On 09/27/2014 10:01 AM, Andrzej Oleś wrote:
Hi Ramon,
many thanks for your feedback an for your nice suggestion! Having more
distinctive image captions is for sure something worth considering. I
personally like the idea of having them typeset in a slightly smaller font
and with boldface label.
On 09/28/2014 07:49 PM, Kasper Daniel Hansen wrote:
3. (well, this is GenomicRanges) It seems like GenomicFiles has a lot of
similarities with SummarizedExperiment. I have a lot of use cases for a
simple class which has a single GRanges slot, and then support stuff like
granges(), start(),
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
On 10/05/2014 01:39 PM, Robert Castelo wrote:
hi,
i have the following warning message when installing the devel version
(0.99.5) of my package 'qpgraph':
** testing if installed package can be loaded
Warning: replacing previous import by 'IRanges::as.vector' when loading
'qpgraph'
* DONE
:19 PM, Martin Morgan mtmor...@fhcrc.org wrote:
On 10/06/2014 07:52 AM, Daniel Schmolze wrote:
I'm getting a vignette error from the BioC build servers that I can't
reproduce locally:
* creating vignettes ... ERROR
Quitting from lines 116-119 (saps.Rmd)
Error: processing vignette 'saps.Rmd
list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Dr. Martin Morgan, PhD
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman
, 2014 at 3:08 AM, Robert Castelo robert.cast...@upf.edu
mailto:robert.cast...@upf.edu wrote:
hi Martin,
On 10/06/2014 07:24 PM, Martin Morgan wrote:
[...]
There are two 'as.vector' generics, one defined in Matrix and one in
BiocGenerics (and made available via IRanges
On 10/07/2014 07:05 PM, Michael Lawrence wrote:
I think the intent there is that if you virtually always need a package to
generate the input or analyze the output of a documented function, it
should be in Depends. If it's a package that is only useful for
demonstration, it should be in
Hi Weijun --
Thanks for the comments...
On 10/08/2014 12:15 PM, Luo Weijun wrote:
Dear all, I noticed that the classical bioc-help email was shut down
completely, instead we have to use the new bioc support forum. I feel that we
can be a little more cautious on this.
First, there should be
On 10/10/2014 08:24 AM, Leonardo Collado Torres wrote:
Hi,
I think that the docs for ?loadDb (AnnotationDbi) need to be updated
as described below.
According to ?loadDb in AnnotationDbi 1.27.19
dbType
dbType - not required
dbPackage
dbPackage - not required
However, R CMD check for
On 10/11/2014 08:41 AM, Vincent Carey wrote:
Is there anything on the order of as([GeneSet], GRanges) around?
no, I don't think so; obviously of use and following a common theme. Martin
On Sat, Sep 20, 2014 at 11:34 PM, Gabe Becker becker.g...@gene.com wrote:
Sean and Vincent,
The goal
Hi Laurent --
On 11/04/2014 01:33 AM, Laurent Gatto wrote:
Something's fishy with my R devel/Bioc 3.1 installation and I fail to
see what is wrong.
I want to install Homo.sapiens:
library(BiocInstaller)
## Bioconductor version 3.1 (BiocInstaller 1.17.1), ?biocLite for help
On 11/04/2014 11:03 AM, Laurent Gatto wrote:
On 4 November 2014 13:41, Martin Morgan wrote:
Hi Laurent --
On 11/04/2014 01:33 AM, Laurent Gatto wrote:
Something's fishy with my R devel/Bioc 3.1 installation and I fail to
see what is wrong.
[...]
bioclite(homo.sapiens)
## bioc_mirror
SYSTEMS ANALYST PROGRAMMER III / IV
The Bioconductor project (http://bioconductor.org) seeks an individual to join
our software development team.
If you're interested, or know someone who is, please visit
https://support.bioconductor.org/p/62737/
for more details!
