, the
child is always a step or two ahead of the main script, so that whenever
the main script asks for the next yield, it gets it immediately instead
of waiting for the child to read from the disk.
So, is this kind of feature appropriate for inclusion into BioConductor?
-Ryan Thompson
deal more straightforward than before. To support the
multi-argument bpvectorize, I also added a function bpmvec, which is
to bpvec as bpmapply is to bplapply.
-Ryan
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc
tryCatch to at least provide a more informative error message
when a subprocess has a missing variable.
-Ryan
withBPExtraErrorText - function(expr) {
tryCatch({
expr
}, simpleError = function(err) {
if (grepl(^object '(.*)' not found$, err$message, perl=TRUE
Another potential easy step we can do is that if FUN function in the
user's workspace, we automatically export that function under the same
name in the children. This would make recursive functions just work, but
it might be a bit too magical.
On 11/3/13, 2:38 PM, Ryan wrote:
Here's an easy
PM, Ryan r...@thompsonclan.org
mailto:r...@thompsonclan.org wrote:
Another potential easy step we can do is that if FUN function in
the user's workspace, we automatically export that function under
the same name in the children. This would make recursive functions
just work
a function refers
to something in the global env.
On Sun Nov 3 21:14:29 2013, Gabriel Becker wrote:
Ryan (et al),
FYI:
f
function() {
x = rnorm(x)
x
}
findGlobals(f)
[1] = { rnorm
x should be in the list of globals but it isn't.
~G
sessionInfo()
R version 3.0.2 (2013-09-25)
Platform
, so I never have to worry about things being undefined
in the forked subprocess. Therefore I cant really dogfood any of the
stuff that might be implemented as a result of this thread.
-Ryan
On Mon Nov 4 03:48:23 2013, Michael Lawrence wrote:
So what is the best practice for ensuring
.
-Ryan
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
The minimize the additional memory used by mclapply, remember that
mclapply works by forking processes, and the advantage of this is that
as long as an object is not modified in either the parent or child,
they will share the memory for that object, which effectively means
that a child process
Ok, sorry to bother you. I'll ask my cluster admin for an update.
On Tue Nov 26 17:24:34 2013, Wei Shi wrote:
Hi Ryan,
It seems you are using a quite old version of Subread. The latest version of
SourceForge Subread is 1.4.2 and the latest version of bioc Rsubread is 1.12.3.
These indexing
That won't work if any vector has fewer than 5 elements. Maybe
lapply(x, head, n=5)
would work?
On Tue Apr 1 09:24:51 2014, Cook, Malcolm wrote:
in the mean time,
lapply(`[`,x,IntegerList(1:5))
??
-Original Message-
From: bioc-devel-boun...@r-project.org
strand info for all reads because the reads must be
directionally extended, which requires strand info. Ditto for counting
the 5-prime and 3-prime ends.
-Ryan
chipseq - function(features, reads, ignore.strand=FALSE,
inter.feature=TRUE,
type=any, maxgap=0L, minoverlap=1L,
width=NULL, fix
these two arguments expect different things than this one
argument expects a different thing depending on the value of another
argument.
-Ryan
On Sun Jun 15 11:17:59 2014, Michael Lawrence wrote:
I just thought there is some benefit for the callback to be the same,
regardless of the iterate setting
I just want to add the perspective that I often browse package
documentation vignettes from the website rather than accessing it from
the R command line. Sometimes it's just easier or more convenient to
view it in a browser. So, when doing this, I sometimes accidentally get
the wrong
() with a '...'
will pass the arguments down; they continue to be passed down until
they are explicitly stated in a function signature (e.g., 'width' and
'fix' in ResizeReads()).
Valerie
On 08/06/2014 11:35 AM, Ryan wrote:
Ok, I had a look at the code, and I think understand now. The help text
my solution also doesn't generalize to multi-step
parallel pipelines.
Thanks,
Jeff
-Ryan
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
.
Thanks,
-Ryan Thompson
[[alternative HTML version deleted]]
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
Yes, a single-assay SummarizedExperiment would be the most common case
for unnamed assays. But I think at the very least there should be a
warning on unnamed assays.
On 3/12/15 9:24 AM, Martin Morgan wrote:
On 03/12/2015 08:12 AM, Tim Triche, Jr. wrote:
What he said
This doesn't make any
Oh wow, I didn't know you could put a DataFrame into a single column of
another DataFrame. That actually solves a problem for me too (I don't
intend to expose nested DataFrames to the users though).
