On this topic, one way of staying abreast of conflicts as you introduce them
during the evolution of a project through use of the `conflicted` library
toward the top of your project, usage modelled as follows:
```
## Force use of package prefixes for ALL conflicting function names
## lacking reg
Hi,
> -Original Message-
> From: Bioc-devel On Behalf Of
> Michael Lawrence
> Sent: Friday, March 09, 2018 1:49 PM
> To: Paul Shannon
> Cc: Gabe Becker ; bioc-devel@r-project.org
> Subject: Re: [Bioc-devel] IGV - a new package in preparation
>
> Couple of things:
>
> 1) Che
Hello,
Jumping in the conversation perhaps late.
If it helps the effort, below are some IGV related R functions I've used in the
past to good effect communicating with IGV running on local/remote host and
issuing GOTO and Save Snapshot commands.
They use utils::write.socket
One things that he
Hi,
Can I ask, is this change under discussion in current release or so far in
Bioconductor devel only (my assumption)?
> On 02/15/2018 08:37 AM, Michael Lawrence wrote:
> > So is as.list() no longer supported for GRanges objects? I have found it
> > useful in places.
>
> Very few places.
> -Original Message-
> From: Bioc-devel [mailto:bioc-devel-boun...@r-project.org] On Behalf Of
> Hervé Pagès
> 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, ex
Hello ,
I am not sure what the best solution is, but, in my hands using Org-mode
version 8.3.2-elpa org-20150929 the reg-expt used to "cleanup extra prompts
left in output" is over-aggressive and will trim session :output at lines
consisting exclusively of blanks and periods such as produced w
Dumb question (?) follows in line:
> That is the plan. Note that we already have elementLengths() that serves the
> same purpose. It was the direct inspiration for lengths().
Why have both?
>
> On Mon, Sep 28, 2015 at 9:41 PM, Peter Hickey
> wrote:
>
> > The lengths() function was added
Yay m- thx
From: Michael Lawrence [mailto:lawrence.mich...@gene.com]
Sent: Tuesday, September 29, 2015 11:16 AM
To: Cook, Malcolm
Cc: Michael Lawrence ; Peter Hickey
; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Adding a lengths() method to List class
The plan is to move to only having
Hi,
>https://github.com/vjcitn/biocMultiAssay/blob/master/vignettes/SEresolver.Rnw
>
>shows some modifications to [ that allow subsetting of SE by
>gene or pathway name
Without reading the code, do you intend that SE[i,j] will , if i is provided
as vector of string, will subset those rows wh
>> Martin,
>>
>> I'm sure you're watching this thread.
>>
>> Can we take it as some "feedback from other developers" that you requested
>> way back in https://stat.ethz.ch/pipermail/bioc-
>devel/2011-October/002854.html when I wished for similar
>>
>
>I don't really have anything
Great.
It sounds like promoting this in
http://www.bioconductor.org/developers/package-guidelines/ might be the path of
least pain/most gain.
The BioConductor project _could_ at some point as a service choose to host a
single bug/issue tracking system which individual package developers could
your question âdo we really need...â, Iâd vote
+2
!Malcolm
From: Michael Lawrence [mailto:lawrence.mich...@gene.com]
Sent: Friday, May 23, 2014 1:31 PM
To: Cook, Malcolm
Cc: Keith Hughitt; Nicolas Delhomme; Martin Morgan; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Bug tracker for
Martin,
I'm sure you're watching this thread.
Can we take it as some "feedback from other developers" that you requested way
back in https://stat.ethz.ch/pipermail/bioc-devel/2011-October/002854.html when
I wished for similar
In any case,
+1,
Malcolm
>-Original Message-
>
>On 05/05/2014 01:00 PM, Cook, Malcolm wrote:
>> Wondering,
>>
>> Is it too off the beaten track to expect
>>
>> `mcols<-`(x,NULL)
>
> > args(`mcols<-`)
> function (x, ..., value)
>
>Arguments after the ellipsis must be na
Wondering,
Is it too off the beaten track to expect
`mcols<-`(x,NULL)
to work?
hint: it does not
>-Original Message-
>From: bioc-devel-boun...@r-project.org
>[mailto:bioc-devel-boun...@r-project.org] On Behalf Of Hervé Pagès
>Sent: Monday, May 05, 2014 1:28 PM
>To: Kasper Daniel
in the mean time,
lapply(`[`,x,IntegerList(1:5))
??
>-Original Message-
>From: bioc-devel-boun...@r-project.org
>[mailto:bioc-devel-boun...@r-project.org] On Behalf Of Michael Lawrence
>Sent: Tuesday, April 01, 2014 9:21 AM
>To: bioc-devel@r-project.org
>Subject: [Bioc-devel] Sub
This is great.
one quick Errata - The link to the RefNet.db package is dead.
!Malcolm
>-Original Message-
>From: bioc-devel-boun...@r-project.org
>[mailto:bioc-devel-boun...@r-project.org] On Behalf Of Valerie Obenchain
>Sent: Tuesday, April 01, 2014 9:36 AM
>To: bioconduc...@r-pro
Hi,
I'm having trouble making a minimal reproducible example, but, pretty reliably
I get the following segfault calling DAVIDWebService in a restored R session:
> david<-DAVIDWebService$new(email="m...@stowers.org")
*** caught segfault ***
address 0x7f5b1bd0e000, cause 'invalid permissions'
Hi,
I just went through this approach in yeast,
regions = gene promoters
assays = H3K3ME1, H3K3ME2, H3K3ME3 ChipSeq
experimental conditions: 7 recombinant knock-outs and knock-ins of
different domains of different genes.
two replicates
So, what I first
Fix confirmed.