Best,
Martin Morgan
On 11/08/2014 08:01 AM, Vincent Carey wrote:
our guidelines state
Packages you depend on must be available via Bioconductor or CRAN; users
and the automated build system have no way to install packages from other
sources.
with increased utility of devtools/install_github perhaps we can relax
On 11/08/2014 08:53 AM, Michael Lawrence wrote:
On Sat, Nov 8, 2014 at 8:01 AM, Vincent Carey st...@channing.harvard.edu
wrote:
our guidelines state
Packages you depend on must be available via Bioconductor or CRAN; users
and the automated build system have no way to install packages from
On 11/09/2014 11:06 AM, Dan Tenenbaum wrote:
- Original Message -
From: Martin Morgan mtmor...@fredhutch.org
To: Laurent Gautier lgaut...@gmail.com, bioc-devel@r-project.org
Sent: Sunday, November 9, 2014 8:26:48 AM
Subject: Re: [Bioc-devel] PPA with built bioconductor packages
On 11/14/2014 02:51 AM, 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 fulfill the requirements of the Bioconductor
Package Guidelines and
On 11/14/2014 01:11 PM, January Weiner wrote:
Dear all,
thanks for your input, it was very helpful. I have some other specific
questions, though:
Martin
You'll want to develop your package on Bioc- and R-devel, as this
is the environment in which your package will be introduced to
the Bioc
On 11/15/2014 12:04 PM, January Weiner wrote:
Dear Martin,
thanks for your description, just a question
mkdir -p ~/src/R-devel
cd ~/src/R-devel
svn co https://svn.r-project.org/R/trunk
tools/rsync-recommended
I think this should be
trunk/tools/rsync-recommended
mkdir -p ~/bin/R-devel
cd
Re-directed from R-devel, where I guess it went by accident.
On 11/18/2014 09:00 AM, Cook, Malcolm wrote:
Hi,
I understand ShortRead::FastqStreamer will read chunks in parallel depending
on the value of ShortRead:::.set_omp_threads
I see this discussed here:
On 11/25/2014 04:46 PM, Peter Hickey wrote:
Hi Martin,
Accessing the names of the assays in a SummarizedExperiment object is very slow
when doing this by what seems that natural way of names(assay(se)). I now see
that it should be done by names(assay(se, withDimnames = FALSE). But I was only
On 11/26/2014 01:39 AM, Joachim Schumann wrote:
Hi everyone,
this morning I got an email from bioconductor.
The message:
According to the Build/check report for BioC 3.0,
the flowCHIC package has the following problem(s):
ERROR for 'R CMD check' on zin1.
The error I get is the following:
This question is better asked on the Bioconductor support site
https://support.bioconductor.org
please re-post the question (and great answer from Ulrich!) there. I think
there's a straight-forward Biostrings solution, too, and I'm sure it will be
posted when the question appears in the
On 11/26/2014 12:11 PM, Hervé Pagès wrote:
Hi guys,
I like the idea of separating the row data from the row ranges.
This could be formalized with 2 distinct accessors: rowData() and
rowRanges(). The former would return a DataFrame, and the latter
NULL or a range-based object (GRanges or
On 12/02/2014 07:04 AM, Paolo Martini wrote:
Dear list,
since my last commit to the release version of clipper, the package has
disappeared from the daily built system of release 3.0 .
Do you have any idea of what's happening?
The devel version is still there... and passes all the checks.
On 12/04/2014 09:56 AM, Michael Love wrote:
I was thinking about a request from someone at Bioc2014 (I can't
remember at the moment)
As an end-user, if I have an object x, how can I *quickly* recall the
main methods for that? As in, without breaking my flow and going to
?myClass or
to discover these without relying on package
break during build / check / install?
Martin Morgan
Michael L and I were not sure how many other packages or R code this
would influence and he was expecting very very few.
Best regards,
Martin Maechler, ETH Zurich
On 01/20/2015 05:06 PM, Dan
:38 PM, Martin Morgan mtmor...@fredhutch.org
mailto:mtmor...@fredhutch.org
wrote:
On 01/21/2015 10:17 AM, avinash sahu wrote:
Hi Dan,
Thanks for the reply and quick support. I am sorry for so many issues,
I
am
somewhat novice in bioconductor
at 6:15 AM, Martin Morgan mtmor...@fredhutch.org wrote:
On 01/22/2015 12:26 AM, Martin Maechler wrote:
Mike wjia...@fhcrc.org
on Tue, 20 Jan 2015 17:16:37 -0800 writes:
I don't think it has been addressed yet in the later commits of
R-devel.