On 6/17/15 7:23 PM, Martin Morgan wrote:
On 06/17/2015 11:41 AM, davide risso wrote:
Dear
digest must have been installed in /usr/local but not pkgmaker,
so removing it broke the dependency chain. No idea how it got into that
state, but problem solved.
On 8/7/15 5:06 PM, Martin Morgan wrote:
On 08/07/2015 04:31 PM, Dan Tenenbaum wrote:
- Original Message -
From: Ryan C
Hopefully this can be fixed soon.
-Ryan
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
interested, you can get it here:
http://mneme.homenet.org/~ryan/SubsettableListOfArrays.R
-Ryan
On 9/18/15 7:41 PM, Michael Lawrence wrote:
> While it's useful (and often necessary) to store the big matrices out
> of core, it would be convenient to store the metadata (the other
> compo
Is it possible to allow the width slot of IRanges to be either a normal
vector or an Rle?
On 11/23/16 6:18 PM, Peter Hickey wrote:
I've been toying with the idea of a fixed/constant width Ranges
subclass. The motivation comes from storing DNA methylation data at CH
loci (non-CpG methylation):
t even for that case, fixed-wdith ranges are not
necessarily usable because a position less than 1kb from the end of a
chromosome would require a truncated range. (What behavior would we
expect from a hypothetical FWRanges class in this case?)
-Ryan
On 11/23/16 8:01 PM, Ryan wrote:
Is it possibl
easily adapt the same code to return a list of all
packages that a function depends on.
-Ryan
On Nov 4, 2013 11:35 AM, Michael Lawrence lawrence.mich...@gene.com
wrote:
The dynamic nature of R limits the extent of these checks. But as Ryan has
noted, a simple sanity check goes a long way
Thanks! I patched my local copy on my own, so I'll be fine until the next
release.
On Mar 25, 2014 3:04 AM, Julian Gehring julian.gehr...@embl.de wrote:
Hi Ryan,
Thank you for the detailed bug report and already providing a fix for
this. I have added your patch to 'les_1.13.2' and pushed
Actually, the code looks like it should be adding these names, so I need to
go back through my code and get back to you on that issue.
On Jul 7, 2015 9:58 AM, Ryan C. Thompson r...@thompsonclan.org wrote:
I've also encoundered another problem, this time I believe related to a
change
They wouldn't be exactly consistent even if they used the same prior count,
since the calculations are not identical. edgeR normalizes the prior count
by each library's normalization factor so that log fold changes are always
squeezed toward zero, while voom, if I understand correctly, does not
and error, and
occasionally R will segfault. Since the bug is random, I've also included a
transcript of me running the script until it crashes, as well as a text
file with the traceback in it.
Can you help me debug the issue here?
Thanks,
-Ryan
[[alternative HTML version deleted
I think the main reason for reusing/subclassing core classes that users can
appreciate is that it makes it much easier for users to integrate multiple
packages into a single workflow. Only the most basic of pipelines uses just
a single Bioconductor package. For instance, an "edgeR" pipeline
for separate installation of other command-line tools.
Regards,
Ryan Thompson
On Sun, Nov 12, 2017 at 2:12 PM Ioannis Vardaxis <ioannis.varda...@ntnu.no>
wrote:
> Hi,
> I have developed a package and is current under review from
> Bioconductor. In the future I am considering
is on CRAN, the
biocLite.R script will become a thin wrapper around it?
-Ryan
On Wed, May 9, 2018 at 3:29 PM Martin Morgan <martin.mor...@roswellpark.org>
wrote:
> Developers --
>
> A preliminary heads-up and request for comments.
>
> Almost since project inception, we've used th
ever need to install it.
For more info, see this old post about the same problem:
https://support.bioconductor.org/p/16932/
Regards,
Ryan
On Thu, May 10, 2018 at 11:58 PM Robert Castelo <robert.cast...@upf.edu>
wrote:
> hi,
>
> this is a question for limma developers.
>
> at every n
an option for a web service like
this, which wants to return a result quickly. Does anyone know a good way
to access this info?
Thanks,
Ryan Thompson
[[alternative HTML version deleted]]
___
Bioc-devel@r-project.org mailing list
https
).
On Tue, Apr 17, 2018 at 11:57 AM Marcel Ramos <marcel.ra...@roswellpark.org>
wrote:
> Hi Ryan,
>
> Thanks for pointing this out.
>
> I'm not sure what you mean by "structured" or "format". We do have
> public facing citations
> which can be found at
ons/BiocFileCache/citation.html>
?
Regards,
Ryan Thompson
On Tue, Apr 17, 2018 at 12:23 PM Ryan Thompson <r...@thompsonclan.org> wrote:
> I wasn't specific about what I meant by "structured" because I'm not
> certain what kind of citation data types CiteAs can handle, though I'd
&g
I don't know if this is helpful for BiocParallel, but there's an extension
for the foreach package that ensures reproducible RNG behavior for all
parallel backends: https://cran.r-project.org/web/packages/doRNG/index.html
Perhaps some of the principles from that package can be re-used?
On Mon,
On Mon, Jan 7, 2019 at 3:26 PM Henrik Bengtsson
wrote:
>
> 1. To achieve fully numerically reproducible RNGs in way that is
> *invariant to the number of workers* (amount of chunking), I think the
> only solution is to pregenerated RNG seeds (using
> parallel::nextRNGStream()) for each
I just submitted a pull request. I'll add tests shortly if I can figure
out how to write them.
On Wed 14 Nov 2012 03:50:36 PM PST, Martin Morgan wrote:
On 11/14/2012 03:43 PM, Ryan C. Thompson wrote:
Here are two alternative implementations of pvec. pvec2 is just a
simple rewrite
of pvec
To be more specific, instead of:
library(parallel)
cl - ... # Make a cluster
parLapply(cl, X, fun, ...)
you can do:
library(parallel)
library(doParallel)
library(plyr)
cl - ...
registerDoParallel(cl)
llply(X, fun, ..., .parallel=TRUE)
On Fri 16 Nov 2012 11:44:06 AM PST, Ryan C. Thompson wrote
In reply to:
On 11/16/2012 09:45 PM, Steve Lianoglou wrote:
But then you have the situation of multi-machines w/ multiple cores --
is this (2) or (3) here? How do you explicitly write code for that w/
foreach mojo? I guess the answer to that is that you let your grid
engine (or whatever your
On Tue 04 Dec 2012 11:31:59 AM PST, Michael Lawrence wrote:
The name pvec is not very intuitive. What about bpchunk? And since the
function passed to bpvectorize is already vectorized, maybe bpvectorize
should be bparallelize? I know everyone has different
intuitions/preferences when it comes to
to generate a list of GRanges similar
in size to your blockRanges object, and I'll test them myself.
-Ryan Thompson
On 01/06/2013 06:00 PM, Dario Strbenac wrote:
Hello,
For a not so large list of GRanges:
length(blockRanges)
[1] 4029
class(blockRanges)
[1] list
Which don't have
matrix (i.e. the part of glmLRT that does all the QR decomposition
stuff). Would you consider splitting this logic into a separate function
that takes a design matrix and contrast matrix and returns the
equivalent reparametrized design matrix and vector of coefficients?
Thanks,
-Ryan
/NE8xsa6bxo
Thanks,
-Ryan
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
I would prefer the droplevels method for SummarizedExperiment, since
this is consistent with the use of droplevels on data.frame objects.
On Wed 12 Mar 2014 03:02:37 PM PDT, Wolfgang Huber wrote:
Hi Martin, Mike
a DESeq2 user brought up the observation that when he subsets a ‘DESeqDataSet’
.
seqinfo(fll)
## Now add a method
setMethod(seqinfo, signature=list(x=BamFileList), function (x)
{
Reduce(merge, lapply(x, seqinfo))
}
)
## Now this returns a good result
seqinfo(fll)
## So does this
seqlengths(fll)
-Ryan Thompson
___
Bioc-devel@r
.
-Ryan Thompson
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
No, I forgot to attach the file. Here is the link:
https://www.dropbox.com/s/7qghtksl3mbvlsl/counting-modes.R
On Wed 30 Apr 2014 02:18:28 PM PDT, Valerie Obenchain wrote:
Hi Ryan,
These sound like great contributions. I didn't get an attachment - did
you send one?
Thanks.
Valerie
On 04/30
, so I basically want to call nearest with a GRanges
of peaks against a GRangesList of TSS (each TSS is a range with a width
of 1 containing the first base pair of a transcript). I don't personally
need a method that works for a GRangesList query.
