- Original Message -
From: Steve Lianoglou lianoglou.st...@gene.com
To: Dan Tenenbaum dtene...@fredhutch.org
Cc: Wolfgang Huber whu...@embl.de, bioc-devel@r-project.org
Sent: Tuesday, April 28, 2015 3:57:25 PM
Subject: Re: [Bioc-devel] Short URLs for packages?
Awesome, thank you
- Original Message -
From: Henrik Bengtsson henrik.bengts...@ucsf.edu
To: bioC-devel bioc-de...@stat.math.ethz.ch
Sent: Sunday, April 26, 2015 7:14:20 PM
Subject: [Bioc-devel] Bioc package pages: List also BugReports for a package?
For affxparser, we've got the following in
- Original Message -
From: Leif Väremo var...@chalmers.se
To: bioc-devel@r-project.org
Sent: Tuesday, April 21, 2015 11:38:31 PM
Subject: [Bioc-devel] build error, piano package
Dear developers,
I am hoping someone can help me with this issue:
The piano package in the devel
- Original Message -
From: Dan Tenenbaum dtene...@fredhutch.org
To: Leonardo Collado Torres lcoll...@jhu.edu
Cc: bioc-devel@r-project.org
Sent: Friday, April 17, 2015 12:47:18 PM
Subject: Re: [Bioc-devel] R 3.3 for snow leopard
- Original Message -
From: Leonardo
- Original Message -
From: Dan Tenenbaum dtene...@fredhutch.org
To: Leonardo Collado Torres lcoll...@jhu.edu
Cc: bioc-devel@r-project.org
Sent: Monday, April 20, 2015 12:32:30 PM
Subject: Re: [Bioc-devel] R 3.3 for snow leopard
- Original Message -
From: Dan
Hi all,
As part of our ongoing response to Michael Love's request for more information
when things happen with the build system, today in the devel (3.2) build
reports we see some packages failing in response to some methods (seqapply(),
mseqapply(), tseqapply(), seqsplit(), and seqby()) being
- Original Message -
From: t kuilman t.kuil...@nki.nl
To: bioc-devel@r-project.org
Sent: Friday, April 17, 2015 11:30:14 PM
Subject: [Bioc-devel] Dependency issue
Hello everyone,
I have tested whether our new package CopywriteR could be installed,
but surprisingly got the
- Original Message -
From: Kevin Rue-Albrecht kevin@ucdconnect.ie
To: Tiphaine Martin tiphaine.mar...@kcl.ac.uk
Cc: Dan Tenenbaum dtene...@fredhutch.org, bioc-devel
bioc-devel@r-project.org
Sent: Friday, April 17, 2015 4:30:24 AM
Subject: Re: [Bioc-devel] BioC 3.1 branch
- Original Message -
From: Leonardo Collado Torres lcoll...@jhu.edu
To: bioc-devel@r-project.org
Sent: Friday, April 17, 2015 12:43:12 PM
Subject: [Bioc-devel] R 3.3 for snow leopard
Hi,
This is not BioC related, but should hopefully be quick.
According to
- Original Message -
From: Sergei Ryazansky s.ryazan...@gmail.com
To: bioc-devel@r-project.org
Sent: Friday, April 17, 2015 1:53:41 PM
Subject: [Bioc-devel] Error after upgrading to R 3.2.0 with loading of GO.db:
2 arguments passed to .Internal(ls)
which requires 3
Hello
- Original Message -
From: Sergei Ryazansky s.ryazan...@gmail.com
To: Dan Tenenbaum dtene...@fredhutch.org
Cc: bioc-devel@r-project.org
Sent: Friday, April 17, 2015 2:18:00 PM
Subject: Re: [Bioc-devel] Error after upgrading to R 3.2.0 with loading of
GO.db: 2 arguments passed
The BioC 3.1 branch is now ready.
Remember, you always have access to 2 versions of your package:
the release and the devel versions.
