Hi Charles,
Small (but needed) correction: It’s CPAN, CRAN is for R.
I have both a new Bio-Graphics and a test BioPerl-Run up on CPAN, but it looks
like there was one additional missing dependency (DB_File) with Bio::Graphics,
which I am adding. There are some odd versioning issues with Bio:
BTW, [1] here was:
https://github.com/sanger-pathogens/Roary/issues/196
Cheers
Sascha
> On 17 Dec 2016, at 23:28, Sascha Steinbiss wrote:
>
> Hi all,
>
> thanks for checking these.
>
>>> roary
>>
>> Build, however when trying to simulate the test suite via
>>
>> cd t/data/genbank_gbff
>> ro
Hi all,
thanks for checking these.
>> roary
>
> Build, however when trying to simulate the test suite via
>
> cd t/data/genbank_gbff
> roary -f out *.gff
>
> Please cite Roary if you use any of the results it produces:
>Andrew J. Page, Carla A. Cummins, Martin Hunt, Vanessa K. Wong, San
Hi,
I checked all rdepends of BioPerl. In summary there are no real new
BioPerl related issues (Sascha, could you please check roary - see
below).
On Fri, Dec 16, 2016 at 01:06:35PM +0100, Andreas Tille wrote:
>
> $ apt-cache rdepends bioperl | grep "^ " | sort | uniq | grep -v -e
> alien-hunt
Hi all,
In the short term, I’m actually listed as co-maint on Bio-Graphics and
BioPerl-Run. I can work on a new release for BioPerl-Run that address those
specific issues (as well as other missing dependencies I found), but
Bio-Graphics has some additional versioning problems with CPAN that ne
Hello everybody, and thanks Carnë for the quick answer !
Le Fri, Dec 16, 2016 at 01:06:35PM +0100, Andreas Tille a écrit :
>
> On Fri, Dec 16, 2016 at 11:38:02AM +, Carnë Draug wrote:
>
> > For example, there is now
> > bio-biblio, bio-eutilities, and bio-coordinates which were previously pa
Hi Carnë,
On Fri, Dec 16, 2016 at 11:38:02AM +, Carnë Draug wrote:
> >> The cause is most probably that libbio-graphics-perl does not work
> >> together with bioperl 1.7.1 (see also #848105). I'm now becoming aware
> >> that with the naive upgrade to bioperl 1.7.1 we have triggered problems
>
On 16 December 2016 at 09:50, Andreas Tille wrote:
> On Thu, Dec 15, 2016 at 02:45:06PM +0100, Andreas Tille wrote:
>> Package: src:gbrowse
>> Severity: serious
>> Justification: FTBFS
>>
>> Hi,
>>
>> when trying to build gbrowse it fails to build from source:
>>
>> ...
>> CGI::param called in lis
Hi,
this is a very *urgent* call to all BioPerl users to raise their
opinion. To verify what else might be broken by the new BioPerl I
tested its rdepends. I stumbled upon bioperl-run which is making
heavy use of
/usr/share/perl5/Bio/Tools/Run/WrapperBase.pm
which is also removed from late
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