[Debian-med-packaging] Patches for sift 4.0.3b-2

[Laszlo Kajan]

Dear Michael!

Thank you very much for the patches! I have a lot of teaching to do this semester - I apologize for the late answer.

I've incorporated your patches to Debian version 4.0.3b-3 (now uploaded), you'll find them here:

 http://anonscm.debian.org/viewvc/debian-med/trunk/packages/sift/trunk/debian/patches/

I managed to fix the remaining issue with the gcc format warning:

--- a/src/Psiblast.c
+++ b/src/Psiblast.c
@@ -95,7 +95,7 @@
         fgets (Buffer, LARGE_BUFF_LENGTH, fp); /* get blank line */
         fgets (Buffer, LARGE_BUFF_LENGTH, fp); /* get first line */;
         get_start_pos = TRUE;
-        while (Buffer != "\n") {
+        while ( strcmp( Buffer, "\n" ) != 0 ) {
                 read_4_alignment_lines (Buffer, alignment, fp, get_start_pos);
                 get_start_pos = FALSE; /* read 1rst 4 alignment lines*/
                                         /* already got the starting pos*/


I appreciate your help with this package very much.

Best regards,

Laszlo

On 17/05/12 14:50, Michael Bienia wrote:
> Hi again,
> 
> found another issue: the package compiles nicely the source in src/ into
> binaries, installs them to and then replaces it with the pre-compiled
> ones from bin :( (the dh_install call for bin/).
> This "works" for amd64 builds as the pre-compiled binaries are x86-64
> ones but fails for i386 as dpkg-shlibs can't find the packages for the
> needed libraries (that's how I noticed this).
> 
> To be sure that they don't end in the binary anymore, I've removed them
> in the clean target.
> 
> Regards,
> Michael
> 
> diff -Nru sift-4.0.3b/debian/rules sift-4.0.3b/debian/rules
> --- sift-4.0.3b/debian/rules	2012-02-27 19:13:37.000000000 +0100
> +++ sift-4.0.3b/debian/rules	2012-05-17 14:31:38.000000000 +0200
> @@ -27,6 +27,15 @@
>  override_dh_auto_clean:
>  	if [ -e src/Makefile ]; then make -j$(parallel) -C src prefix=$(prefix) distclean; fi
>  	rm -f $(MAN1)
> +	# remove pre-compiled binaries from bin
> +	rm -f bin/choose_seqs_via_psiblastseedmedian
> +	rm -f bin/clump_output_alignedseq
> +	rm -f bin/consensus_to_seq
> +	rm -f bin/fastaseqs
> +	rm -f bin/info_on_seqs
> +	rm -f bin/process_alignment
> +	rm -f bin/psiblast_res_to_fasta_dbpairwise
> +	rm -f bin/seqs_from_psiblast_res
>  
>  override_dh_auto_build: man
>  	make -j$(parallel) -C src prefix=$(prefix) VERSION=$(VERSION) deps.mk && \