Thanks very much.
.-Original Message-
.From: datas...@ebi.ac.uk [mailto:datas...@ebi.ac.uk]
.Sent: Thursday, February 14, 2013 10:04 AM
.To: Cook, Malcolm
.Cc: bioc-devel@r-project.org; zhuj...@mail.nih.gov
.Subject: RE: [Bioc-devel] SRAdb listSRAfile returns empty
: Thursday, February 14, 2013 6:54 AM
.To: Cook, Malcolm
.Cc: bioc-devel@r-project.org; zhuj...@mail.nih.gov
.Subject: RE: [Bioc-devel] SRAdb listSRAfile returns empty datatable with
filetype='fastq' (rasko) (SUB#832914)
.
.Dear Malcolm,
.
.We have reverted minor differences in
-boun...@r-project.org] On Behalf Of Cook, Malcolm
.Sent: Wednesday, February 13, 2013 5:18 PM
.To: 'bioc-devel@r-project.org'; 'zhuj...@mail.nih.gov'
.Subject: [Bioc-devel] SRAdb listSRAfile returns empty datatable with
filetype='fastq'
.
.Hi Jack,
.
.Do you hap
Hi Jack,
Do you happen to know if EBI is refreshing or otherwise administering their
archive of SRA fastqs?
I find that if I change the type to 'sra', I get a quick list of paths. But
if go after the 'fastq', the result yesterday, which worked, is coming back
empty this afternoon.
Any ideas
Marc et. al.,
A colleague of mine (cc:ed) is experiencing memory bloat using
makeTranscriptDBFromGFF on dmel GFF from Flybase.org
I told him of my success in using Ensembl's GTF-ization but that I would check
in with you (et al).
So
Do you have any advice/warnings/gothcas/toldyasos/cave
From: Marc Carlson [mailto:mcarl...@fhcrc.org]
.Sent: Saturday, February 09, 2013 3:57 AM
.To: Cook, Malcolm
.Cc: 'bioc-devel@r-project.org'
.Subject: Re: [Bioc-devel] [GenomicFeatures] no pkgName found.
makeTxDbPackage() called after txdb created from GFF3 file
.
.Hi Malcolm,
.
.In
.Hi Tengfei,
.
.Yes that looks like an oversight. Thanks for reporting that! I will
.extend makeTxDbPackage so that it's more accommodating of these newer
.transcriptDbs. If you want to help me out, you could call saveDb() on
.your gmax189 object and send me the .sqlite file that you save i
d 1.37.1 (devel).
>
> Thanks for reporting this.
> H.
>
>
> On 11/08/2012 09:40 AM, Cook, Malcolm wrote:
> > Hi,
> >
> > I find there is some form of namespace conflict between the GenomicRanges
> > package and 'graph'
> >
> > A session sh
> I think this is now fixed in Rsamtools 1.10.2 / 1.11.9, available in svn now
> and
> biocLite, hopefully, Saturday 10am Seattle time.
Excellent. I have confirmed the fix works for me.
~Malcolm
>
> Martin
>
> On 11/09/2012 07:03 AM, Cook, Malcolm wrote:
> >
Excellent news. Thanks for the sleuthing and fix.
~Malcolm
> -Original Message-
> From: Hervé Pagès [mailto:hpa...@fhcrc.org]
> Sent: Friday, November 09, 2012 12:10 AM
> To: Cook, Malcolm
> Cc: bioc-devel@r-project.org
> Subject: Re: graph package conflict with Gen
.now',TRUE))
My workaround for now is to perform system calls to do the zipping and tabix
indexing. So, no urgency, but,
sessionInfo() is as below.
Thanks,
~Malcolm
From: Michael Lawrence
[mailto:lawrence.mich...@gene.com]<mailto:[mailto:lawrence.mich...@gene.com]>
Sent: Frida
rtracklayer developers (Michael/Vincent/Robert),
I find that tabix indexed exporting too many bed files causes an error.
The session following my signature reproduces the error.
It provides sessionInfo() details prior to the code causing the error because
sessionInfo() FAILS with 'too many op
Hi,
I find there is some form of namespace conflict between the GenomicRanges
package and 'graph'
A session showing reproducible issue, and workaround, follows.
Thanks for your help and attention.
Malcolm Cook
Computational Biology - Stowers Institute for Medical Research
PS: The issue appea
Excellent. thanks exactly what I hoped to find.
Dan Tenenbaum wrote:
On Tue, Nov 6, 2012 at 12:59 PM, Laurent Gatto wrote:
> On 6 November 2012 20:50, Cook, Malcolm wrote:
>> Kasper,
>>
>> Yes, right, the NEWS file.
>>
>> In practice I find that the
d
VariantAnnotation
I guess what I want is svn log available from web/RSS.
Any hopes out there?
Thx
~Malcolm
> -Original Message-
> From: Kasper Daniel Hansen [mailto:kasperdanielhan...@gmail.com]
> Sent: Tuesday, November 06, 2012 2:32 PM
> To: Cook, Malcolm
> Cc: Bioc
Is there a generic way to learn what is changed or new in a "released" package
since its release?
For instance, IRanges was released as 1.16.0 but is now at 1.16.4.
I'd like to know what was changed in this released version.
I do already know that I can monitor changes to devel with either
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