Hi,
I tried debuild -rfakeroot
but it still fails. I cannot build anymore the package.
dpkg-source -b ncbi-blast-2.2.25+-src
dpkg-source: info: using source format `3.0 (quilt)'
dpkg-source: warning: patches have not been applied, applying them now
(use --no-preparation to override)
hi,
after updating to your code, there is a compil (configure) error at
build time:
configure: error: Do not know how to build MT-safe with compiler
/usr/bin/g++
Maybe a missing dependency, do you have any idea?
Olivier
Le 5/29/11 6:12 PM, Aaron M. Ucko a écrit :
Olivier Sallou
That's a puzzling error; please send your c++/config.log, which should shed
more light on it. nbsp;Thanks!
-- Sent from my Palm Pre
On May 30, 2011 3:44, Olivier Sallou lt;olivier.sal...@irisa.frgt; wrote:
hi,
after updating to your code, there is a compil (configure) error at
build time:
Here is config.log
25+-src/c++$ cat config.log
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.
It was created by ncbi-tools++ configure 0.0, which was
generated by GNU Autoconf 2.59. Invocation command line was
$
It looks like you're trying to run the whole build under fakeroot, which is
unnecessary. nbsp;I can improve debian/rules to allow for that, but would
regardless recommend switching to debuild -rfakeroot.
Sorry you ran into trouble!
Olivier Sallou olivier.sal...@irisa.fr writes:
configure: error: Do not know how to build MT-safe with compiler
/usr/bin/g++
Updating debian/rules to r6893 should fix that, though I'd still
recommend using fakeroot only as needed (e.g., via debuild -rfakeroot).
Once again, thanks for pointing
since we are on the subject, i have been trying to compile ncbi-blast
on my own, for my own use. i would like to enable ever single one of
it's features; eg, UUIDs . or xalan. I cannot find any info on how to
activate UUIDs (it's not an option in ./configure --help) and I cannot
find the proper
Mai 2011 13:57:28
Objet: Re: blast+ packaging
since we are on the subject, i have been trying to compile ncbi-blast
on my own, for my own use. i would like to enable ever single one of
it's features; eg, UUIDs . or xalan. I cannot find any info on how to
activate UUIDs (it's not an option
-
De: George Marselis geo...@marsel.is
À: Debian Med Project List debian-med@lists.debian.org
Envoyé: Dimanche 29 Mai 2011 13:57:28
Objet: Re: blast+ packaging
since we are on the subject, i have been trying to compile ncbi-blast
on my own, for my own use. i would like to enable ever single one
Olivier Sallou olivier.sal...@irisa.fr writes:
please feel free to commit in my dir. It will indeed be easier than merging.
Done, thanks. I also threw in some improvements to the copyright file that
I'd meant to propose earlier:
* Remove the stanza for (c++/)scripts/projects/xmlwrapp/*, whose
Olivier Sallou olivier.sal...@irisa.fr writes:
for info I could make a few changes ot blast+ packaging:
Please don't let the length of this message alarm you; as I mentioned,
you're off to a great start, but there are plenty of details to packaging
anything well, and BLAST is no exception.
Olivier Sallou olivier.sal...@irisa.fr writes:
did you had time to look at ncbi-blast+ package before pushing it ?
I'm trying out your packaging now; although I will have some further
suggestions (detailed patch to follow later this week), I must say that
you've gotten off to a great start, and
Olivier Sallou olivier.sal...@irisa.fr writes:
did you had time to look at ncbi-blast+ package before pushing it ?
I'm terribly sorry, but I still haven't had time. Perhaps this weekend.
--
Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org)
http://www.mit.edu/~amu/ |
Hi,
for info I could make a few changes ot blast+ packaging:
- rename package to ncbi-blast+ (instead of -plus).
- create a ncbi-blast+-legacy which adds some scripts for legacy blast
that calls the blasT_legacy perl script to keep available previous
command line (shell scripts in
Hi,
thanks for your reviews.
I won't have time to progress in next 2 weeks.
I will refresh svn and have a look at this time
For boost, I did not know what was exactly required, I just saw that it was
required for compil.
For zlib etc... included in code, I think we should keep the copies
Olivier Sallou olivier.sal...@irisa.fr writes:
thanks for your reviews.
I won't have time to progress in next 2 weeks.
I will refresh svn and have a look at this time
No problem; I know how that goes.
I'd like to be as close as possible form original source code for maintenance
That's
Hi Olivier,
I'm having a look at the package now. I've pushed some changes to SVN
already - I hope you don't mind. To explain...
I don't think you need to repack the source in this case. The
guidelines say to rename the tarball file, but not to change the
contents unless there is a pressing
Tim Booth ava...@fastmail.fm writes:
I'm having a look at the package now. I've pushed some changes to SVN
already - I hope you don't mind. To explain...
Thanks for getting the review process started! I'll give more feedback
once I've had time to take a closer look at the packaging, but in
Hi Olivier,
On Wed, Apr 27, 2011 at 02:35:55PM +0200, Olivier Sallou wrote:
Has anyone started something? Or should I go for it ?
If you are brave enough to tackle this there are several people who
would be happy about this (and some other programs depend from it.
I would strongly advise to CC
Hi,
thanks for the info.
Regarding binaries size vs compiled from source, I know that by default,
compilation is done with debug enabled, and
increase size/lower performance.
For uscan I did not have a look yet, for the moment I will try to get
compilation done...
The legacy_blast.pl is given
Hello,
On 04/27/2011 02:35 PM, Olivier Sallou wrote:
I see in tasks the ncbi Blast+ software, not packaged.
Has anyone started something? Or should I go for it
packages/ncbi-tools-cxx
I once had a closer look at ... but then there was something
with the build the let me stop ... don't
Hi Olivier,
This was on my RADAR but I'm currently about to tackle AmplicoNoise
(must remember to file an ITP before I start...) so please go ahead. I
had a look at it at the sprint and this is what I found:
1) This may have been down to our rubbish wireless link but there
appeared to be
Tim Booth ava...@fastmail.fm writes:
1) This may have been down to our rubbish wireless link but there
appeared to be something stopping automated downloads (ie. Uscan) from
NCBI. I know they do have anti-leeching on some of their sites. Do you
get any problems?
This shouldn't be a
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