BIONF / fDOG

Feature-aware Directed OrtholoG search
GNU General Public License v3.0
9 stars 3 forks source link

Cannot install FASTA36 #36

Closed bheimbu closed 11 months ago

bheimbu commented 11 months ago

Hello,

I'm having problems to install fDOG. See below for error message

$ fdog.setup -d $HOME/bin/fdog/
*** Creating local NCBI taxonomy database...
*** Installing dependencies...
=> Dependencies in /home/uni08/bheimbu/.local/lib/python3.9/site-packages/fdog/data/dependencies.txt already installed!
=> FASTA36 (https://github.com/wrpearson/fasta36)
Downloading https://github.com/wrpearson/fasta36/archive/refs/tags/v36.3.8h_04-May-2020.tar.gz
...-126156800%, 1 MB, 7856 KB/s, 0 seconds passed ... done!
Compiling fasta36. Please wait...
gcc -g -O -msse2  -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit  -DM10_CONS  -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP  -D_LARGEFILE64_SOURCE  -DBIG_LIB64 -DCOMP_THR -DCOMP_MLIB -c comp_lib9.c -o comp_mthr9.o
In file included from comp_lib9.c:43:0:
/opt/sw/rev/21.12/haswell/oneapi-2022.0.0/intel-20.0.4-bn2ws2/include/limits.h:37:54: Fehler: missing binary operator before token "("
     defined(__has_include_next) && __has_include_next(<limits.h>)
                                                      ^
comp_lib9.c: In Funktion »main«:
comp_lib9.c:913:17: Fehler: »FLT_MAX« nicht deklariert (erste Benutzung in dieser Funktion)
     zbestcut = -FLT_MAX;
                 ^
comp_lib9.c:913:17: Anmerkung: jeder nicht deklarierte Bezeichner wird nur einmal für jede Funktion, in der er vorkommt, gemeldet
comp_lib9.c: In Funktion »init_beststats«:
comp_lib9.c:3046:25: Fehler: »FLT_MIN« nicht deklariert (erste Benutzung in dieser Funktion)
   (*best)[0].rst.escore=FLT_MIN; /* for E()-values, lower is best */
                         ^
comp_lib9.c:3047:21: Fehler: »FLT_MAX« nicht deklariert (erste Benutzung in dieser Funktion)
   (*best)[0].zscore=FLT_MAX; /* for Z-scores, bigger is best */
                     ^
make: *** [comp_mthr9.o] Fehler 1
ERROR: Cannot install FASTA36!

before that I have done...

$ fas.setup -t ./ --check
Annotation tools can be found at /usr/users/bheimbu/annotation_tools. FAS is ready to run!
You should test fas.doAnno with this command:
==> fas.doAnno -i test_annofas.fa -o testFas_output <==

Any help is highly appreciated,

Bastian

bheimbu commented 11 months ago

Found the solution by myself, had to module load gcc. The 'base' compiler of our HPC is outdated.

Cheers Bastian