Right now the release version of your package (which is not
officially released yet but will be tomorrow if
everything goes well) is in the 3.1 branch and
- Original Message -
From: Henrik Bengtsson henrik.bengts...@ucsf.edu
To: Dan Tenenbaum dtene...@fredhutch.org
Cc: bioc-devel bioc-devel@r-project.org
Sent: Thursday, April 16, 2015 6:57:45 PM
Subject: Re: [Bioc-devel] BioC 3.1 branch created
On Thu, Apr 16, 2015 at 1:23 PM, Dan
Hello BioC developers,
We will be creating the Bioconductor 3.1 branch today at 12:30 PM
Seattle time. (19:30 UTC). This is about an hour from now.
Please stop all commits to trunk before 12:30PM and do not resume until
further notice.
We will send another email when it is OK to resume
- Original Message -
From: Bastian Schiffthaler bast...@bioinformatics.upsc.se
To: Martin Morgan mtmor...@fredhutch.org
Cc: bioc-devel@r-project.org
Sent: Wednesday, April 15, 2015 2:21:08 AM
Subject: Re: [Bioc-devel] Docker granularity: containers for individual R
packages,
- Original Message -
From: Michael Love michaelisaiahl...@gmail.com
To: bioc-devel@r-project.org
Sent: Wednesday, April 8, 2015 11:03:02 AM
Subject: [Bioc-devel] request for more notices about build issues
dear core Bioc-ers,
It would be nice to have more devel mailing list
- Original Message -
From: Ulrich Bodenhofer bodenho...@bioinf.jku.at
To: Dan Tenenbaum dtene...@fredhutch.org
Cc: Hervé Pagès hpa...@fhcrc.org, m...@bioinf.jku.at, Johannes Palme
jpa...@aon.at, bioc-devel@r-project.org
Sent: Monday, April 13, 2015 11:22:11 AM
Subject: Re: [Bioc
Hi Ulrich,
- Original Message -
From: Ulrich Bodenhofer bodenho...@bioinf.jku.at
To: bioc-devel@r-project.org
Cc: Hervé Pagès hpa...@fhcrc.org, m...@bioinf.jku.at, Johannes Palme
jpa...@aon.at
Sent: Monday, April 13, 2015 3:37:37 AM
Subject: [Bioc-devel] OpenMP on Mac OS Mavericks
Robert, you just need to put MafDb.ExAC.r0.3.sites in Depends, Suggests, or
Imports.
Dan
- Original Message -
From: Robert Castelo robert.cast...@upf.edu
To: bioc-devel@r-project.org
Sent: Friday, April 10, 2015 2:33:04 PM
Subject: [Bioc-devel] MafDb.ExAC.r0.3.sites missing from
- Original Message -
From: Michael Lawrence lawrence.mich...@gene.com
To: Tim Triche, Jr. tim.tri...@gmail.com
Cc: Michael Lawrence lawrence.mich...@gene.com, bioc-devel@r-project.org,
Paul Shannon pshan...@fredhutch.org
Sent: Monday, April 6, 2015 4:48:41 PM
Subject: Re:
Try updating to R-alpha (3.2.0) instead of R-devel (3.3.0).
Dan
- Original Message -
From: Nicolas Delhomme nicolas.delho...@umu.se
To: Dan Tenenbaum dtene...@fredhutch.org
Cc: bioC-devel bioc-de...@stat.math.ethz.ch
Sent: Friday, March 27, 2015 11:12:00 AM
Subject: Re: [Bioc-devel
The builder for submitted packages uses the devtools package and this is a bug
in devtools:
https://github.com/hadley/devtools/issues/717
You can ignore it.
