sbml/SBMLDocument.h:305:
/usr/local/Cellar/libsbml/5.20.4/include/sbml/SBMLErrorLog.h:317:8: warning: 'SBMLErrorLog::add' hides overloaded virtual functions [-Woverloaded-virtual]
  void add (const std::list<SBMLError>& errors);
       ^
/usr/local/Cellar/libsbml/5.20.4/include/sbml/xml/XMLErrorLog.h:200:16: note: hidden overloaded virtual function 'XMLErrorLog::add' declared here: type mismatch at 1st parameter ('const std::list<XMLError> &' vs 'const std::list<SBMLError> &')
  virtual void add (const std::list<XMLError>& errors);
               ^
/usr/local/Cellar/libsbml/5.20.4/include/sbml/xml/XMLErrorLog.h:211:16: note: hidden overloaded virtual function 'XMLErrorLog::add' declared here: type mismatch at 1st parameter ('const std::vector<XMLError *> &' vs 'const std::list<SBMLError> &')
  virtual void add (const std::vector<XMLError*>& errors);
               ^
In file included from SBML.cpp:5:
In file included from /usr/local/Cellar/libsbml/5.20.4/include/sbml/SBMLTypes.h:48:
In file included from /usr/local/Cellar/libsbml/5.20.4/include/sbml/SBMLDocument.h:305:
/usr/local/Cellar/libsbml/5.20.4/include/sbml/SBMLErrorLog.h:326:8: warning: 'SBMLErrorLog::add' hides overloaded virtual functions [-Woverloaded-virtual]
  void add (const std::vector<SBMLError>& errors);
       ^
/usr/local/Cellar/libsbml/5.20.4/include/sbml/xml/XMLErrorLog.h:200:16: note: hidden overloaded virtual function 'XMLErrorLog::add' declared here: type mismatch at 1st parameter ('const std::list<XMLError> &' vs 'const std::vector<SBMLError> &')
  virtual void add (const std::list<XMLError>& errors);
               ^
/usr/local/Cellar/libsbml/5.20.4/include/sbml/xml/XMLErrorLog.h:211:16: note: hidden overloaded virtual function 'XMLErrorLog::add' declared here: type mismatch at 1st parameter ('const std::vector<XMLError *> &' vs 'const std::vector<SBMLError> &')
  virtual void add (const std::vector<XMLError*>& errors);
               ^
3 warnings generated.
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 cobrar.so GLPK.o RcppExports.o SBML.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/homebrew/Cellar/gcc/12.2.0/lib/gcc/12 -L/opt/homebrew/Cellar/glpk/5.0/lib -lglpk -L/opt/homebrew/Cellar/gmp/6.2.1_1/lib -lgmp -L/usr/local/Cellar/libsbml/5.20.4/lib -lsbml -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: ignoring file '/usr/local/Cellar/libsbml/5.20.4/lib/libsbml.5.20.4.dylib': found architecture 'x86_64', required architecture 'arm64'
installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-cobrar/00new/cobrar/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘cobrar’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-cobrar/00new/cobrar/libs/cobrar.so':
  dlopen(/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-cobrar/00new/cobrar/libs/cobrar.so, 0x0006): symbol not found in flat namespace '_BiolQualifierType_fromString'
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/cobrar’
Warning: installation of package ‘/var/folders/bj/gpwqmjsj6c1bwfknb93mxtf00000gn/T//RtmpHmALia/file8d4376b65963/cobrar_0.1.1.tar.gz’ had non-zero exit status

[Waschina]

Hi @Calvin2077 ,

there seems to be an issue with the glpk installation. Which commands did you use to install the dependencies GLPK and LIBSBML?

A general comment: Please use code blocks when posting code and logs (I edited your comment above)

[Calvin2077]

Thank you for getting back to me and for editing my post (still very new at this)

To install GLPK and LIBSBML I entered in on my terminal app
brew install glpk brewsci/bio/libsbml

[Waschina]

I don't know what causes the issue. I will try to test the installation again on a MacOS when time allows.