PoonLab / Kaphi

Kernel-embedded ABC-SMC for phylodynamic inference
GNU Affero General Public License v3.0
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Can't compile igraph #10

Closed ArtPoon closed 7 years ago

ArtPoon commented 7 years ago

Current objective is to implement and call the kernel function from R:

Currently unable to compile code due to this error:

is2882:Kaphi art$ R CMD INSTALL pkg
* installing to library ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library’
* installing *source* package ‘Kaphi’ ...
** libs
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 Kaphi.so kernel.o newick_lexer.o newick_parser.o newick_parser.tab.o rinterface.o rinterface_extra.o tree.o treekernel.o treestats.o util.o -Ligraph/src -ligraph -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: library not found for -ligraph
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [Kaphi.so] Error 1
ERROR: compilation failed for package ‘Kaphi’
* removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Kaphi’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Kaphi’

There is no libigraph available in igraph subdirectory because I haven't been able to get it to compile.

ArtPoon commented 7 years ago

Duplicate of #3

ArtPoon commented 7 years ago

Static library was hiding out in .libs. Apparently it managed to build after all, just didn't specify the correct path in Makevars.

ArtPoon commented 7 years ago

However, make check tests all fail...