Re: How to deal with clapack - is it (or a replacement) packaged
Hi Ghislain,
On Wed, Apr 20, 2016 at 09:35:32PM +0100, Ghislain Vaillant wrote:
> You should be able to use the packaged lapacke instead of clapack.
>
> Both should respect the same LAPACK API.
I somehow brute forced a patch
--- a/include/external_libs.h
+++ b/include/external_libs.h
@@ -39,8 +39,8 @@
#else
#ifndef SKIP_LAPACK
-#include <f2c.h>
-#include <clapack.h>
+/* #include <f2c.h> */
+#include <lapacke.h>
#define LAPACK_INT integer
#define LAPACK_DOUBLE doublereal
#endif /*ifndef SKIP_LAPACK */
into the preliminary packaging which is now available in Git[1] but its
probably not that simple since
./munge-help.sh consEntropy.help_src > consEntropy.help
gcc -O3 -Wall -I/build/phast-1.4/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4/src/util/../..\" -I/build/phast-1.4/src/util/../../src/lib/pcre -fno-strict-al
In file included from /build/phast-1.4/src/util/../../include/vector.h:19:0,
from /build/phast-1.4/src/util/../../include/matrix.h:18,
from /build/phast-1.4/src/util/../../include/misc.h:21,
from indelHistory.c:15:
/build/phast-1.4/src/util/../../include/external_libs.h:45:23: error: unknown type name 'doublereal'
#define LAPACK_DOUBLE doublereal
^
/build/phast-1.4/src/util/../../include/matrix.h:348:31: note: in expansion of macro 'LAPACK_DOUBLE'
void mat_to_lapack(Matrix *m, LAPACK_DOUBLE *arr);
^
/build/phast-1.4/src/util/../../include/external_libs.h:45:23: error: unknown type name 'doublereal'
#define LAPACK_DOUBLE doublereal
^
/build/phast-1.4/src/util/../../include/matrix.h:355:33: note: in expansion of macro 'LAPACK_DOUBLE'
void mat_from_lapack(Matrix *m, LAPACK_DOUBLE *arr);
^
Makefile:17: recipe for target 'indelHistory.o' failed
So I wonder whether it is harder to adapt the code or rather package
clapack. Upstream is in CC - may be someone might try to explain the
advantage of lapacke over clapack.
Kind regards
Andreas.
> On 20/04/16 20:50, Andreas Tille wrote:
> >Hi folks,
> >
> >I wonder whether somebody has dealt with CLAPACK. A search via
> >
> > apt-file search clapack
> >
> >uncovers some clapack.h but it seems I need to package this first.
> >
> >Any hint would be welcome before I start with this.
> >
> >Kind regards
> >
> > Andreas.
> >
> >----- Forwarded message from "Ramani, Ritika" <rramani@cshl.edu> -----
> >
> >Date: Wed, 20 Apr 2016 18:50:09 +0000
> >From: "Ramani, Ritika" <rramani@cshl.edu>
> >To: Andreas Tille <andreas@an3as.eu>
> >CC: PhastHelp <phasthelp@cshl.edu>, Debian Med Project List <debian-med@lists.debian.org>
> >Subject: RE: Please provide release tags for Phast on Github and may be you could uncover Debian packaging code
> >
> >Hey Andreas,
> >CLAPACK is different from the Lapack package you mention. Clapack provides LAPACK for non Fortran compilers using f2c. - http://www.netlib.org/clapack/
> >Thanks!
> >Ritika
> >
> >________________________________________
> >From: Andreas Tille [andreas@an3as.eu]
> >Sent: Wednesday, April 20, 2016 2:11 PM
> >To: Ramani, Ritika
> >Cc: PhastHelp; Debian Med Project List
> >Subject: Re: Please provide release tags for Phast on Github and may be you could uncover Debian packaging code
> >
> >Hi Ritika,
> >
> >On Wed, Apr 20, 2016 at 05:40:45PM +0000, Ramani, Ritika wrote:
> >>Hello Andreas,
> >>Thank you so much for your message.
> >
> >Thanks a lot for your quick response.
> >
> >>I have tagged the releases on Github. Our last released version was v1.3 in March 2013. But we are planning on releasing a new version soon. I have tagged this version as pre-release v1.4 on Github so you can use that for the Debian mirror.
> >
> >Thanks for the tagging and the information about the new version.
> >
> >>We do have the source tarball for v1.3 available on the phast website if you select the source option. Here is the link to download the source for v1.3 - http://compgen.cshl.edu/phast/downloads/phast.v1_3.tgz
> >
> >Fine. May be it was just me. The tagging on Github is perfectly
> >sufficient anyway.
> >
> >>I had used the same v1.3 source code to package into debian with CLAPACK.
> >>
> >>How do you plan to add phast to the mirror considering it has the CLAPACK dependency?
> >
> >Debian has the liblapacke-dev[1]. Is this any difference to CLAPACK? If
> >yes we need to package CLAPACK first. I have not yet investigated into
> >this question.
> >
> >>Let me know if you need any more information.
> >
> >Thanks, I'll do.
> >
> >Kind regards
> >
> > Andreas.
> >
> >
> >[1] http://www.netlib.org/lapack/
> >
> >--
> >http://fam-tille.de
> >
> >
> >----- End forwarded message -----
> >
>
>
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http://fam-tille.de
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