And that piece of code
On 02/08/2015 05:31 AM, de...@gmx.de wrote:
Hi everyone,
I am trying to install the edgeR package on Linux Mint 17 Cinnamon 64-bit.
I have installed R the normal way via
sudo apt-get install r-base
Have you also
sudo apt-get install r-base-dev
? This is needed to install
On 01/21/2015 10:17 AM, avinash sahu wrote:
Hi Dan,
Thanks for the reply and quick support. I am sorry for so many issues, I am
somewhat novice in bioconductor. I am replying to your comments inline.
On Wed, Jan 21, 2015 at 6:55 PM, Dan Tenenbaum dtene...@fredhutch.org
wrote:
See my
On 01/16/2015 03:00 PM, Dario Strbenac wrote:
Thank you for the detailed explanation. I understand the cause now. Actually,
the exact problem is that, in runTest, I have a condition that depends on the
previous function calls :
if(any(grepl(runTests, deparse(sys.calls()
If runTest was
On 02/11/2015 05:52 AM, Elena Grassi wrote:
Hello,
I've just submitted a package and I'm trying to address the last
issues thanks to the automated building system (if it's inappropriate
to ask here before hearing from the reviewer please ignore this mail
and excuse me!).
I am still getting
.
On Wed, Feb 18, 2015 at 8:38 AM, Philip Lijnzaad
p.lijnz...@umcutrecht.nl mailto:p.lijnz...@umcutrecht.nl
wrote:
On 02/18/2015 05:13 PM, Martin Morgan wrote:
On 02/18/2015 08:05 AM, Philip Lijnzaad wrote:
Dear
On 02/18/2015 08:05 AM, Philip Lijnzaad wrote:
Dear all,
looking up the documentation on functions like follow() and precede() is
very hard, since they are only documented under the topic nearest-methods,
which currently (GenomicRanges package 1.18.4) can only be found using the
?
Thanks in advance,
- Gord Brown
Details:
R v3.1.2, and also the latest devel version
gnu make 3.81, 3.82, 4.1
centos linux 6.6
*
*
Message: 3
Date: Fri, 23 Jan 2015 19:36:46 -0800
From: Martin Morgan mtmor...@fredhutch.org mailto:mtmor...@fredhutch.org
To: Michael Lawrence
On 01/29/2015 06:41 AM, Thomas Lin Pedersen wrote:
Hi
I’m querying on whether there are any plans on supporting random access reading
of fasta files in the sense that it is possible to upfront specify the indexes
of sequences that should be read in.
I’m working on a package for comparative
On 01/23/2015 06:22 PM, Michael Lawrence wrote:
Here is a quote from Brian's email to CRAN maintainers:
The set of make programs in use for R is shifting (BSD make seems to
be no longer in use by Apple or FreeBSD; dmake and pmake variants are
appearing) and we have taken the POSIX
On 02/10/2015 01:51 AM, Guangchuang Yu wrote:
Dear all,
I found the vignette of my package DOSE is missing,
http://bioconductor.org/packages/devel/bioc/html/DOSE.html.
I am pretty sure the I don't have .Rbuildignore file and the vignette,
DOSE.Rnw, passing the build with knit2pdf.
Not only it
On 03/09/2015 07:36 AM, Kasper Daniel Hansen wrote:
On Mon, Mar 9, 2015 at 10:30 AM, Vincent Carey st...@channing.harvard.edu
wrote:
I am glad you are keeping this discussion alive Kasper.
On Mon, Mar 9, 2015 at 10:06 AM, Kasper Daniel Hansen
kasperdanielhan...@gmail.com wrote:
It sounds
datasets utils
methods base
other attached packages:
[1] GenomicRanges_1.19.42 GenomeInfoDb_1.3.13 IRanges_2.1.41
S4Vectors_0.5.21
[5] BiocGenerics_0.13.6 RUnit_0.4.28 devtools_1.7.0
knitr_1.9
[9] BiocInstaller_1.17.5
On Wed, Mar 4, 2015 at 3:03 PM, Martin Morgan mtmor
.