Dan
- Original Message -
From: Glyn Bradley glyn.x.brad...@gsk.com
To: bioc-devel@r-project.org
Sent: Tuesday, March 24,
On March 23, 2015 9:18:57 AM PDT, Tim Triche, Jr. tim.tri...@gmail.com
wrote:
Packages are (read: should be, IMHO) published, citable pieces of
research, though. Imagine if a paper you cite were silently updated
without the doi/citation changing. That wouldn't be good
I don't disagree, but
- Original Message -
From: Vincent Carey st...@channing.harvard.edu
To: Eric Frichot eric.fric...@gmail.com
Cc: bioc-devel@r-project.org
Sent: Sunday, March 22, 2015 11:42:52 AM
Subject: Re: [Bioc-devel] development vs release version
On Sun, Mar 22, 2015 at 2:27 PM, Eric Frichot
- Original Message -
From: Jianhong Ou jianhong...@umassmed.edu
To: bioc-devel@r-project.org
Sent: Thursday, March 19, 2015 8:36:28 AM
Subject: [Bioc-devel] How to remove warnings when load BiocGenerics,
AnnotationDbi and GenomeInfoDb
Hi,
How could we mask the warnings when
- Original Message -
From: Vladislav Petyuk pet...@gmail.com
To: bioc-devel@r-project.org
Sent: Friday, March 20, 2015 2:43:03 PM
Subject: [Bioc-devel] Mavericks Not Supported message
Hi,
Could someone tell me about the possible causes of ...NOT
SUPPORTED...NOT
SUPPORTED...NOT
-project.org/pipermail/rcpp-devel/2015-March/008524.html
So when this new toolchain (and R-devel built against it) is available, I will
be installing it on the devel windows build machine.
Thanks,
Dan
- Original Message -
From: Dan Tenenbaum dtene...@fredhutch.org
To: bioc-devel bioc
- Original Message -
From: Yinming Jiao 20907...@zju.edu.cn
To: Dan Tenenbaum dtene...@fredhutch.org
Cc: bioc-devel@r-project.org, Andrew Teschendorff and...@picb.ac.cn
Sent: Tuesday, March 17, 2015 10:29:16 PM
Subject: Re: Re: [Bioc-devel] FEM package updation build frequence
- Original Message -
From: Levi Waldron levi.wald...@hunter.cuny.edu
To: bioc-devel@r-project.org
Sent: Monday, March 16, 2015 11:30:54 AM
Subject: [Bioc-devel] developer profiles on bioconductor.org
Since our Seattle team is always looking for extra work (!), I was
thinking
it
- Original Message -
From: Kasper Daniel Hansen kasperdanielhan...@gmail.com
To: Tiphaine Martin tiphaine.mar...@kcl.ac.uk
Cc: Dan Tenenbaum dtene...@fredhutch.org, bioc-devel
bioc-devel@r-project.org
Sent: Monday, March 16, 2015 6:43:40 PM
Subject: Re: [Bioc-devel] Bioconductor
- Original Message -
From: Steven Barrett steven.j.barr...@gsk.com
To: bioc-devel@r-project.org
Sent: Monday, March 16, 2015 8:54:58 AM
Subject: [Bioc-devel] No vignette contents page/fig refs with Devtools build
Hello,
I have a problem with the automated vignette construction
- Original Message -
From: Charles Determan Jr deter...@umn.edu
To: Bioc-devel@r-project.org
Sent: Friday, March 13, 2015 11:57:24 AM
Subject: [Bioc-devel] Submitting a new package
I have finished a new package recently that I would like to submit to
bioconductor. I have read
- Original Message -
From: Charles Determan Jr deter...@umn.edu
To: Dan Tenenbaum dtene...@fredhutch.org
Cc: Bioc-devel@r-project.org
Sent: Friday, March 13, 2015 12:04:12 PM
Subject: Re: [Bioc-devel] Submitting a new package
Thanks Dan, could you confirm that the email
- Original Message -
From: Michael Love michaelisaiahl...@gmail.com
To: Dan Tenenbaum dtene...@fredhutch.org
Cc: bioc-devel@r-project.org
Sent: Friday, March 13, 2015 6:24:56 PM
Subject: Re: [Bioc-devel] testthat instructions for website
On Mar 13, 2015 9:13 PM, Dan
- Original Message -
From: Michael Love michaelisaiahl...@gmail.com
To: bioc-devel@r-project.org
Sent: Friday, March 13, 2015 6:06:39 PM
Subject: [Bioc-devel] testthat instructions for website
hi Bioc team,
Can we add some testthat instructions to the unit testing page:
Hi all,
This is relevant (and possibly quite important) to all package maintainers
whose packages contain C or C++ code, or depend on one that does.
