On 09/30/2014 10:00 PM, Dario Strbenac wrote:
Hello,
When I try to install the development version of Repitools in R 3.1.1, I get an
error :
useDevel()
biocLite("Repitools")
** preparing package for lazy loading
Error : objects ‘Seqinfo’, ‘seqlevels’ are not exported by
'namespace:GenomicRan
Hello,
When I try to install the development version of Repitools in R 3.1.1, I get an
error :
useDevel()
biocLite("Repitools")
** preparing package for lazy loading
Error : objects ‘Seqinfo’, ‘seqlevels’ are not exported by
'namespace:GenomicRanges'
What needs to be changed ?
--
A!!! Thanks!
I forgot to check those help pages. The error messages didn't lead me
there, but I should have checked again regardless. Anyhow, maybe it
would be useful to check the OS in those functions and prompt a
warning or error that is more informative.
In my case, I added a warning in th
- Original Message -
> From: "Karl Stamm"
> To: bioc-devel@r-project.org
> Sent: Tuesday, September 30, 2014 3:45:37 PM
> Subject: Re: [Bioc-devel] new package build problems
>
> Hello all, I'm running into some problems submitting my first
> bioconductor
> package. Hope someone can hel
Hello all, I'm running into some problems submitting my first bioconductor
package. Hope someone can help.
I've got the package building and checking successfully on three of the
four build servers, and a strange error on the last. The OSX *oaxaca* host
reports a warning during CHECK. Reviewing th
Hi,
Import and manipulation of BigWig files in rtracklayer make use of the
Kent C library and are not supported on windows.
This is documented at
?import.bw
?`BigWigFile-class`
This problem isn't specific to an 'over the network' example. Trying to
import() a local BigWig on Windows will al
The answer on Windows is simple: BigWig is not supported on that platform.
There is probably a simple fix, if someone were to just go into Windows and
use gdb to fix the Windows implementation of the abstraction layer.
The problem on Dans' linux seems to be lack of permission for writing to
/tmp.
Hi Gabe,
It would help to have a common baseline. Please show the output for
writing the Illumina file you sent originally:
library(VariantAnnotation)
fl <- "NA12877_S1.genome.vcf.gz"
vcf <- readVcf(fl, "", param=ScanVcfParam(info=NA))
dim(vcf)
gc()
print(system.time(writeVcf(vcf, tempfile())
Hi Thomas,
One possible solution is the example below that conforms to the format
Laurent suggested to you. Another variation on it is to read the html from
a file in /inst/ and assign it to a character variable:
myhtml <- readLines("/path/to/index.html")
app <- list(
ui = HTML(myhtml),
hi Kasper and Valerie,
In Kasper's original email:
"I would like to be able to write a MAP function which takes
ranges, file
instead of just
range, file
And then chunk over say 1,000s of ranges. I could then have an
argument to reduceByXX called something like rangeSize, which is kind
of yiel
Thanks Dan!
On Tue, Sep 30, 2014 at 1:19 PM, Dan Tenenbaum wrote:
>
>
> - Original Message -
> > From: "James W. MacDonald"
> > To: "Dan Tenenbaum"
> > Cc: "bioc-devel"
> > Sent: Tuesday, September 30, 2014 10:14:00 AM
> > Subject: Re: [Bioc-devel] hedgehog Subversion server upgrade
- Original Message -
> From: "James W. MacDonald"
> To: "Dan Tenenbaum"
> Cc: "bioc-devel"
> Sent: Tuesday, September 30, 2014 10:14:00 AM
> Subject: Re: [Bioc-devel] hedgehog Subversion server upgrade Tuesday 9/30
>
>
> Hi Dan,
>
>
> I got this when I tried to commit a change.
>
Hi Dan,
I got this when I tried to commit a change.
Transmitting file data ..svn: Commit failed (details follow):
svn: Commit blocked by pre-commit hook (exit code 1) with output:
Use of the encoding pragma is deprecated at
/extra/svndata/gentleman/svnroot/bioconductor/hooks/
check-case-insensiti
The switchover has happened, hedgehog is a new server now. Please let me know
if you run into any issues with it.
Dan
- Original Message -
> From: "Dan Tenenbaum"
> To: "bioc-devel"
> Sent: Monday, September 29, 2014 9:34:36 AM
> Subject: Fwd: [Bioc-devel] hedgehog Subversion server up
Valerie,
Apologies for this taking much longer than it should have. The changes in
Bioc-devel have wreaked havoc on the code we use to to generate and process
the data we need to write out, but the fault is mine for not getting on top
of it sooner.
I'm not seeing the speed you mentioned above in
Hm... weird. I can get it to work on our linux cluster.
> ## Attempt with 1 file
ode_v10/bigwig/HSB97.AMY.bw')wnload.alleninstitute.org/brainspan/MRF_BigWig_Genc
> seql <- seqlengths(bw)
>
> seql
chr1 chr10 chr11 chr12 chr13 chr14 chr15 chr16
249250621 135534747 1
Hello,
I ran into an issue interacting with BigWig files over the network
with `rtracklayer`. For some reason, the issue is Windows-specific and
I don't understand why.
Basically, I run the short code at
https://gist.github.com/lcolladotor/0ab8ab3d904d21110637 It works on a
Mac, but it fails on W
- Original Message -
> From: "Antti Honkela"
> To: bioc-devel@r-project.org
> Sent: Tuesday, September 30, 2014 5:58:03 AM
> Subject: [Bioc-devel] Problems creating Git-SVN bridge to an organisation
> repo
>
> It seems GitHub has changed their handling of organisation repos to
> be
- Original Message -
> From: "Leonardo Collado Torres"
> To: bioc-devel@r-project.org
> Cc: "Dan"
> Sent: Tuesday, September 30, 2014 8:00:53 AM
> Subject: Cannot interact with a BigWig file on the web with rtracklayer
> (Windows specific)
>
> Hello,
>
> I ran into an issue interacti
Thanks Herve,
That would be great indeed.
Florian
On 29/09/14 21:23, "Hervé Pagès" wrote:
>Hi Florian,
>
>True. These restrictions don't make much sense these days anymore!
>Some of them are gone in the devel version of BSgenome. The
>BSgenomeForge vignette in devel now says:
>
> The sequence
It seems GitHub has changed their handling of organisation repos to be
incompatible with current Git-SVN bridge creation.
1. As far as I can tell, you cannot simply add members to a team, but
only send invitations. It seems bioc-sync does not accept these at least
immediately.
2. Additionall
Hi there,
I have had this issue as well when submitting my package. In my case it
turned out that the Windows build apparently can't handle bibtex/biblatex
very well. Looks like your build also stops at bibtex. If you have just a
few references, you might just put them in the old-fashioned way (i.
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