Following up on the discussion this morning about refining the
guidelines for using existing classes and generics, I am wondering if
there is such a thing as too much dependency. Say there is a package
that has a useful class, but it depends/imports 10 other packages (none
of which I would imp
You can solve the package size issue by putting your example data in a
separate "experiment data" package
(http://www.bioconductor.org/packages/release/data/experiment/).
Stephanie
On 2/27/13 3:03 AM, Davide Rambaldi wrote:
Hi all,
I am working on a library called flowFit, the purpose of thi
Hi all,
There is a non-exported function in VariantAnnotation called
.toDNAStringSetList that converts a vector of comma-separated character
strings to a DNAStringSetList. I'd like to use this code in a package
I'm working on. Would it make sense to export this from Biostrings? If
not, wha
NAStringSetList constructor, so
I'm glad it will be starting tomorrow.
Stephanie
On 4/19/13 12:35 PM, Hervé Pagès wrote:
Hi Stephanie,
On 04/19/2013 11:55 AM, Stephanie M. Gogarten wrote:
Hi all,
There is a non-exported function in VariantAnnotation called
.toDNAStringSetList that conver
I had this issue with GWASTools/GWASdata at one point. There is only
one copy of an experiment data package, so if you change it, it will
break the current release version of bsseq. The solution I came up with
was to add new objects with different names to the data package, and
change my exam
Hi Valerie,
The asVCF method in SeqArray is failing as of today with a (to me)
mysterious error. I get it for the test files chr22.vcf.gz, ex2.vcf,
and gl_chr1.vcf in extdata of VariantAnnotation, but not for
SeqArray/extdata/CEU_Exon.vcf. Do you have any suggestions of where I
might look t
subscript contains NAs
One solution is use %in% which does not return NAs.
Browse[2]> x %in% ""
LogicalList of length 5
[[1]] FALSE
[[2]] FALSE
[[3]] FALSE FALSE
[[4]] FALSE
[[5]] FALSE FALSE
Valerie
On 11/22/2013 03:11 PM, Stephanie M. Gogarten wrote:
Hi Valerie,
The asVCF metho
Dear Bioconductors,
The Department of Biostatistics at the University of Washington, Seattle
has a position open for a Research Scientist/Engineer 4. Basic
responsibilities are to provide data analysis, programming, experimental
design, interpretation and reporting of results for statistical
I would say rows 1 and 3 are SNVs, but not row 4. For this application
I think a variant has to be an SNV or not, as you can't pass half a
variant. (I suppose you could remove the ALT values with length > 1 and
set those genotypes to missing, but that is both complicated and
unexpected behavi
On 7/8/14 12:27 PM, Hervé Pagès wrote:
On 07/08/2014 11:58 AM, Leonardo Collado Torres wrote:
Hello,
Thank you everyone for the replies and help!
I did not know that it was due to S4Vectors::extractROWS nor what
Hervé exposed about the upcoming changes to them.
Regarding "probably it is not
Are tags in "My Tags" automatically Watched? Or should I enter those
tags in both fields?
I really like the option to get email when my packages are mentioned. I
think it will mean that users get help faster, since those of us who are
not constantly watching the mailing list will see relevan
I am guilty of doing this today, but I have (I think) a good reason.
I'm making a bunch of changes that are all related to each other, but
are being implemented and tested in stages. I'd like to use svn to
commit when I've made a set of changes that works, so I can roll back if
I break somethi
On 11/14/14, 9:20 AM, Laurent Gatto wrote:
Dear January,
On 14 November 2014 10:51, January Weiner wrote:
Dear all,
I am building my first Bioconductor package and, before wasting
everyone's time with a faulty submission, I would like to clarify
certain things.
1) The package seems to ful
On 12/2/14 8:17 AM, Dan Tenenbaum wrote:
- Original Message -
From: "Julian Gehring"
To: bioc-devel@r-project.org
Cc: "Felix Klein"
Sent: Tuesday, December 2, 2014 2:19:01 AM
Subject: [Bioc-devel] RSS package feeds not updated
Hi,
some/many of the package build RSS feeds [1] don'
Using the URLs exactly as given on the "Source Control" HOWTO results in
the following error:
svn co
https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/MYPACKAGENAME
svn merge -c140
https://hedgehog.fhcrc.org/gentleman/bioconductor/trunk/madman/Rpacks/MYPACKAGENAME
sv
Why is it that packages with no changes still get new version numbers at
every release? For example, my experiment data package GWASdata has not
changed since the last release, but the version was bumped from 1.4.0 to
1.6.0. I imagine most users expect that a change in version number
indicates
gdsfmt is another option for storing large datasets on disk, similar to
HDF5. Take a look at packages SNPRelate, GWASTools and SeqArray which
all use it to store genotype data.