A new toolchain is available for building R and R packages on Windows. This
toolchain uses gcc 4.9.2 whereas the old one used gcc 4.6.3.
Another
Hi,
- Original Message -
From: Rainer Johannes johannes.rai...@eurac.edu
To: bioc-devel@r-project.org
Sent: Wednesday, March 11, 2015 1:06:15 PM
Subject: [Bioc-devel] Strange warning message on build server moscato2
dear all!
I have submitted a new package that builds nicely on
- Original Message -
From: Dan Tenenbaum dtene...@fredhutch.org
To: bioc-devel bioc-devel@r-project.org
Sent: Friday, February 27, 2015 10:12:44 AM
Subject: [Bioc-devel] Bioconductor 3.1 release schedule now available
Hi all,
The next version of Bioconductor will be 3.0 and its
- Original Message -
From: Michael Lawrence lawrence.mich...@gene.com
To: Hervé Pagès hpa...@fredhutch.org
Cc: Michael Lawrence lawrence.mich...@gene.com, bioc-devel@r-project.org,
James Macdonald
jmac...@u.washington.edu
Sent: Wednesday, February 18, 2015 11:12:13 AM
Subject:
- Original Message -
From: Ryan r...@thompsonclan.org
To: stephen piccolo stephen_picc...@byu.edu
Cc: bioC-devel bioc-de...@stat.math.ethz.ch
Sent: Friday, February 6, 2015 9:37:24 AM
Subject: [Bioc-devel] Error in citation info for SPAN.UPC
Hi Stephen,
I noticed that there's
- Original Message -
From: Dan Tenenbaum dtene...@fredhutch.org
To: Ryan r...@thompsonclan.org
Cc: bioC-devel bioc-de...@stat.math.ethz.ch, stephen piccolo
stephen_picc...@byu.edu
Sent: Friday, February 6, 2015 10:13:16 AM
Subject: Re: [Bioc-devel] Error in citation info
- Original Message -
From: Elena Grassi grass...@gmail.com
To: bioc-devel@r-project.org
Sent: Monday, January 26, 2015 1:14:59 AM
Subject: [Bioc-devel] unit tests for C code inside a package
Hi,
I'm writing a package that calculates total affinity (see PMID
21335606 and
- Original Message -
From: Levi Waldron levi.wald...@hunter.cuny.edu
To: bioc-devel@r-project.org
Sent: Sunday, January 25, 2015 9:33:56 AM
Subject: Re: [Bioc-devel] Announcing Docker containers for Bioconductor
Perhaps docker should be mentioned on
- Original Message -
From: Levi Waldron levi.wald...@hunter.cuny.edu
To: Dan Tenenbaum dtene...@fredhutch.org
Cc: bioc-devel@r-project.org
Sent: Sunday, January 25, 2015 11:45:23 AM
Subject: Re: [Bioc-devel] Announcing Docker containers for Bioconductor
On Sun, Jan 25
in bioconductor. I am replying to your
comments inline.
On Wed, Jan 21, 2015 at 6:55 PM, Dan Tenenbaum
dtene...@fredhutch.org
mailto:dtene...@fredhutch.org
wrote:
See my comments below.
- Original Message
- Original Message -
From: Kevin Ushey kevinus...@gmail.com
To: Laurent Gatto lg...@cam.ac.uk
Cc: bioc-devel bioc-de...@stat.math.ethz.ch
Sent: Friday, January 23, 2015 4:58:40 PM
Subject: Re: [Bioc-devel] portable make syntax
If I understand correctly, all versions of `make` on
See my comments below.
- Original Message -
From: avinash sahu avinash.s...@gmail.com
To: Karim Mezhoud kmezh...@gmail.com
Cc: bioc-devel@r-project.org
Sent: Wednesday, January 21, 2015 7:50:38 AM
Subject: Re: [Bioc-devel] Package submission with library requirement
Thanks for
- Original Message -
From: avinash sahu avinash.s...@gmail.com
To: bioc-devel@r-project.org
Sent: Tuesday, January 20, 2015 8:49:06 AM
Subject: [Bioc-devel] release new package bioccheck failing
Hi All,
I am trying to release a package https://github.com/vinash85/GOAL in
- Original Message -
From: avinash sahu avinash.s...@gmail.com
To: bioc-devel@r-project.org
Sent: Tuesday, January 20, 2015 8:49:06 AM
Subject: [Bioc-devel] release new package bioccheck failing
Hi All,
I am trying to release a package https://github.com/vinash85/GOAL in
- Original Message -
From: Dan Tenenbaum dtene...@fredhutch.org
To: Mike wjia...@fhcrc.org
Cc: Bioc-devel@r-project.org
Sent: Tuesday, January 20, 2015 5:01:52 PM
Subject: Re: [Bioc-devel] Latest R-devel revision breaks flowCore and other
flow packages
Hi Mike
Hi Mike,
- Original Message -
From: Mike wjia...@fhcrc.org
To: Bioc-devel@r-project.org
Cc: Dan Tenenbaum dtene...@fhcrc.org
Sent: Tuesday, January 20, 2015 4:56:43 PM
Subject: [Bioc-devel] Latest R-devel revision breaks flowCore and other flow
packages
Dan,
First of all
There is no shared memory on windows so you need to make sure you require() any
necessary packages on each node.
Dan
On January 15, 2015 5:00:22 PM PST, Dario Strbenac dstr7...@uni.sydney.edu.au
wrote:
Hello,
The development version of ClassifyR won't build on Windows. It happens
for a code
[moving this to bioc-devel]
- Original Message -
From: Keith Satterley ke...@wehi.edu.au
To: r-de...@r-project.org
Sent: Tuesday, January 13, 2015 9:50:40 PM
Subject: [Rd] Is the tcltk failure in affylmGUI related to R bug 15957
I maintain the package affylmGUI. It works when
- Original Message -
From: Dan Tenenbaum dtene...@fredhutch.org
To: Elena Grassi grass...@gmail.com
Cc: bioc-devel@r-project.org
Sent: Thursday, January 8, 2015 10:18:50 AM
Subject: Re: [Bioc-devel] Announcing Docker containers for Bioconductor
- Original Message
- Original Message -
From: Elena Grassi grass...@gmail.com
To: Dan Tenenbaum dtene...@fredhutch.org
Cc: bioc-devel@r-project.org
Sent: Thursday, January 8, 2015 8:45:37 AM
Subject: Re: [Bioc-devel] Announcing Docker containers for Bioconductor
On Thu, Jan 8, 2015 at 4:43 PM, Dan
- Original Message -
From: Elena Grassi grass...@gmail.com
To: bioc-devel@r-project.org
Sent: Thursday, January 8, 2015 5:11:50 AM
Subject: Re: [Bioc-devel] Announcing Docker containers for Bioconductor
Thanks, this is really useful and I was looking forward to it after
having
We're pleased to announce the availability of Docker containers for
Bioconductor.
With Bioconductor containers, we hope to enhance
* reproducibility: If you run some code in a container today,
you can run it again in the same container (with the same tag)
years later and know that nothing
- Original Message -
From: Karim Mezhoud kmezh...@gmail.com
To: bioc-devel@r-project.org
Sent: Friday, January 2, 2015 4:22:44 AM
Subject: [Bioc-devel] BiocCheck result
Dear all,
I have these comments and did not found solution for silencing them.
1 - What about Vignette?
- Original Message -
From: Karim Mezhoud kmezh...@gmail.com
To: Dan Tenenbaum dtene...@fredhutch.org
Cc: bioc-devel@r-project.org
Sent: Friday, January 2, 2015 12:15:31 PM
Subject: Re: [Bioc-devel] BiocCheck result
Dear Dr Dan,
Thanks,
With GUI package the vignette does
- Original Message -
From: Charles Determan Jr deter...@umn.edu
To: bioc-devel@r-project.org
Sent: Wednesday, December 31, 2014 11:41:09 AM
Subject: [Bioc-devel] BiocCheck Error 'duplicate label install'?
Greetings,
Apologies if this is a double post, I was over zealous in my
- Original Message -
From: Dario Strbenac dstr7...@uni.sydney.edu.au
To: bioc-devel@r-project.org
Sent: Thursday, December 11, 2014 5:00:11 PM
Subject: [Bioc-devel] biovizBase Installation rbind Problem
Hello,
I can't install biovizBase, although I have the correct versions of
- Original Message -
From: Dan Tenenbaum dtene...@fredhutch.org
To: Dario Strbenac dstr7...@uni.sydney.edu.au
Cc: bioc-devel@r-project.org
Sent: Thursday, December 11, 2014 5:10:34 PM
Subject: Re: [Bioc-devel] biovizBase Installation rbind Problem
- Original Message
- Original Message -
From: Kevin Rue-Albrecht kevin@ucdconnect.ie
To: Stephanie M. Gogarten sdmor...@u.washington.edu
Cc: bioc-devel@r-project.org, Dan Tenenbaum dtene...@fredhutch.org
Sent: Wednesday, December 3, 2014 3:09:58 AM
Subject: Re: [Bioc-devel] RSS package feeds
- Original Message -
From: Dan Tenenbaum dtene...@fredhutch.org
To: Kevin Rue-Albrecht kevin@ucdconnect.ie
Cc: bioc-devel@r-project.org
Sent: Wednesday, December 3, 2014 7:49:10 AM
Subject: Re: [Bioc-devel] RSS package feeds not updated
- Original Message -
From
- Original Message -
From: Paolo Martini paolo.mart...@unipd.it
To: bioc-devel@r-project.org
Sent: Tuesday, December 2, 2014 7:04:32 AM
Subject: [Bioc-devel] Info On Clipper release version!
Dear list,
since my last commit to the release version of clipper, the package
has
- Original Message -
From: Julian Gehring julian.gehr...@embl.de
To: bioc-devel@r-project.org
Cc: Felix Klein fkl...@embl.de
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't
- Original Message -
From: Stephanie M. Gogarten sdmor...@u.washington.edu
To: bioc-devel@r-project.org, Dan Tenenbaum dtene...@fredhutch.org
Sent: Tuesday, December 2, 2014 4:19:14 PM
Subject: Re: [Bioc-devel] RSS package feeds not updated
On 12/2/14 8:17 AM, Dan Tenenbaum
- Original Message -
From: Martin Morgan mtmor...@fredhutch.org
To: Joachim Schumann joachim.schum...@ufz.de, bioc-devel@r-project.org
Sent: Wednesday, November 26, 2014 9:00:07 AM
Subject: Re: [Bioc-devel] BioC 3.0 CHECK ERROR
On 11/26/2014 01:39 AM, Joachim Schumann wrote:
Hi
- Original Message -
From: Martin Morgan mtmor...@fredhutch.org
To: Dan Tenenbaum dtene...@fredhutch.org
Cc: Joachim Schumann joachim.schum...@ufz.de, bioc-devel@r-project.org
Sent: Wednesday, November 26, 2014 5:33:22 PM
Subject: Re: [Bioc-devel] BioC 3.0 CHECK ERROR
On 11/26
Hi Robert,
- Original Message -
From: Robert Castelo robert.cast...@upf.edu
To: bioc-devel@r-project.org
Sent: Friday, November 21, 2014 8:40:07 AM
Subject: [Bioc-devel] MacOS-specific error in
VariantAnnotation::locateVariants() in devel
hi,
I have encountered an error using
- Original Message -
From: January Weiner january.wei...@gmail.com
Cc: bioc-devel bioc-devel@r-project.org
Sent: Friday, November 14, 2014 1:11:32 PM
Subject: Re: [Bioc-devel] Help with creating first Bioconductor package
Dear all,
thanks for your input, it was very helpful. I
- Original Message -
From: Laurent Gautier lgaut...@gmail.com
To: Martin Morgan mtmor...@fredhutch.org
Cc: bioc-devel@r-project.org, Dan Tenenbaum dtene...@fredhutch.org
Sent: Monday, November 10, 2014 9:57:00 AM
Subject: Re: [Bioc-devel] PPA with built bioconductor packages
Hi everyone (especially package maintainers),
As you know, we recently switched the Bioconductor mailing list to a QA site
at https://support.biooconductor.org .
