[Debian-med-packaging] Bug#848236: Remaining issue with gbrowse - any help (Was: Urgent call to BioPerl users (Was: Bug#848236: src:gbrowse: ...)
Fields, Christopher J
cjfields at illinois.edu
Mon Jan 16 00:42:47 UTC 2017
That’s great news Lincoln, fantastic!
chris
From: Lincoln Stein <lincoln.stein at gmail.com<mailto:lincoln.stein at gmail.com>>
Date: Sunday, January 15, 2017 at 3:25 PM
To: Andreas Tille <andreas at fam-tille.de<mailto:andreas at fam-tille.de>>
Cc: Scott Cain <scott at scottcain.net<mailto:scott at scottcain.net>>, "848236 at bugs.debian.org<mailto:848236 at bugs.debian.org>" <848236 at bugs.debian.org<mailto:848236 at bugs.debian.org>>, Chris Fields <cjfields at illinois.edu<mailto:cjfields at illinois.edu>>, Debian Med Project List <debian-med at lists.debian.org<mailto:debian-med at lists.debian.org>>, Charles Plessy <charles at plessy.org<mailto:charles at plessy.org>>, Olivier Sallou <olivier.sallou at irisa.fr<mailto:olivier.sallou at irisa.fr>>, Sascha Steinbiss <satta at debian.org<mailto:satta at debian.org>>, Carnë Draug <carandraug+dev at gmail.com<mailto:carandraug+dev at gmail.com>>
Subject: Re: Remaining issue with gbrowse - any help (Was: Urgent call to BioPerl users (Was: Bug#848236: src:gbrowse: ...)
Hi,
The bug in the memory adaptor that Scott found turns out to have been from using the old perl 1.6.9 installed by the Debian package. Updating to 1.7.1 (1.007001) fixes the problem.
I have merged all GBrowse changes into git version 2.56 and have made a CPAN release. I think you can go ahead and package it.
Lincoln
On Thu, Jan 12, 2017 at 11:37 PM, Andreas Tille <andreas at fam-tille.de<mailto:andreas at fam-tille.de>> wrote:
Thanks to you both. I think the only question targeted directly at my
was the "how much time question": On Februrar 5 is full freeze. You
need to cut 10 days from this since a package has a 10 day migration
time until it makes it from unstable to the release candidates in
testing. So this would make 2017-01-25 - but if there is a single (even
unrelated to gbrowse) issue that might prevent the migration gbrowse is
doomed. So I'd recommend to get something out until beginning of next
week.
Kind regards
Andreas.
On Thu, Jan 12, 2017 at 02:23:42PM -0500, Scott Cain wrote:
> I made a few changes in a branch off that security-bug-fixes branch that
> quieted several warning messages, though I still need to sort out at least
> one problem (the memory adaptor doesn't seem to be reading fasta files, but
> also doesn't emit a warning about a problem). Lincoln, if you want to look
> at this pull request, you could pull those changes into the security bug
> fix branch:
>
> https://github.com/GMOD/GBrowse/pull/59<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_GMOD_GBrowse_pull_59&d=DwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=2cLlU7FOZAQeYfnsvzIC5kmMFA3W1qju00t4ePCEY_M&s=MRYHErWK47BZKLu5X5Zja0-5WQgLMmD7d7YvnXf0p2c&e=>
>
> Scott
>
>
> On Thu, Jan 12, 2017 at 1:57 PM, Lincoln Stein <lincoln.stein at gmail.com<mailto:lincoln.stein at gmail.com>>
> wrote:
>
> > Hi Andreas,
> >
> > I was able to remove the vast majority of the warnings and other
> > incompatibility issues, but need to do more testing to identify areas of
> > the code that were not covered. How much time do I have? If you want to go
> > with a fully functional version that may issue warnings when the user takes
> > certain rare actions, it is the "security-bug-fixes" branch at
> > https://github.com/GMOD/GBrowse<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_GMOD_GBrowse&d=DwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=2cLlU7FOZAQeYfnsvzIC5kmMFA3W1qju00t4ePCEY_M&s=k8qhFQlbBsMMPYcq1symbVU2QqCdO8CadJ4_x2ffWaE&e=>
> >
> > Lincoln
> >
> > On Thu, Jan 12, 2017 at 1:39 PM, Andreas Tille <andreas at an3as.eu<mailto:andreas at an3as.eu>> wrote:
> >
> >> Hi Lincoln,
> >>
> >> On Wed, Dec 21, 2016 at 06:25:46PM -0500, Lincoln Stein wrote:
> >> > I am devoting several days over the Christmas holidays to fixing the
> >> > various outstanding bugs in gbrowse. Stay tuned!
> >>
> >> Did you managed to managed to work on this? If not we probably can not
> >> include gbrowse in the next Debian stable release which would be a
> >> shame.
> >>
> >> Kind regards
> >>
> >> Andreas.
> >>
> >> --
> >> http://fam-tille.de<https://urldefense.proofpoint.com/v2/url?u=http-3A__fam-2Dtille.de&d=DwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=2cLlU7FOZAQeYfnsvzIC5kmMFA3W1qju00t4ePCEY_M&s=TQQSNkmnOUGCcyYl2u8qy3cyXjn6xWm6i8Dkk95cWGs&e=>
> >>
> >
> >
> >
> > --
> > *Lincoln Stein*
> >
> > Scientific Director (Interim), Ontario Institute for Cancer Research
> > Director, Informatics and Bio-computing Program, OICR
> > Senior Principal Investigator, OICR
> > Professor, Department of Molecular Genetics, University of Toronto
> >
> > <http://goog_1828306398<https://urldefense.proofpoint.com/v2/url?u=http-3A__goog-5F1828306398&d=DwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=2cLlU7FOZAQeYfnsvzIC5kmMFA3W1qju00t4ePCEY_M&s=s-FUwZzW_lF3fQ_9GJzd8mGyFqA3Lq05-XSK_fZORQ0&e=>>
> > *Ontario Institute for Cancer Research*
> > MaRS Centre
> > 661 University Avenue
> > Suite 510
> > Toronto, Ontario
> > Canada M5G 0A3
> >
> > Tel: 416-673-8514<tel:416-673-8514> <(416)%20673-8514>
> > Mobile: 416-817-8240<tel:416-817-8240> <(416)%20817-8240>
> > Email: lincoln.stein at gmail.com<mailto:lincoln.stein at gmail.com>
> > Toll-free: 1-866-678-6427<tel:1-866-678-6427> <(866)%20678-6427>
> > Twitter: @OICR_news
> >
> > *Executive Assistant*
> > *Frances Dirnbeck*
> > Tel: 647-259-4253<tel:647-259-4253> <(647)%20259-4253>
> > Email:frances.dirnbeck at oicr.on.ca<mailto:Email%3Afrances.dirnbeck at oicr.on.ca> <stacey.quinn at oicr.on.ca<mailto:stacey.quinn at oicr.on.ca>>
> > www.oicr.on.ca<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.oicr.on.ca&d=DwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=2cLlU7FOZAQeYfnsvzIC5kmMFA3W1qju00t4ePCEY_M&s=lAnUSPJ5MwR_fE48YxQd_76zWZxa5G2Rv9jGSgFmuOU&e=>
> >
> > This message and any attachments may contain confidential and/or
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> >
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D. scott at scottcain dot
> net
> GMOD Coordinator (http://gmod.org/<https://urldefense.proofpoint.com/v2/url?u=http-3A__gmod.org_&d=DwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=2cLlU7FOZAQeYfnsvzIC5kmMFA3W1qju00t4ePCEY_M&s=LbuoK2hvzPfJ7ELGZ3-bkGOJ4N0q5sKwEyLM-i-jn0Q&e=>) 216-392-3087<tel:216-392-3087>
> Ontario Institute for Cancer Research
--
http://fam-tille.de<https://urldefense.proofpoint.com/v2/url?u=http-3A__fam-2Dtille.de&d=DwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=2cLlU7FOZAQeYfnsvzIC5kmMFA3W1qju00t4ePCEY_M&s=TQQSNkmnOUGCcyYl2u8qy3cyXjn6xWm6i8Dkk95cWGs&e=>
--
Lincoln Stein
Scientific Director (Interim), Ontario Institute for Cancer Research
Director, Informatics and Bio-computing Program, OICR
Senior Principal Investigator, OICR
Professor, Department of Molecular Genetics, University of Toronto
<https://urldefense.proofpoint.com/v2/url?u=http-3A__goog-5F1828306398&d=DwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=2cLlU7FOZAQeYfnsvzIC5kmMFA3W1qju00t4ePCEY_M&s=s-FUwZzW_lF3fQ_9GJzd8mGyFqA3Lq05-XSK_fZORQ0&e=>
Ontario Institute for Cancer Research
MaRS Centre
661 University Avenue
Suite 510
Toronto, Ontario
Canada M5G 0A3
Tel: 416-673-8514
Mobile: 416-817-8240
Email: lincoln.stein at gmail.com<mailto:lincoln.stein at gmail.com>
Toll-free: 1-866-678-6427
Twitter: @OICR_news
Executive Assistant
Lisa Duncan
Tel: 647-260-7970<tel:(647)%20260-7970>
Email: lisa.duncan at oicr.on.ca<mailto:stacey.quinn at oicr.on.ca>
www.oicr.on.ca<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.oicr.on.ca&d=DwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=2cLlU7FOZAQeYfnsvzIC5kmMFA3W1qju00t4ePCEY_M&s=lAnUSPJ5MwR_fE48YxQd_76zWZxa5G2Rv9jGSgFmuOU&e=>
This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization.
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