Martin
Best,
Kasper
On Tue, Mar 10, 2015 at 3:50 PM, Henrik Bengtsson henrik.bengts...@ucsf.edu
mailto:henrik.bengts...@ucsf.edu wrote:
On Tue, Mar 10, 2015 at 12:30 PM, Martin Morgan mtmor...@fredhutch.org
mailto:mtmor...@fredhutch.org wrote:
On 03/10/2015 11:08 AM, Kasper
On 03/10/2015 11:08 AM, Kasper Daniel Hansen wrote:
Ok, I had to manually remove the BiocInstaller package, restart R and then
run biocLite and I am now on BiocInstaller 1.17.5 ~ Bioconductor 3.0
any idea how BiocInstaller 1.16.x was installed in the R-3.2 library? I think
install.packages()
On 03/12/2015 08:12 AM, Tim Triche, Jr. wrote:
What he said
This doesn't make any sense from an API perspective. When would a user ever
expect to see unnamed assay matrices?
When there's a single assay?
--t
On Mar 12, 2015, at 7:46 AM, Kasper Daniel Hansen
kasperdanielhan...@gmail.com
On 03/24/2015 02:31 AM, Wolfgang Huber wrote:
Before we start a religious war, can we make progress on the pragmatic goal of
making it possible to provide such URLs to people?
There are two concepts
- ‘the package' - a specific version, running in a specific environment,
‘frozen’, etc. (Gabe)
On 04/01/2015 05:08 AM, Michael Lawrence wrote:
It would be nice if someone from Seattle would weigh in on this.
I was hoping to weigh in with 'it's done' but will instead with 'it will be
done'.
A second aspect of Jesper's data that took me a little by surprise and is
related to Michael's
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 setting a
repo or using BiocInstaller::bioLite. Here is an example using a fresh R
installation
On 03/04/2015 10:03 AM, Peter Haverty wrote:
Michael has a good point. The complexity of the BioC universe of classes
hurts our ability to attract new users. More classes would be a minus there
... but a small set of common, explicit APIs would simplify things.
Rectangular things implement the
Let me take this belated opportunity to introduce Jim Hester
jhes...@fredhutch.org to the Bioconductor developer community.
Jim is working in the short term on SummarizedExperiment, including the
refactoring efforts he introduced yesterday as well as coercion methods to and
from ExpressionSet
A /trunk/madman/Rpacks/annotate/DESCRIPTION
added the start of some annotation functionality
H.
On 02/27/2015 04:37 PM, Hervé Pagès wrote:
On 02/27/2015 03:28 PM, Martin Morgan wrote:
I noticed that we're at r99955 in svn
On 03/23/2015 09:55 AM, Gabe Becker wrote: Thus it is more likely that a
person will do the right thing if it happens
to be the most convenient thing IMHO. Anything to advance this strategy
would be a step in the right direction
Bioc core team: This may be getting a bit off topic, but has
On 04/03/2015 04:37 AM, Andrea Rau wrote:
Hello,
I am the maintainer of a Bioconductor package called 'HTSFilter' that
imports DESeq2. On today's build report, I see that my package (as well
as DESeq2 and all of the other packages that import it) is showing an
error message which seems to arise
On 04/21/2015 02:18 PM, Ryan C. Thompson wrote:
Hello,
Often when sequence data is delivered to me, I receive each sample in several
input files. Generally I want to get them into a single file ASAP, and the
filterFastq step would be a convenient place to do it. Is there any possibility
to add
On 04/22/2015 10:28 AM, Jim Hester wrote:
I typically use pipe() in these circumstances which avoids using any
additional storage
readLines(pipe(cat file1 file2))
It should work with filterFastq assuming it can read from connections
rather than just files, but I have not tested it to be
On 04/24/2015 09:07 AM, James W. MacDonald wrote:
A poster on the support site reported some warnings issued when running
hyperGTest() from GOstats. I tracked this down to the ls() function from
AnnotationDbi, when it dispatches on AnnDbBimap objects. The method is:
setMethod(ls,
?