If you haven't registered on this site, please do so now. If you ever
subscribed to the Bioconductor list, you already have an
Hi Laurent,
- Original Message -
From: Martin Morgan mtmor...@fredhutch.org
To: Laurent Gatto lg...@cam.ac.uk, bioc-devel@r-project.org
Sent: Tuesday, November 4, 2014 5:41:04 AM
Subject: Re: [Bioc-devel] error: 2 arguments passed to .Internal(ls) which
requires 3
Hi Laurent --
- Original Message -
From: Leonardo Collado Torres lcoll...@jhu.edu
To: bioc-devel@r-project.org
Cc: Jeff Leek jtl...@gmail.com
Sent: Friday, October 31, 2014 4:05:11 AM
Subject: [Bioc-devel] More than 1 citation in landing page
Hi,
I'm wondering if it's possible to display
- Original Message -
From: Hervé Pagès hpa...@fredhutch.org
To: Laurent Gatto lg...@cam.ac.uk, bioc-devel@r-project.org
Sent: Thursday, October 30, 2014 10:52:14 AM
Subject: Re: [Bioc-devel] experiment data package versioning
Hi Laurent,
On 10/30/2014 10:31 AM, Laurent Gatto
- Original Message -
From: Vincent Carey st...@channing.harvard.edu
To: Henrik Bengtsson h...@biostat.ucsf.edu
Cc: bioC-devel bioc-de...@stat.math.ethz.ch
Sent: Thursday, October 23, 2014 7:45:13 PM
Subject: Re: [Bioc-devel] Documentation on how to update a BioC experimental
- Original Message -
From: Felix Klein felix.kl...@embl.de
To: bioc-devel@r-project.org
Sent: Wednesday, October 22, 2014 4:02:09 AM
Subject: [Bioc-devel] Cant sign up on support site!
Hello,
somehow I cannot sign up on the support site by entering a new email
address and
- Original Message -
From: Julian Gehring julian.gehr...@embl.de
To: bioc-devel@r-project.org
Sent: Friday, October 17, 2014 1:10:13 AM
Subject: [Bioc-devel] Link posting guide in support forum
Hi,
Can we embed the posting guide
- Original Message -
From: Robert Castelo robert.cast...@upf.edu
To: Kevin Rue-Albrecht kevin@ucdconnect.ie
Cc: bioc-devel@r-project.org
Sent: Thursday, October 16, 2014 3:24:32 AM
Subject: Re: [Bioc-devel] 'BiocInstaller' package not in repository error
during nightly build
- Original Message -
From: Hervé Pagès hpa...@fhcrc.org
To: Tiphaine Martin tiphaine.mar...@kcl.ac.uk, Michael Lawrence
lawrence.mich...@gene.com, Dan Tenenbaum
dtene...@fhcrc.org
Cc: bioc-devel@r-project.org
Sent: Thursday, October 16, 2014 11:43:32 AM
Subject: Re: [Bioc-devel
- Original Message -
From: zhao shilin zhaoshi...@gmail.com
To: Dan Tenenbaum dtene...@fhcrc.org
Cc: bioc-devel bioc-devel@r-project.org
Sent: Wednesday, October 15, 2014 8:51:26 PM
Subject: Re: [Bioc-devel] Bioonductor package tracker has moved
Hello Dan,
It seems that I
- Original Message -
From: Tim Triche, Jr. tim.tri...@gmail.com
To: Dan Tenenbaum dtene...@fhcrc.org
Cc: zhao shilin zhaoshi...@gmail.com, bioc-devel
bioc-devel@r-project.org
Sent: Wednesday, October 15, 2014 9:32:14 PM
Subject: Re: [Bioc-devel] Bioonductor package tracker has
- Original Message -
From: Leonardo Collado Torres lcoll...@jhu.edu
To: bioc-devel@r-project.org
Sent: Tuesday, October 14, 2014 7:05:21 AM
Subject: [Bioc-devel] Git-svn bridge for BioC 3.0
Hi,
I know it might be too early for this, but well, given Dan's BioC 3.0
branch
- Original Message -
From: Tiphaine Martin tiphaine.mar...@kcl.ac.uk
To: bioc-devel@r-project.org
Sent: Monday, October 13, 2014 1:29:08 PM
Subject: [Bioc-devel] runnable examples for internal function ?
