Finally, I found this which might be a suitable option:
metadata(BSgenome.Dmelanogaster.UCSC.dm3)$genome
>"dm3"
But happy to hear about alternatives.
Best,
Diego
On Sat, Jul 18, 2020 at 12:56 AM Diego Diez wrote:
>
> I found that the providerVersion method has been depre
: Fri Jun 26 18:49:17 2020 -0700
A couple of changes to GenomeDescription objects
- The GenomeDescription() constructor looses its 'provider_version'
argument.
- The providerVersion() accessor is now deprecated.
On Sat, Jul 18, 2020 at 12:46 AM Diego Diez wrote:
>
cs"
So it seems providerVersion has lost the BSgenome method. Is this an
intentional change or something that needs to be fixed?
Thank you.
Diego
On Thu, Jul 16, 2020 at 2:38 PM Diego Diez wrote:
>
> Dear all,
>
> I am finding an error when running the following code:
>
&
Dear all,
I am finding an error when running the following code:
> library(BSgenome.Dmelanogaster.UCSC.dm3)
Loading required package: BSgenome
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: rtracklayer
> dm3 <- BSgenome.Dmelanogaster.UCSC
Hi Nitesh,
Thank you for the explanation. Now everything is clear.
Best,
Diego
On Mon, Jul 10, 2017 at 10:55 PM, Turaga, Nitesh
wrote:
> Hi Diego,
>
> This is a good question.
>
> Please note, that when you do a 'git clone¹, you are getting the commit
> history of every branch, and master(trunk
Dear all,
Great to know that the git transition is moving forward. I tested
cloning (https) several packages and I noticed a significant
difference in the repository size between svn and git. Two examples
showing the output (svn/git) of du -k:
Biobase: 4968 / 8720
limma: 6284 / 20296
Looking bri
Hi Ramon,
My experience with this issue is that it requires reinstalling the
depending packages from source (but not ggplot2 itself).
Alternatively, this should be fixed (I think) once all dependent
packages are rebuilt with the newest ggplot2 installed. See this
related post in the ggtree package
Nice addition, thank you. Just want to note that now the 3.1 page says
"April 17, 2005". Thats a long time ago! I guess it means "April 17,
2015".
Diego
On Sat, Oct 17, 2015 at 3:30 AM, Hervé Pagès wrote:
> On 10/16/2015 10:52 AM, Dan Tenenbaum wrote:
>>
>>
>>
>> - Original Message -
>>>
git status
> 2210 vim DESCRIPTION
> 2211 git status
> 2212 git add *
> 2213 git status
> 2214 git rebase --continue
> 2215 git rebase --skip
> 2216 git status
> 2217 git svn dcommit --add-author-from
> 2218 git status
>
> /Jesper
>
> On Fr
at 3:08 PM, Diego Diez wrote:
> Dear all,
>
> I am having some problem with the git mirror and I would appreciate
> some light into how could it be solved.
>
> I have forked my package "codelink" in github and work on a local copy
> in my computer. I
Dear all,
I am having some problem with the git mirror and I would appreciate
some light into how could it be solved.
I have forked my package "codelink" in github and work on a local copy
in my computer. I used the information in
http://www.bioconductor.org/developers/how-to/git-mirrors/ to set
Hi Dan,
On Fri, Apr 4, 2014 at 11:05 PM, Dan Tenenbaum wrote:
> Hi Diego,
>
> - Original Message -
>> From: "Diego Diez"
>> To: "bioc-devel"
>> Sent: Friday, April 4, 2014 12:44:20 AM
>> Subject: [Bioc-devel] Bioconductor
Dear all,
sorry if double posting this. I sent it two days ago using a different
email not registered at bioc-devel and it seems (as for the archives)
it has not reached destination.
FYI, it seems the OSX build R 3.1.0 beta has split into snowleopard
and mavericks builds:
http://r.research.att.c
Hi,
I have been following this conversation with a lot of interest. I have
an R package with a shiny interface to another package recently
accepted in bioc-devel (rTRM). I was planning to submit it soon, as
the package is finished.
So my question is, should I hold the submission off until the
que
Hi
however unlike an iphone Bioconductor is only (as far as I know)
supported for the current release. We all do our best to help users
when they find problems and in most cases when I have suggested they
upgrade they have done so- solving their problems. If they were more
aware of being using an
Hi
I second improving the awareness of users about new Bioc releases and
also personally do not mind loud messages while I am
installing/upgrading packages, even if it is each time I source/run
biocLite(). Indeed for old releases that I maintain for old projects
very rarely have to install a new p
Hi,
I have no objection and I am willing to support this generic in the
package codelink. I agree that it is better to wait for the next
release cycle so that we maintainers have enough time to make the
changes.
Thank you,
Diego
On Wed, Feb 20, 2013 at 7:44 AM, Hervé Pagès wrote:
> Hi Laurent,
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