Martin Morgan
Warning: namespace 'GenomeInfoDb' is not available and has been replaced
by .GlobalEnv when processing object ''
Warning: namespace 'GenomeInfoDb' is not available and has been replaced
by .GlobalEnv when processing object ''
Warning: namespace 'GenomeInfoDb' is not available and has
On 05/18/2015 06:06 AM, Christian Arnold wrote:
Thanks for your input, highly appreciated!
I can see that the semantics of [ are violated, so I agree that
overwriting the subset method is probably a better way to go.
Essentially, the object stores several, individual-specific count
matrices
and users have a chance to make
changes to their own packages and work flows.
Feedback is of course always welcome.
Best,
Martin Morgan
Bioconductor
--
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
, Martin Morgan mtmor...@fredhutch.org wrote:
On 04/10/2015 04:34 AM, Rainer Johannes wrote:
hi Martin,
but if that's true, then I will never have a way to test whether the
recipe actually works, right?
I guess I don't really know what I'm talking about, and that insert=FALSE
is intended
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,
On 04/09/2015 05:57 AM, Ludwig Geistlinger wrote:
Here you go ...
sessionInfo()
R Under development (unstable) (2015-03-09 r67969)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: Debian GNU/Linux 8 (jessie)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3]
On 06/05/2015 08:51 AM, Robert Castelo wrote:
hi,
importing an OBO file with GSEABase::getOBOCollection() I have observed missing
children in the imported ontology. Here is an example with the Sequence
Ontology:
Thanks Robert, the import went ok, but the coercion to graphNEL was flawed. This
On 06/08/2015 11:43 PM, Rainer Johannes wrote:
dear Robert and Ludwig,
the EnsDb packages provide all the gene/transcript etc annotations for all
genes defined in the Ensembl database (for a given species and Ensembl
release). Except the column/attribute entrezid that is stored in the
internal
On 06/09/2015 02:52 AM, Simon Anders wrote:
Hi
My two cents:
On 04/06/15 19:50, James W. MacDonald wrote:
In other words, for me it is a common practice to do something like this:
fit - lmFit(eset, design)
fit2 - eBayes(fit)
gns - select(chippackage, featureNames(eset), c(ENTREZID,SYMBOL))
On 06/24/2015 10:42 AM, Michael Lawrence wrote:
In order for R to find those symbols reliably, you need to import
those functions into your NAMESPACE, and therefore you should ensure
yes
that the Biobase package is listed on the Depends line of your
DESCRIPTION. Your package directly depends
On 06/17/2015 11:41 AM, davide risso wrote:
Dear list,
I'm creating an R package to store RNA-seq data of a somewhat large project
in which I'm involved.
One of the initial goals is to compare different pre-processing pipelines,
hence I have multiple expression matrices corresponding to the
On 05/28/2015 06:32 AM, Robert M. Flight wrote:
Thanks for the feedback Wolfgang. I never thought to look at how many
packages in Bioconductor have a baseName and baseName2 to see how often
this is done. I assume based on the existence of Roxygen2 and ggplot2 that
there were initial versions of
On 08/12/2015 02:01 PM, Vincent Carey wrote:
It seems to me we may need a class to manage related annotation
structures. For example, the chromImpute segmentations of the genome
defined for various cell types. I would like to be able to take a region
of the genome (say a SNP) and ask how the
On 08/24/2015 07:37 AM, Charles Determan wrote:
This initially came to my attention with this question on StackOverflow (
http://stackoverflow.com/questions/32139378/travis-ci-failing-to-install-bioconductor?noredirect=1#comment52184421_32139378).
I have noticed that my own bioconductor package
On 07/30/2015 09:02 AM, Alejandro Reyes wrote:
Dear Leonard,
Thanks a lot for reporting this. It should be fixed in the version that
I just committed to the svn (DEXSeq 1.5.10).