Hi,
I would like to know if I need to add a runnable example for each
Hello BioC developers,
We will be creating the Bioconductor 3.0 branch today at 2:30 PM
Seattle time. (21:30 UTC). This is about an hour from now.
Please stop all commits to trunk before 2:30PM and do not resume until
further notice.
We will send another email when it is OK to resume commits.
The BioC 3.0 branch is now ready.
Remember, you always have access to 2 versions of your package:
the release and the devel versions.
Right now the release version of your package (which is not
officially released yet but will be on Tuesday if
everything goes well) is in the 3.0 branch and
- Original Message -
From: Kevin Rue-Albrecht kevin@ucdconnect.ie
To: Dan Tenenbaum dtene...@fhcrc.org
Cc: bioc-devel@r-project.org
Sent: Friday, October 10, 2014 8:03:25 AM
Subject: Re: [Bioc-devel] no more commits allowed before release ?
Hi Dan,
Ok good, you have
- Original Message -
From: Yinming Jiao 20907...@zju.edu.cn
To: bioc-devel@r-project.org
Sent: Thursday, October 9, 2014 7:46:38 PM
Subject: [Bioc-devel] package ‘FEM’ is not available (for R version 3.0.2)
Dear All,
I have a package, FEM, which is published few days ago.
Package developers --
Each Bioconductor release is accompanied by release notes that mention
new packages and other significant project developments. For the
forthcoming release we will include release notes for
individual packages, so that users have an easy way to survey changes
in their
- Original Message -
From: Luo Weijun luo_wei...@yahoo.com
To: bioc-devel@r-project.org, Martin Morgan mtmor...@fhcrc.org
Sent: Wednesday, October 8, 2014 3:51:22 PM
Subject: Re: [Bioc-devel] Keep the bioc-help email list running?
Martin,
Thanks for all the details/info. I see
This is fixed now.
http://bioconductor.org/spb_reports/STATegRa_0.99.4_buildreport_20141007100210.html
Dan
- Original Message -
From: Gordon Ball gordon.b...@ki.se
To: Andrzej Oleś andrzej.o...@gmail.com, Dan Tenenbaum
dtene...@fhcrc.org
Cc: jmac...@u.washington.edu, bioc-devel@r
- Original Message -
From: Leo Lahti leo.la...@iki.fi
To: bioc-devel@r-project.org
Sent: Monday, October 6, 2014 7:25:03 AM
Subject: [Bioc-devel] Fwd: Rmarkdown built html vignette not included in
final package tarball
Hi Sean, thanks again. Even this does not seem to help. The
- Original Message -
From: Leo Lahti leo.la...@iki.fi
To: Dan Tenenbaum dtene...@fhcrc.org
Cc: bioc-devel@r-project.org
Sent: Monday, October 6, 2014 7:55:07 AM
Subject: Re: [Bioc-devel] Fwd: Rmarkdown built html vignette not included in
final package tarball
Hi Dan
- Original Message -
From: Daniel Schmolze s...@schmolze.com
To: bioc-devel@r-project.org
Sent: Monday, October 6, 2014 7:52:49 AM
Subject: [Bioc-devel] odd vignette dependency issue
I'm getting a vignette error from the BioC build servers that I can't
reproduce locally:
What's
- Original Message -
From: Henrik Bengtsson h...@biostat.ucsf.edu
To: jmac...@u.washington.edu
Cc: bioc-devel@r-project.org
Sent: Friday, October 3, 2014 6:56:59 AM
Subject: Re: [Bioc-devel] RMarkdown for vignettes
I think it requires Bioc core to make a statement that pandoc
- 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
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: [Bioc
- 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
- 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
301 - 400 of 559 matches
Mail list logo