-Ryan
On Fri 23 May 2014 11:13:24 AM PDT
Hi Valerie,
I got really busy around May and never got a chance to thank you for
adding this option to summarizeOverlaps! So thank you!
-Ryan
On Thu 01 May 2014 04:25:33 PM PDT, Valerie Obenchain wrote:
GenomicAlignments 1.1.8 has a 'preprocess.reads' argument. This should
be a function
be documented.
-Ryan
On Tue 05 Aug 2014 05:12:41 PM PDT, Ryan C. Thompson wrote:
Hi Valerie,
I got really busy around May and never got a chance to thank you for
adding this option to summarizeOverlaps! So thank you!
-Ryan
On Thu 01 May 2014 04:25:33 PM PDT, Valerie Obenchain wrote
experience with svn or with
git-svn, but this seems like exactly the use case for it.
-Ryan
On Fri 05 Sep 2014 04:50:49 PM PDT, Peter Haverty wrote:
Hi all,
I respectfully disagree. One should certainly check in each discrete unit
of work. These will often not result in something that is ready
either reported it with a patch or explained what I tried
and where I got stuck.
-Ryan
On Mon 06 Oct 2014 05:55:02 PM PDT, Michael Lawrence wrote:
Makes sense to me. Just wondering: if S4Vectors were say on github,
would this be something that you would be comfortable resolving via a
pull request
I thought CRAN packages weren't allowed to depend on Bioconductor
packages for exactly this reason.
On 03/02/2015 03:18 PM, Laurent Gatto wrote:
Dear all,
I had never realised that CRAN packages that depended on Bioc packages
could actually not be installed with install.packages without
things might be complicated because dplyr uses S3 and S4Vectors uses S4.
Can anyone offer any pointers?
-Ryan
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
That's not ideal because it's duplicating storage unnecessarily.
On 04/22/2015 04:07 AM, Aedin wrote:
This is one instance were a system or simple unix command is very easy
system('cat *.fastq all.fastq')
---
On Apr 22, 2015, at 6:00, bioc-devel-requ...@r-project.org wrote:
Re:
, but it seems
unexpected that graphite cannot handle a pathway included in its own
package.
-Ryan Thompson
sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: Ubuntu 14.04.2 LTS
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME
Thanks Ivana,
I've forwarded your message to the bioc-devel list so graphite
developers can see it.
-Ryan
On 06/16/2015 12:46 PM, ihnat...@iba.muni.cz wrote:
Hello,
this problem is caused by the presence of interaction type
control(In(INHIBITION-COMPETITIVE)) which is missing
This is great to hear. I sometimes want to delve into the source code of
a package's internals, but doing so through the SVN web interface is
clunky. Being able to use Github's repo browsing functionality for Bioc
packages is great.
On 06/16/2015 12:00 PM, Dan Tenenbaum wrote:
Dear
a test for
string equality. I believe the solution is to replace that test with:
all(sprintf(%i, pmi) == rownames(pms))
-Ryan
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
will have length zero and ifelse does NOT do lazy
evaluation.
On 07/06/2015 12:21 PM, Ryan C. Thompson wrote:
Hello,
I just encountered a bug in frmaTools that makes it impossible to use
on certain array platforms. The following lines in
makeVectorsAffyBatch fail on an AffyBatch object
MASS_7.3-41
[28] GenomicRanges_1.20.5 colorspace_1.2-6 stringi_0.5-2
[31] munsell_0.4.2 affyio_1.36.0
On 07/07/2015 06:52 AM, Matthew McCall wrote:
Ryan,
Thanks for pointing these out. I'll look into them soon, but I imagine
your assessment is correct.
Best,
Matt
On Mon, Jul 6, 2015
Konsole output Hello,
I was recently setting up the latest version of R Bioc on a system,
installing all packages from scratch, and I ran into an error while
installing bumphunter. It failed to install because it couldn't load the
digest package. After installing this package manually,
From base, according to my R console:
subset
standardGeneric for subset defined from package base
function (x, ...)
standardGeneric(subset)
environment: 0x4eb60c8
Methods may be defined for arguments: x
Use showMethods(subset) for currently available ones.
On 07/29/2015 10:40 AM, Steve
.
I leave it up to the developers of the SRAdb package to decide whether
or not this is a bug, but I think it should at least be documented that
the sort order of the output of sraConvert is arbitrary and will not
necessarily match the input.
-Ryan
66 matches
Mail list logo
