Re: MOM: Probe
Hi,
On Sat, Aug 08, 2015 at 09:23:40AM +0430, Malihe Asemani wrote:
> Thank you Micheal for the proposed name :)
> What do you think Andreas? Is it OK now?
Besides the name I have checked your commits
...
cc -c autobondrot.c
cc -o probe probe.o dots.o abin.o readPDBrecs.o geom3d.o utility.o select.o parse.o atomprops.o stdconntable.o autobondrot.o -lm
readPDBrecs.o: In function `parseAtomNumber':
readPDBrecs.c:(.text+0x313): undefined reference to `hy36decode'
readPDBrecs.o: In function `parseResidueNumber':
readPDBrecs.c:(.text+0x346): undefined reference to `hy36decode'
collect2: error: ld returned 1 exit status
Makefile.linux:11: recipe for target 'probe' failed
...
When checking where this function is defined:
$ grep -R hy36decode
hybrid_36_c.c:/*! C port of the hy36encode() and hy36decode() functions in the
hybrid_36_c.c: const char* errmsg = hy36decode(width, "A1T5", 4, &result);
hybrid_36_c.c:hy36decode(unsigned width, const char* s, unsigned s_size, int* result)
hybrid_36_c.c: ie_range = "internal error hy36decode: integer value out of range.";
readPDBrecs.c: const char* errmsg = hy36decode(5, &line[6], 5, &atomno);
readPDBrecs.c: const char* errmsg = hy36decode(4, &line[22], 4, &resid);
hybrid_36_c.h:hy36decode(unsigned width, const char* s, unsigned s_size, int* result);
I think there is just hybrid_36_c.o missing in the list of linked object
files. (This is just an assumption - please try.)
You need to use
quilt new fix_build_issue.patch
quilt edit Makefile.linux
if this does not work please ask Michael - he previously confirmed that
he was able to build the program.
Hints for the rename:
I'd recommend to move the git repository on git.debian.org:/git/debian-med.
Please also look into the metadata of this repository to reflect the
changed name.
The renaming inside d/control and d/changelog should be clear.
The tricky part is that also the binary needs to be renamed since it is
taken in the Debian name space which you can check via
$ apt-file search /usr/bin/probe
mirmon: /usr/bin/probe
So providing the binary as /usr/bin/king-probe is probably also simple
but I recently implemented a method to keep the original binary name for
users who explicitly declare themselves as Debian Med users. You can
find an example in the plink package. Since this is also maintained in
SVN and you seem to have trouble to check this out I'd recommend to use
apt-get source plink
to have a look into the way how this is done.
Feel free to keep on asking in case something might remain unclear.
Kind regards
Andreas.
--
http://fam-tille.de
Reply to: