- Original Message -
> From: "t kuilman"
> To: bioc-devel@r-project.org
> Sent: Friday, April 17, 2015 11:30:14 PM
> Subject: [Bioc-devel] Dependency issue
>
> Hello everyone,
>
> I have tested whether our new package CopywriteR could be installed,
> but surprisingly got the message th
Hello everyone,
I have tested whether our new package CopywriteR could be installed, but
surprisingly got the message that it could not be installed under R 3.1.2:
Warning message:
package ‘CopywriteR’ is not available (for R version 3.1.2)
All the dependencies of CopywriteR have R >= 3.1.0 or
Sorry, I was confused. You're right, there's not much point in keeping it
compressed.
On Fri, Apr 17, 2015 at 10:14 AM, Hervé Pagès wrote:
> On 04/17/2015 10:00 AM, Michael Lawrence wrote:
>
>> Is that the case here? He has an Rle as an mcol in the GRanges, so in
>> general expanding it will not
Thanks, it fixed the issue.
2015-04-18 0:24 GMT+03:00 Dan Tenenbaum :
>
>
> - Original Message -
> > From: "Sergei Ryazansky"
> > To: "Dan Tenenbaum"
> > Cc: bioc-devel@r-project.org
> > Sent: Friday, April 17, 2015 2:18:00 PM
> > Subject: Re: [Bioc-devel] Error after upgrading to R 3.2
Hej Leonardo,
I had the same doubts when Maverick came out, but eventually went for it. Since
then, I have been running R and RStudio on OSX Yosemite - since Yosemite got
out - and never had any problems. There are been some issues originally with
Maverick but these are history. You might need
- Original Message -
> From: "Sergei Ryazansky"
> To: "Dan Tenenbaum"
> Cc: bioc-devel@r-project.org
> Sent: Friday, April 17, 2015 2:18:00 PM
> Subject: Re: [Bioc-devel] Error after upgrading to R 3.2.0 with loading of
> GO.db: 2 arguments passed to .Internal(ls)
> which requires 3
>
Yes, I did the upgrading of Bioconductor as well, but the result was the
same:
> library("BiocInstaller", lib.loc="~/Rlibs")Bioconductor version 3.0
> (BiocInstaller 1.16.2), ?biocLite for help
> biocLite()BioC_mirror: http://bioconductor.orgUsing Bioconductor version 3.0
> (BiocInstaller 1.16.
- Original Message -
> From: "Sergei Ryazansky"
> To: bioc-devel@r-project.org
> Sent: Friday, April 17, 2015 1:53:41 PM
> Subject: [Bioc-devel] Error after upgrading to R 3.2.0 with loading of GO.db:
> 2 arguments passed to .Internal(ls)
> which requires 3
>
> Hello everyone,
>
> aft
Somewhere in GO.db a direct call to the ls .Internal is being made
(probably a speed hack) apparently. The API for .Internal(ls()) has
changed in R 3.2.0. This call should be replaced with "names", which now
works on environments in R 3.2.0, and is way faster than the direct call to
.Internal(ls()
Hello everyone,
after updating to fresh R 3.2.0 from R 3.1.3, GO.db, org.Dm.eg.db and
org.Hs.eg.db are failed to load (sorry for non-english environment):
>library("GO.db")Error : .onLoad не удалось в loadNamespace() для 'GO.db',
>подробности:
вызов: ls(envir, all.names = TRUE)
ошибка: 2 арг
- Original Message -
> From: "Leonardo Collado Torres"
> To: bioc-devel@r-project.org
> Sent: Friday, April 17, 2015 12:43:12 PM
> Subject: [Bioc-devel] R 3.3 for snow leopard
>
> Hi,
>
> This is not BioC related, but should hopefully be quick.
>
> According to
> http://cran.r-project
Hi,
This is not BioC related, but should hopefully be quick.
According to
http://cran.r-project.org/doc/manuals/r-devel/R-admin.html#Installing-R-under-OS-X
"there may be a separate installer package, R-3.3.0-snowleopard.pkg". I'm
not seeing any at http://r.research.att.com/. Has anyone heard if
On 04/17/2015 10:00 AM, Michael Lawrence wrote:
Is that the case here? He has an Rle as an mcol in the GRanges, so in
general expanding it will not align with the other components.
Not sure what you mean. Can you give an example?
H.
On Fri, Apr 17, 2015 at 9:42 AM, Hervé Pagès mailto:hpa...
Is that the case here? He has an Rle as an mcol in the GRanges, so in
general expanding it will not align with the other components.
On Fri, Apr 17, 2015 at 9:42 AM, Hervé Pagès wrote:
> Hi,
>
> I think we should just expand the Rle internally. That will produce
> a numeric vector of the length
Hi,
I think we should just expand the Rle internally. That will produce
a numeric vector of the length of the GRanges i.e. it will be the
same size as the start and end components of the GRanges object itself.
No big deal at all.
I'll make that change.
H.
On 04/17/2015 09:00 AM, Michael Lawren
On 04/17/2015 08:59 AM, Leonard Goldstein wrote:
Hi all,
I ran into a segfault error when trying to read paired-end RNA-seq
alignments with scanBam (see below). This seems to be a problem
introduced in Rsamtools version 1.19.35 (1.19.34 works fine). In case
you need the BAM file for testing, ple
Ideally it should be supported, but it would take some work as the coverage
stuff is all in C. Could you give more details on your use case? For
example, if you already have a range for every position on the chromosome,
you could just extract the score column. I'm guessing it's more complicated
tha
Hi all,
I ran into a segfault error when trying to read paired-end RNA-seq
alignments with scanBam (see below). This seems to be a problem
introduced in Rsamtools version 1.19.35 (1.19.34 works fine). In case
you need the BAM file for testing, please let me know. Many thanks for
your help.
Leonar
Dear all, I'm puzzled by the following behaviour:
Given
n <- 10
gr <- GRanges(seqnames=Rle('A', n),
ranges=IRanges(1:n, width=1),
score=Rle(5,n))
If I do
coverage(gr,weight='score')
I get
Error in .normarg_shift_or_weight(weight, "weight",
- Original Message -
> From: "Kevin Rue-Albrecht"
> To: "Tiphaine Martin"
> Cc: "Dan Tenenbaum" , "bioc-devel"
>
> Sent: Friday, April 17, 2015 4:30:24 AM
> Subject: Re: [Bioc-devel] BioC 3.1 branch created
>
>
>
>
> Hi Tiphaine,
>
> I have followed both of your links,. and they
Dear Martin,
> On 17 Apr 2015, at 14:00, Martin Morgan wrote:
>
> On 04/13/2015 02:48 AM, Thomas Maurel wrote:
>> Dear Martin,
>>
>> I have investigated with our Web team and we believe that the command
>> attempts to open a number of concurrent sessions in order to download all of
>> the files
On 04/13/2015 02:48 AM, Thomas Maurel wrote:
Dear Martin,
I have investigated with our Web team and we believe that the command
attempts to open a number of concurrent sessions in order to download all of
the files. If that is the case then the problem is that our ftp server is
configured to lim
Hi Kevin,
Thanks,
I will try it later and check whether I have still this issue to connect it.
Tiphaine
From: Kevin Rue-Albrecht
mailto:kevin@ucdconnect.ie>>
Date: Friday, 17 April 2015 11:30
To: Tiphaine Martin
mailto:tiphaine.mar...@kcl.ac.uk>>
Cc: Dan Tenenbaum mailto:dtene...@fredhutch
Hi Tiphaine,
I have followed both of your links,. and they both work for me. Probably
just a glitch in the connection ?
Hi Dan,
I have a quick question of my own,
I would like to bridge the new release branch to my Github "release"
repository, but:
- In the dropdown of the bridge creation, r
Hi Dan,
When I try to access on my package, I have ³Internal Server Error². Maybe
I make a mistake somewhere.
https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/
coMET
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/coMET
Regards,
Tiphaine
On 17/04/2015 05:44
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