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BDI-pathogens / phyloscanner

Phylogenetics between and within hosts at once, all along the genome.
GNU General Public License v3.0
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Couldn't compile software using "make" command #74

Closed manisenthils closed 1 year ago

manisenthils commented 1 year ago

Hello people, I have been downloading and installing all the necessary tools and software one by one using the Phyloscanner installation notes. Now I got an error in the "make" command. I tried solving it by searching for "nadd '' variable in several files. And tried exporting it and deleting that line manually but nothing got me out of this!!! I pasted the error bellow . I hope someone can give me the solution!

/usr/include/features.h:194:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 194 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~ gcc -o makedirectionlist mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o MSalignmm.o makedirectionlist.o defs.o fft.o fftFunctions.o addfunctions.o -Denablemultithread -std=c99 -O3 -lm -lpthread /usr/bin/ld: defs.o:(.bss+0x4): multiple definition of `nadd'; makedirectionlist.o:(.bss+0x10): first defined here collect2: error: ld returned 1 exit status make: *** [Makefile:203: makedirectionlist] Error 1

ChrisHIV commented 1 year ago

Now I got an error in the "make" command

For which software? (Note that installing each separate piece of software that phyloscanner requires is not the same as 'installing phyloscanner'.) I haven't seen that error before. If googling it doesn't help you, perhaps the authors of whichever software you are trying to make can advise.