In function `print_usage': nw_cmdline.c undefined reference to `string_buff_strlen'

[tseemann]

This is bash install.sh result now:

for file in ; do rm -r $file; done
for file in ; do rm $file; done
gcc -o needleman_wunsch -O3 -DCOMPILE_TIME='"Thu Mar 24 22:43:30 AEDT 2016"' -DSCORE_TYPE='int' -Wall \
-I . -I ./libs/utility_lib -I ./libs/string_buffer \
-I ./libs/bioinf -I ./libs/alignment_scoring \
nw_cmdline.c needleman_wunsch.c \
./libs/alignment_scoring/*.c ./libs/utility_lib/utility_lib.c \
./libs/bioinf/bioinf.c ./libs/string_buffer/string_buffer.c -lz
In file included from nw_cmdline.c:32:0:
./libs/string_buffer/string_buffer.h:93:13: warning: inline function 'string_buff_set_char' declared but never defined
 inline void string_buff_set_char(STRING_BUFFER *sbuf, const t_buf_pos index,
             ^
<snip>
mp/ccuBmjhi.o: In function `print_usage':
nw_cmdline.c:(.text+0xce): undefined reference to `string_buff_strlen'
/tmp/ccuBmjhi.o: In function `align_from_file':
nw_cmdline.c:(.text+0x679): undefined reference to `string_buff_strlen'
nw_cmdline.c:(.text+0x69c): undefined reference to `string_buff_strlen'
/tmp/cceFyvb3.o: In function `read_fastq_entry':
bioinf.c:(.text+0x3ec): undefined reference to `string_buff_strlen'
bioinf.c:(.text+0x434): undefined reference to `string_buff_strlen'
bioinf.c:(.text+0x4c2): undefined reference to `string_buff_get_char'
bioinf.c:(.text+0x516): undefined reference to `string_buff_strlen'
bioinf.c:(.text+0x521): undefined reference to `string_buff_strlen'
/tmp/cceFyvb3.o: In function `read_fasta_entry':
bioinf.c:(.text+0x6c4): undefined reference to `string_buff_strlen'
bioinf.c:(.text+0x704): undefined reference to `string_buff_strlen'
/tmp/cceFyvb3.o: In function `seq_file_read':
bioinf.c:(.text+0x8cc): undefined reference to `string_buff_strlen'
collect2: error: ld returned 1 exit status
Makefile:25: recipe for target 'all' failed
make: *** [all] Error 1

[tseemann]

You have 2 string_buffer folders in your repo - one in /lib and one below needleman_wunch.

The second one is incomplete.

And they are both out of date and potentially violate GCC rules about static and inline.

[iqbal-lab]

OOut of date is deliberate. Isaac broke the API compatibility at some point and it would need a lot of upstream changes. An update is on the timeline, it's a bit of a pain there's no way to have one (dev ) branch using one commit, and the master continuing on the old commit til the dev is tested and ready for merge

[iqbal-lab]

I'll look into it

[abeu9727]

We are trying to install Cortex and encountering the same error. Has there been any progress for correcting the error?

[tseemann]

Ping @iqbal-lab