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
Thanks Herve,
That would be great indeed.
Florian
On 29/09/14 21:23, Hervé Pagès hpa...@fhcrc.org 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
- Original Message -
From: Leonardo Collado Torres lcoll...@jhu.edu
To: bioc-devel@r-project.org
Cc: Dan dtene...@fhcrc.org
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
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
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
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 dtene...@fhcrc.org
To: bioc-devel bioc-devel@r-project.org
Sent: Monday, September 29, 2014 9:34:36 AM
Subject: Fwd:
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/
- Original Message -
From: James W. MacDonald jmac...@uw.edu
To: Dan Tenenbaum dtene...@fhcrc.org
Cc: bioc-devel bioc-devel@r-project.org
Sent: Tuesday, September 30, 2014 10:14:00 AM
Subject: Re: [Bioc-devel] hedgehog Subversion server upgrade Tuesday 9/30
Hi Dan,
I got
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 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(
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,
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
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
- Original Message -
From: Karl Stamm karl.st...@gmail.com
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
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
Dear all,
I am trying to use Rcpp to write some files in C++ for use in R.
Below is an example for a cpp-file (crossp.cpp). Then I use
sourceCpp(crossp.cpp) in R and the corresponding function is
availabe in R.
Now I have to question related to this worklfow:
1) Is there a way to see the source
On 30 September 2014 at 13:00, Martin Spindler wrote:
| I am trying to use Rcpp to write some files in C++ for use in R.
Please subscribe to rcpp-devel, and post on that list.
Dirk
--
http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
I have access to a cluster on which I have been supplied with R 3.1.0 which
appears to have been built using the intel compiler tools.
The following minimal Fortran file:
subroutine truth(lind)
logical lind
lind = .TRUE.
end
Compiles thusly:
arcadia R CMD SHLIB truth.f
On 30/09/2014, 7:41 AM, Barry Rowlingson wrote:
I have access to a cluster on which I have been supplied with R 3.1.0 which
appears to have been built using the intel compiler tools.
The following minimal Fortran file:
subroutine truth(lind)
logical lind
lind = .TRUE.
On Tue, Sep 30, 2014 at 12:53 PM, Duncan Murdoch murdoch.dun...@gmail.com
wrote:
This appears to be user error. According to Writing R Extensions, the
Fortran type corresponding to R logical is INTEGER, not LOGICAL.
Oh yes, a very old and long-standing user error. I assume the CRAN checks
On 30/09/2014 8:39 AM, Barry Rowlingson wrote:
On Tue, Sep 30, 2014 at 12:53 PM, Duncan Murdoch
murdoch.dun...@gmail.com mailto:murdoch.dun...@gmail.com wrote:
This appears to be user error. According to Writing R Extensions, the
Fortran type corresponding to R logical is INTEGER,
In S+ and S it was valid to pass logicals to .Fortran, where they got
mapped into the
appropriate bit pattern. (The trouble was that 'appropriate' was
compiled into the program -
so you were locked into our compiler vendor's choice). Passing them
between Fortran
code and C code has always been
E.g. I am seeing:
dir - file.path(tempdir(), test-tar)
dir.create(dir)
setwd(dir)
dir.create(foo, showWarnings = FALSE)
file.create(foo/bar.R)
tar(test.tar, files = foo/bar.R)
dir.create(untarred)
untar(test.tar, exdir = untarred)
list.files(untarred,
Sounds like a bug to me, at least in documentation. I would say
that it ignores them by accident. I doubt that skipping files is
intended.
The problem appears to be that the 'files' argument to tar() becomes
the 'path' argument to list.files(), and the spec for 'path' is not
a whole lot more
I have a question about shallow copies in R. Since R 3.1.0, subsetting
a dataframe with respect to its columns no longer result in deep
copies. This is an amazing change in my opinion. Now, subsetting a
data.frame by rows (or subsetting a matrix by columns or rows) still
does deep copies. In
On Tue, Sep 30, 2014 at 2:20 PM, Matthieu Gomez
gomez.matth...@gmail.com wrote:
I have a question about shallow copies in R. Since R 3.1.0, subsetting
a dataframe with respect to its columns no longer result in deep
copies. This is an amazing change in my opinion. Now, subsetting a
data.frame
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