Question: Inability to install R package "sybilSBML"
0
gravatar for simone.moro.2
2.8 years ago by
simone.moro.20 wrote:

Hello,

I can't install package sybilSBML in R, this is the error message that I get:

ERROR: loading failed * removing ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/sybilSBML’ Warning in install.packages : installation of package ‘sybilSBML’ had non-zero exit status

What do you think is the possible reason?

Thanks

R software error • 1.4k views
ADD COMMENTlink written 2.8 years ago by simone.moro.20
1

And the command you ran was?

ADD REPLYlink written 2.8 years ago by Jenez520

install.packages("sybilSBML")

ADD REPLYlink written 2.8 years ago by simone.moro.20
1

Presumably there was more to the error message further up when it was actually compiling stuff.

ADD REPLYlink written 2.8 years ago by Devon Ryan91k

This is the all report:

> install.packages("sybilSBML")
Package which is only available in source form, and may need compilation of C/C++/Fortran:
  ‘sybilSBML’
Do you want to attempt to install these from sources?
y/n: y
installing the source package ‘sybilSBML’


* installing *source* package ‘sybilSBML’ ...
** package ‘sybilSBML’ successfully unpacked and MD5 sums checked
checking for gcc... clang
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 accepts -g... yes
checking for clang option to accept ISO C89... none needed
checking how to run the C preprocessor... clang -E
checking for pkg-config... no
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... 
rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking sbml/SBMLTypes.h usability... yes
checking sbml/SBMLTypes.h presence... yes
checking for sbml/SBMLTypes.h... yes
checking for library containing readSBML... none required
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -I/usr/local/include -I/usr/include/sbml -I/usr/local/include/sbml -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c init.c -o init.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -I/usr/local/include -I/usr/include/sbml -I/usr/local/include/sbml -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c sbml.c -o sbml.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -I/usr/local/include -I/usr/include/sbml -I/usr/local/include/sbml -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c sybilSBML.c -o sybilSBML.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o sybilSBML.so init.o sbml.o sybilSBML.o -L/usr/local/lib -L/usr/lib -lsbml -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.2/Resources/library/sybilSBML/libs
** R
** inst
** preparing package for lazy loading
Warning: package ‘Matrix’ was built under R version 3.2.5
Warning: package ‘sybil’ was built under R version 3.2.5
Warning: package ‘lattice’ was built under R version 3.2.5
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: package ‘Matrix’ was built under R version 3.2.5
Warning: package ‘sybil’ was built under R version 3.2.5
Warning: package ‘lattice’ was built under R version 3.2.5
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/Library/Frameworks/R.framework/Versions/3.2/Resources/library/sybilSBML/libs/sybilSBML.so':
  dlopen(/Library/Frameworks/R.framework/Versions/3.2/Resources/library/sybilSBML/libs/sybilSBML.so, 6): Library not loaded: /Users/fbergmann/Development/libsbml/build/lib/libsbml.5.dylib
  Referenced from: /Library/Frameworks/R.framework/Versions/3.2/Resources/library/sybilSBML/libs/sybilSBML.so
  Reason: image not found
Errore: loading failed
Execution interrupted
ERROR: loading failed
* removing ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/sybilSBML’
Warning in install.packages :
  installation of package ‘sybilSBML’ had non-zero exit status

The downloaded source packages are in
‘/private/var/folders/sr/3jkht91d67g5vcqnnhfjn3lr0000gn/T/RtmpiExNBC/downloaded_packages’
ADD REPLYlink modified 2.8 years ago by Devon Ryan91k • written 2.8 years ago by simone.moro.20

Did you delete /Users/fbergmann/Development/libsbml/build/lib/libsbml.5.dylib?

ADD REPLYlink written 2.8 years ago by Devon Ryan91k

Have you installed LibSBML? From the quick start guide:

The package sybilSBML depends on a working installation of LibSBML [Bornstein et al., 2008] available from the SBML homepage (in particular libraries and header files). See INSTALL for installation instructions and platform specific details.

ADD REPLYlink written 2.8 years ago by Neilfws48k
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