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PoonLab / Kaphi

Kernel-embedded ABC-SMC for phylodynamic inference
GNU Affero General Public License v3.0
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make configure.ac script #135

Open ArtPoon opened 6 years ago

ArtPoon commented 6 years ago

On master branch, when running R CMD INSTALL pkg I get the following error:

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 blank.o dQAL-6.3.o kernel.o newick_lexer.o newick_parser.o tree.o treekernel.o treestats.o util.o -Ligraph/src/.libs -ligraph -L/usr/local/lib -lgsl -lJudy -lgmp -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: library not found for -lgmp

I've used MacPorts to install libgmp and modified LD_LIBRARY_PATH to include the path to this library, but haven't been able to fix this problem yet.

ArtPoon commented 6 years ago

Needed to go into src/Makevars and change -L/usr/local/lib to -L/opt/local/lib.
We need to add a configure.ac script to generate platform-specific Makevars files.

ArtPoon commented 5 years ago

do we still need libgmp?