GitLab

On leca-34:

Running into this error at compilation:

build/temp.linux-x86_64-3.4/pyrex/obitools3/apps/progress.c: In function ‘__pyx_pf_9obitools3_4apps_8progress_11ProgressBar_2__call__’:
build/temp.linux-x86_64-3.4/pyrex/obitools3/apps/progress.c:1727:9: error: format not a string literal and no format arguments [-Werror=format-security]
         ((void)fprintf(stderr, __pyx_k__5));
         ^
cc1: some warnings being treated as errors
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1

On luke21 (ALL RESOLVED NOW but writing here to keep track):

1. The inline functions were not read properly and had to turn them into macros.

2. Then, when trying to run an obi command, ran into this error:

   obi import --fastq -d 'tdms' -v 'Import big fastq' '150529_SND405_A_L004_GWM-656.filtered.fastq'
   Traceback (most recent call last):
     File "/scratch_r730/home/cmercier/devel/obitools3/OBITools3-0.00.0/bin/obi", line 29, in <module>
       from obitools3.apps.config import getConfiguration     # @UnresolvedImport
     File "python/obitools3/apps/config.pyx", line 16, in init obitools3.apps.config (build/temp.linux-x86_64-3.5/pyrex/obitools3/apps/config.c:2477)
       from _curses import version
   ImportError: libncurses.so.5: cannot open shared object file: No such file or directory

   Fixed with this import: module load ncurses/5.9_gcc-4.6.2

3. Then had to add all C files in all *.cfiles Cython files.