While debugging the DEXSeq code, I noticed that summarizedOverlaps is
giving me an error, which I think its a bug
On 08/04/2015 03:06 AM, Vincent Carey wrote:
Thanks for all input. Henrik's comments deserve to be in WRE or developer
doc for bioc, IMHO.
yes, was there any attempt to get something more in WRE? Martin
On Tue, Aug 4, 2015 at 3:02 AM, Henrik Bengtsson henrik.bengts...@ucsf.edu
wrote:
You
On 08/04/2015 06:43 AM, Nathan Olson wrote:
We are starting to work on an infrastructure for annotation of 16S metagenomic
sequencing datasets and would like your comments and/or contributions. Below are
links to two github repositories: metagenomeFeatures and greengenes13.5MgDb.
The
On 07/23/2015 10:41 AM, Hervé Pagès wrote:
Hi Mike,
On 07/22/2015 04:13 PM, Michael Love wrote:
it's slightly annoying to write
foo - function(x) {
if ( ! is.numeric(x) ) stop(x should be numeric)
if ( ! length(x) == 2 ) stop(x should be length 2)
c(x[2], x[1])
}
That's a little
On 08/28/2015 02:51 PM, Dan Tenenbaum wrote:
- Original Message -
From: Laurent Gatto lg...@cam.ac.uk
To: Dan Tenenbaum dtene...@fredhutch.org
Cc: Kasper Daniel Hansen kasperdanielhan...@gmail.com, bioC-devel
bioc-de...@stat.math.ethz.ch, Laurent
Gatto lg...@cam.ac.uk
Sent: Friday,
On 06/08/2016 04:44 AM, Yu, Guangchuang wrote:
Dear all,
I found many peoples still using (and asking questions of) out-dated branch
of Bioconductor packages that are no longer maintained.
I think it would be great to have a message notifying them when they are
browsing the web page of
in the community who would like to
take responsibility for this? Otherwise we will close this resource.
Feel free to contact me on or off list,
Martin Morgan
Bioconductor
This email message may contain legally privileged and/or...{{dropped:2
On 06/09/2016 10:06 AM, James W. MacDonald wrote:
You should post this on the support site (https://support.bioconductor.org),
using the 'News' item description. This bioc-devel is intended for
discussion of issues with development of packages, not really for
announcing new packages.
actually
ase of version 3.3." *
On Thu, Jun 9, 2016 at 10:09 AM, Martin Morgan <
martin.mor...@roswellpark.org> wrote:
On 06/09/2016 10:06 AM, James W. MacDonald wrote:
You should post this on the support site (
https://support.bioconductor.org), using the 'News' item
description. This bioc-
On 06/14/2016 10:10 PM, Kasper Daniel Hansen wrote:
In my case its an annotation package thats >100MB. But I could imagine
experiment package doing that as well.
very large packages don't play well with SVN or the repository, e.g.,
placing storage burden on repository mirrors. ExperimentHub
On 06/15/2016 05:32 AM, Rue-Albrecht, Kevin C wrote:
Hi all,
I think my previous email didn’t get through because of screenshots
paste in the email.
Apologies for the relatively basic question, but… can anyone tell me
how to produce the alphabetical index of man pages that appears in
RStudio
Hi Jil --
On 05/28/2016 02:36 PM, Jil Sander wrote:
Dear all,
I am very new to the package development process and I am facing a
beginner's issue I suppose.
The main function of my package automatically saves output files of
intermediate steps (PDF result files as well as R objects
of nightly build seem necessary anyway, to account for changes
in packages outside Bioconductor control.
Martin Morgan
Yours,
Steffen
On Mi, 2016-06-22 at 22:46 -0400, Kasper Daniel Hansen wrote:
That's crazy. Not so much that I have to do it once, but that I
apparently
will have to do this going
On 06/20/2016 09:22 PM, Leonardo Collado Torres wrote:
I was going to say that for the tutorial users it might be easier to
use devtools::install_github('Bioconductor-mirror/GenomicRanges')
FWIW biocLite("Bioconductor-mirror/GenomicRanges") invokes
install_github(). Martin
rather than svn.
On 06/18/2016 12:58 AM, Leonardo Collado Torres wrote:
Hi,
I get the same error while hosting the data somewhere else or when using
RawGit's url. That is:
library('downloader')
download('
http://www.biostat.jhsph.edu/~lcollado/recount/metadata_clean_sra.Rdata',
destfile = 'test2.Rdata')
The appropriate place for the this question is the support site; no need
to cross-post https://support.bioconductor.org/p/79460/
Martin
On 03/09/2016 11:22 PM, huizhu.gmail wrote:
Dear all,
When I run "makeTxDbFromGFF", I got the error message ... Error in
get(name, envir =
not declared in the "imports" line of the DESCRIPTION).
I don't know if the newest version of BiocCheck still complains about
them now.
The right solution is to declare them in the Imports: line, too.
Martin
-Steve
-Original Message----- From: Martin Morgan
[mailto:
Hi Aaron --
On 03/15/2016 08:40 AM, Aaron Taudt wrote:
I am trying to register my native routines as recommended by BiocCheck. I
followed the instructions in "Writing R Extensions" and have implemented
the following code in "init.cpp". However, the routines are still not
registered.
#include
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2016-03-15 14:09 GMT+01:00 Martin Morgan <martin.mor...@roswellpark.org
<mailt
As we exchanged in separate email, I think that the SIZE of this data
does NOT require that you produce an annotation package.
The package guidelines
http://bioconductor.org/developers/package-guidelines/#correctness say
that the package should occupy less than 4MB on disk. Your package has
On 04/07/2016 03:54 AM, Karim Mezhoud wrote:
unfortunately,
Bioconductor version 3.3 (BiocInstaller 1.21.4), ?biocLite for help
Bioconductor does not yet support R version 3.4.0
The release of Bioconductor on May 4 and the next release in the fall
will both be based on the R-3.3.* series,
On 03/17/2016 10:35 AM, Martin Morgan wrote:
On 03/17/2016 10:29 AM, Peter Hickey wrote:
Thanks, Aaron. I implemented a similar workaround, but I think it
would be nice to have in the core Bioconductor implementation. I had a
quick poke around GenomicAlignments::readGAlignmentPairs
On 03/22/2016 08:34 AM, Gmail2 wrote:
Dear Bioc-dev guys,
I recently fixed some bugs in my package SICtools and commit the changes into
Release_3_2. To my surprise, it seems that the source in the website
(http://bioconductor.org/packages/3.2/bioc/html/SICtools.html
On 03/22/2016 07:53 AM, Glyn Bradley wrote:
Hi,
We’ve got CausalR back up both in the 3.2 release and devel, but although we
committed the same package (with different version number) to both release and
devel, the landing pages are showing
build:OK in release but build:warnings in devel.
the biocLite.R script has been changed to use bioc-devel when the R
version is 'too new'.
Worth pointing out perhaps that Bioconductor will not use R-devel again
for another six months -- after our next release, both release and devel
versions of Bioconductor will use the R-3-3-branch,
Best regards,
Xiaobin
On 22 Mar 2016, at 13:55, Martin Morgan <martin.mor...@roswellpark.org
<mailto:martin.mor...@roswellpark.org>> wrote:
On 03/22/2016 08:34 AM, Gmail2 wrote:
Dear Bioc-dev guys,
I recently fixed some bugs in my package SICtools and commit the
changes into R
packages submitted by
that date through the preview process in time to be included in the release.
Also, a reminder that we will switch to an open review system at the
start of the next release cycle; further details to follow...
https://support.bioconductor.org/p/76472/
Martin Morgan
On 04/02/2016 08:01 AM, Krithika Bhuvaneshwar wrote:
Hello
We are authors of the newly accepted CINdex package.
We have not received our SVN credentials yet. I believe today is the last
day to make changes to the package before the new release .
Credentials were sent to the maintainer
On 04/25/2016 03:53 PM, Michael Lawrence wrote:
Yea, this is a bug in R, in my opinion. The class cache circumvents
the namespace imports. In my working copy I've fixed it by falling
back to the namespace search when there are multiple hits. That at
least fixes this case.
This also fixes it
On 04/26/2016 05:28 PM, Michael Lawrence wrote:
> On Tue, Apr 26, 2016 at 2:16 PM, Martin Morgan
> <martin.mor...@roswellpark.org> wrote:
>> >
>> >On 04/26/2016 04:47 PM, Michael Lawrence wrote:
>>> >>
>>> >>On Tue,
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