kResults/3.12/bioc-LATEST/ChemmineOB/
>
> Cheers,
> H.
>
>
> On 3/17/21 10:23 AM, Thomas Girke wrote:
> > Awesome, thanks!
> >
> > On Tue, Mar 16, 2021 at 11:40 PM Hervé Pagès > <mailto:hpages.on.git...@gmail.com>> wrote:
> >
> > Hi T
providing openbabel3 for Ubuntu 18.04. Will take a
> > look ASAP.
> >
> > @Thomas: Yes, the Ubuntu 18.04 builds are only used for the BioC 3.12
> > builds (release). BioC 3.13 and further BioC releases are/will be using
> > Ubuntu >= 20.04.
> >
> > Best,
> &g
8.04 system,
> > let us know and we will do that. The best thing would be to be able to
> > use a .deb package for this. The easiest the procedure, the more
> > likely people that are still using Ubuntu 18.04 will be able to
> > install ChemmineOB.
> >
> > Best,
> >
uted. Each test runs fine in isolation.
>
> Thanks
>
> Kevin
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> ___
in
> to BiocCredentials and activate your account.
>
> Best,
>
> Nitesh
>
> > On Dec 17, 2018, at 9:53 PM, Thomas Girke wrote:
> >
> > Dear Nitesh,
> >
> > Could you please add a new developer to my BioC packages systemPipeR and
> > systemPipe
Dear Nitesh,
Could you please add a new developer to my BioC packages systemPipeR and
systemPipeRdata to provide commit/push access for the corresponding git
repositories on git.bioconductor.org. The person's name is Daniela Cassol
(new postdoc in my group) and her email is danicas...@gmail.com.
Great thanks!
Thomas
On Wed, Feb 21, 2018 at 3:11 AM Martin Morgan
wrote:
> Thanks Thomas, countLines() in ShortRead 1.37.3 and later) will return
> numeric() rather than integer() and hence support large files.
>
> Martin
>
> On 02/20/2018 10:08 PM, Thomas Girke wrot
Dear Martin,
countLines in ShrotRead returns the line counts as integers which appears
to create problems with large FASTQ files (>536.8 Mio lines) due to R's
integer limit (2^31-1). When the integer limit is reached/exceeded it seems
that countLines returns negative values not reflecting the numb
19:50:57 2017 +
>
> bump x.y.z versions to odd y after creation of 3_5 branch
>
> git-svn-id: file:///home/git/
> hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/systemPipeR@129129
> bc3139a8-67e5-0310-9ffc-ced21a209358
>
>
> Give me a thumbs up and I’ll go ahead.
quot;%h %ad %an (%cn) %s" --date-order --date=iso
After duplicated commit pairs have been identified, one can check with diff
or vimdiff whether their content is identical:
git --no-pager show > zzz1
git --no-pager show > zzz2
vimdiff zzz1 zzz2
Thomas
On Fri, Sep 8, 2017 at 9
receive
> hooks code, which we have since fixed. I’m glad to have made the shift to
> Git, and hope the community enjoys it.
>
> Best Regards,
>
> Nitesh
>
>
> > On Sep 8, 2017, at 2:59 PM, Thomas Girke wrote:
> >
> > Dear Martin and Nitesh,
> >
>
fficial Bioconductor branch) rather than merging?
>
> I know it'll get hairy here, and maybe no easy or complete or simple
> solution... maybe seeing the steps required for alternative solutions
> would make the branch swap solution more palatable :)
: 2016-11-30
+Version: 2.28.1
+Date: 2017-6-30
Author: Y. Eddie Cao, Kevin Horan, Tyler Backman, Thomas Girke
Maintainer: Thomas Girke
Description: ChemmineR is a cheminformatics package for analyzing
drug-like small molecule data in R. Its latest version contains
functions for efficient processing
Great thanks. I will add some ideas later this week or next week.
Thomas
On Wed, Jun 29, 2016 at 12:44 PM Martin Morgan <
martin.mor...@roswellpark.org> wrote:
> On 06/29/2016 03:42 PM, Thomas Girke wrote:
> > Yes, a "readSummarizedExperiment" would be a "mo
ror, please notify the sender immediately by
> e-mail and delete this email message from your computer. Thank you.
> On 06/29/2016 01:57 PM, Thomas Girke wrote:
> > Hi Vince and Martin,
> >
> > It was great seeing you at the Bioc conference, and thanks for all your
> >
t; > > Sent: Monday, October 26, 2015 12:39 PM
> > > To: Thomas Girke ; Arora, Sonali
> > > ; bioc-devel@r-project.org
> > > Subject: Re: [Bioc-devel] systemPipeR error - Error in NSBS(i, x,
> exact = exact,
> > > upperBoundIsStrict = !allow.ap
extremely useful.
Thomas
On Mon, Oct 26, 2015 at 10:38 AM Hervé Pagès wrote:
> Hi Thomas,
>
> On 10/25/2015 01:06 PM, Thomas Girke wrote:
> > I fixed this in systemPipeR versions 1.4.3/1.5.3. The reason for this
> error
> > was that the tx_type column contains only
is generated
from a GFF.
Thanks,
Thomas
On Fri, Oct 23, 2015 at 12:49:09AM +, Thomas Girke wrote:
> Thanks. Good to know. I have never tried this with an txdb instance
> from makeTxDbFromUCSC(). Will fix this over the weekend.
> Thomas
>
>
>
> On Thu, Oct 22, 2015 at
Thanks. Good to know. I have never tried this with an txdb instance from
makeTxDbFromUCSC(). Will fix this over the weekend.
Thomas
On Thu, Oct 22, 2015 at 5:39 PM Arora, Sonali wrote:
> Hi Thomas,
>
> I get the following error when I try to obtain the feature types using
> the function genFeatu
st/doc/HtmlStyle.html
>
> Kasper
>
> On Wed, Jul 29, 2015 at 10:39 PM, Thomas Girke
> wrote:
>
>> Perfect, if your update in Bioc-devel eliminates the awkward bullets in
>> front of the numbers. The lack of numbered content tables in Bioc-release
>> may be something
t;> It would be great to expand on the BiocStyle vignette and discuss
>> citations and other issues and also include a clear template file. I am
>> planning on doing some pull request along those lines soon; I have been
>> testing Rmd -> HTML extensively for a course I am
A simple formatting issue:
Since support for table of contents in R markdown vignettes has become
available, it seems like an amazing solution for many online
documentation needs in the future.
What would help me to fully to adopt to it, is a solution to get rid of
the bullets in a numbered tabl
to BiocParallel that works
> for all backends. I've been trying out the futile.logger package which
> looks promising for logging at both the system and user levels. We're
> also exploring more interactive debugging when an error is thrown.
>
>
> Valerie
rough BiocParallel?
Again sorry for the unnecessary noise.
Thomas
On Tue, Sep 23, 2014 at 06:59:11PM -0700, Thomas Girke wrote:
> Hi Valerie,
>
> Thanks for looking into this.
>
> Yes, if I include the bogus 'MYR' in *.tmpl then I am getting the same
> error in R-rele
University of California, Riverside
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> there's a problem with how R devel is being called on the cluster?
>
> Michel Lang (cc'd) implemented BatchJobs in BiocParallel. I'd like to
> get his opinion on how he wants to handle this type of error.
> Michel, let me know if you need more details, I
Hi Martin, Micheal and Vincent,
If I run the following code, with the release version of BiocParallel then it
works (took me some time to actually realize that), but with the development
version I am getting an error shown after the test code below. If I run the
same test with BatchJobs from the
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