Re: Patch for cd-hit and source for documentation
Hi Limin,
thanks for considering the Debian patches and keeping me informed about
the new release. I have some further hints for you that I came across
when building the Debian package:
1. Enable hardening flags
Debian tries to support some security hardening features which will be
enabled by setting some specific compiler options[1]. To support this
the Makefile needs to propagate those options but unfortunately yours is
not doing this. If you apply the patch available from
http://anonscm.debian.org/viewvc/debian-med/trunk/packages/cd-hit/trunk/debian/patches/use-dpkg-buildflags.patch?view=markup
this could be done smoothly.
2. Use MPI
The Debian package is now builded using "openmp=yes" - I hope you like
this.
3. Manpages
Debian tries to provide manpages for every program in /usr/bin. I'm
using help2man in the build process of the package to get the best out
of the executables from their usage advises. You can see the commands
I'm using in the debian/rules file[2]. When doing so I detected some
errors in Perl scripts. I was able to fix some minor ones and you can
find a patch here:
http://anonscm.debian.org/viewvc/debian-med/trunk/packages/cd-hit/trunk/debian/patches/enable_help2man.patch?view=markup
However I stumbled about more serious things I would like you to
consider checking. For instance if you would
use strict;
in psi-cd-hit.pl this would result in:
$ ./psi-cd-hit.pl
Global symbol "$restart_in" requires explicit package name at ./psi-cd-hit.pl line 32.
Global symbol "$restart_in" requires explicit package name at ./psi-cd-hit.pl line 39.
Global symbol "$host_no" requires explicit package name at ./psi-cd-hit.pl line 44.
Global symbol "$bl_dir" requires explicit package name at ./psi-cd-hit.pl line 44.
Global symbol "$bl_dir" requires explicit package name at ./psi-cd-hit.pl line 44.
Global symbol "$host_no" requires explicit package name at ./psi-cd-hit.pl line 45.
Global symbol "$print_db" requires explicit package name at ./psi-cd-hit.pl line 60.
Global symbol "$restart_seg" requires explicit package name at ./psi-cd-hit.pl line 64.
Global symbol "$reformat_seg" requires explicit package name at ./psi-cd-hit.pl line 67.
Global symbol "$print_db" requires explicit package name at ./psi-cd-hit.pl line 72.
Global symbol "$db_out" requires explicit package name at ./psi-cd-hit.pl line 73.
Global symbol "$db_out" requires explicit package name at ./psi-cd-hit.pl line 73.
Execution of ./psi-cd-hit.pl aborted due to compilation errors.
That's not good and you might like to consider fixing this. If you
would do so this would fix the
Name "main::.*" used only once:
errors when calling the script without any argument.
Finally I would like to say that it would be perfectly OK if you rather
would address your responses to debian-med@lists.debian.org than to me
in private. On one hand this increases your chances we will deal with
your message and you might also get more visibility for CD-HIT.
Kind regards and thanks for providing cd-hit as free software
Andreas.
[1] http://wiki.debian.org/Hardening
[2] http://anonscm.debian.org/viewvc/debian-med/trunk/packages/cd-hit/trunk/debian/rules?view=markup
On Wed, Apr 25, 2012 at 04:33:55PM -0700, Limin Fu wrote:
> I just made a new stable release (
> http://code.google.com/p/cdhit/downloads/list) which includes the fix from
> Andreas among a few other minor fixings and improvements. I also included
> the documentation files in the tarball (and the repository on googlecode).
>
> Limin
>
>
> On Wed, Apr 25, 2012 at 10:43 AM, Weizhong Li <liwz@sdsc.edu> wrote:
>
> >
> > Thank you Andreas for your email.
> >
> > We appreciate your efforts in helping cd-hit package. We will apply the
> > patch in our future releases.
> >
> > I am sorry that I forgot about LaTex document, will fix it.
> >
> > Thnaks again,
> > Weizhong,
> >
--
http://fam-tille.de
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