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tjunier / newick_utils

shell tools for processing phylogenetic trees
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Compilation error #30

Open cmfield opened 2 years ago

cmfield commented 2 years ago

I am attempting to build the software within our easybuild system with GCC 10.2.0, CMake 3.18.4 and I get this error at the make step:

ld.gold: error: CMakeFiles/nw_ed.dir/address_parser.c.o: multiple definition of 'address_parser_status'

I'm not sure what I'm doing wrong.. compiling without libxml or lua in case that matters..

zwets commented 2 years ago

This is fixed by commit df19bf28d83f15a343e9f6d2777230061b3e969a in PR #31

cmfield commented 2 years ago

This changes the error:

CMakeFiles/nw_ed.dir/tree_editor.c.o:tree_editor.c:function main: error: undefined reference to 'address_parser_status' CMakeFiles/nw_ed.dir/address_parser.c.o:address_parser.c:function adsparse: error: undefined reference to 'address_parser_status'

hinz1 commented 5 months ago

Same here. Did you ever get it to compile...?

giacomomutti commented 4 months ago

After struggling I found a solution using the same compilation as the bioconda recipe. 

wget https://github.com/tjunier/newick_utils/archive/da121155a977197cab9fbb15953ca1b40b11eb87.tar.gz -O newick_utils.tar.gz
tar zxvf newick_utils.tar.gz 
cd newick_utils-da121155a977197cab9fbb15953ca1b40b11eb87/
export CFLAGS="${CFLAGS} -fcommon"
export CXXFLAGS="${CXXFLAGS} -fcommon"
autoreconf -fi
./configure  --without-guile --without-lua --with-libxml
make

If you dont use the -fcommon flags it fails. I managed with gcc 13.2 and make 4.3