Stephanie
On 11/5/15 8:41 AM, Fischer, Bernd wrote:
Hi Christian,
you should have a look at packages that for parti
I was notified today that the ncdf package is deprecated and will be
removed from CRAN in January. Since this date does not correspond with a
Bioconductor release, is it possible to add ncdf to the Bioconductor
"extra" repository for the duration of this release? I will modify
GWASTools to use
How long does it usually take for a new package added to Imports to
become available on the build machines? I updated GWASTools on January 4
to depend on ncdf4 instead of ncdf, but the build report for 2/3
machines still says "ncdf4 not available".
thanks,
Stephanie
__
I have a build error for SeqVarTools, but it didn't show up in the
package RSS feed. The last message I got via RSS was "NotNeeded" for
install.
Stephanie
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Which core team member should we contact to add a new maintainer to an
existing package?
thanks,
Stephanie
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Hi Estefania,
After you commit to your github repository, you will need to explicitly
push those changes to svn to get them into Bioconductor devel. I
recommend following the instructions under "Dealing with prior history /
merge conflicts" on this page:
http://www.bioconductor.org/developer
Try following the steps under "Dealing with prior history / merge
conflicts" on the git mirror page:
http://www.bioconductor.org/developers/how-to/git-mirrors/
Using "git cherry-pick" instead of rebase seems to avoid a lot of errors.
Stephanie
On 4/5/17 8:18 AM, Lluís Revilla wrote:
Dear all,
Dear Core Team,
What do you think about adding the following generics to BiocGenerics?
colData
rowRanges
ref
alt
qual
filt
header
fixed
info
geno
They are currently defined by both
VariantAnnotation/SummarizedExperiment and SeqArray. Given the
increasingly widespread use of VCF files, it seem
Array and VariantAnnotation in the same
session, as they would have to add the package name with "::" to
disambiguate the methods.
Martin
On Fri, May 19, 2017 at 8:39 AM, Stephanie M. Gogarten
wrote:
Dear Core Team,
What do you think about adding the following generics
I tried following the instructions in scenario 9 after adding a remote:
$ git remote add upstream https://git.bioconductor.org/packages/GENESIS.git
$ git fetch --all
Fetching origin
Fetching upstream
warning: no common commits
When I merge both upstream and origin, I see all my commits in
duplic
If we followed the steps here:
https://www.bioconductor.org/developers/how-to/git/maintain-github-bioc/
How much, if any, of this will need to be redone after the repositories
are regenerated? In particular, if I don't have an unknown user, will
the regenerated commits be equal to the previous
thanks,
Stephanie
On 8/21/17 1:23 PM, Martin Morgan wrote:
On 08/21/2017 03:17 PM, Stephanie M. Gogarten wrote:
If we followed the steps here:
https://www.bioconductor.org/developers/how-to/git/maintain-github-bioc/
How much, if any, of this will need to be redone after the
repositories are r
Hi Nitesh,
Does this mean that merge commits are not allowed? I have been
developing features on branches and then merging back into the master
branch with a merge commit, which helps me keep track of which commits
go together in a single feature. But when I just tried to push upstream,
I was
Hi,
If one wanted to move some code from an existing Bioconductor package
into its own, separate package for ease of maintenance, would that
constitute a new package submission with the full review process? Or is
there some expedited submission available?
We are refactoring the GENESIS packa
Can we move the "asVCF" generic to BiocGenerics?
thanks,
Stephanie
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t's not
attached until the method is called (with requireNamespace)?
thanks,
Stephanie
The VCF class is defined in the VariantAnnotation package so it
would be weird to have the asVCF() generic in BiocGenerics.
Cheers,
H.
On 10/13/2017 01:55 PM, Stephanie M. Gogarten wrote:
Can we move
Dear Yaoyong,
Can you remove the R version dependency from your DESCRIPTION file
entirely? That will eliminate the warning, but will also not suggest to
users that they need a newer version of R than is necessary. R 2.3.0 was
released in 2006, so it seems highly unlikely that anyone would be
Is this a new policy? Will packages that currently have multiple
maintainers be required to remove all but one?
All three of the packages I maintain have multiple maintainers listed.
In two cases, I added a second maintainer to the packages before I went
on parental leave, to ensure that someo
One possible point of confusion: Laurent's workflow includes maintaining
separate branches "master" and "devel", which he syncs to his own Github
repo and Bioconductor's git repo respectively. However, the
documentation on the bioc website
(https://bioconductor.org/developers/how-to/git/) assum
This sentence seems to indicate that the original format
\link[base]{rbind} should work:
"Because they have been frequently misused, the HTML help system looks
for topic foo in package pkg if it does not find file foo.html."
On 1/17/18 8:56 AM, James W. MacDonald wrote:
On Wed, Jan 17, 2018
Rather than a class union, how about an internal function that is called
by the methods for both matrix and DelayedArray:
setGeneric("myNewRowMeans", function(x,...) {
standardGeneric("myNewRowMeans")})
#' @importFrom DelayedArray rowMeans
.myNewRowMeans <- function(x,...){
# a lot of co
Are there any plans to have another BioC on the west coast in the near
future?
thanks,
Stephanie
On 9/10/18 1:32 PM, Levi Waldron wrote:
Hi all,
I'm organizing a planning committee for Bioc2019 in New York City (at NYU
and Rockefeller University), June 24-26. There is lots to be done includin
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