So a preliminary diagnosis is that some packages are not building even though
they build in the nightly builds. The problem could be a newer compiler, newer
R-devel, slightly different OS (debian vs ubuntu) or something else.
Investigating further. However, in the meantime, bioconductor/devel_ba
Thanks!
In the meanwhile I went for a DIY solution - but it would be great to have the
image again up(dated) and running.
Federico
From: Dan Tenenbaum
Sent: Friday, March 4, 2016 10:46 PM
To: Marini, Federico
Cc: Martin Morgan; bioc-devel
Subject: Re: [B
Yes, it looks like devel_sequencing has not updated for a while. I'll look into
that.
Dan
- Original Message -
> From: "Federico Marini"
> To: "Dan Tenenbaum"
> Cc: "Martin Morgan" , "bioc-devel"
>
> Sent: Friday, March 4, 2016 1:40:54 PM
> Subject: Re: [Bioc-devel] Imports, depends
Hi Dan,
I pulled the devel_sequencing image - took the most up to date a couple of days
ago.
Probably even if the rocker/rstudio-daily is indeed updated daily the bioc
container isn't?
Federico
From: Dan Tenenbaum
Sent: Friday, March 4, 2016 10:05 PM
To
Can you be more specific about which docker image you pulled?
Dan
- Original Message -
> From: "Federico Marini"
> To: "Martin Morgan" , "bioc-devel"
>
> Sent: Thursday, March 3, 2016 1:20:46 AM
> Subject: Re: [Bioc-devel] Imports, depends and warnings
> You're right, sorry for the m
Thank you all for the useful suggestions and links.
I like the idea of using a CC0 license. That's likely what I will go for.
Best,
davide
On Fri, Mar 4, 2016 at 7:42 AM Tim Triche, Jr. wrote:
> I was going to mention droit d'auteur under EU common law, but somehow
> that seemed more in Hervé
Using the integrated help system is nice, but isn't always ideal.
Just for example: when I'm ssh'd into my work cluster I don't get a nice web
page, I instead get the ascii-formatted version, which is considerably harder
to read and doesn't include proper links. Running a second local instance
I can reproduce the error quite consistently by running either R CMD build or
by sourcing the Stangled vignette.
Here is my sessionInfo after doing the latter. If you are running an older R
devel please update it.
> sessionInfo()
R Under development (unstable) (2016-02-25 r70222)
Platform: x86_6
I was going to mention droit d'auteur under EU common law, but somehow that
seemed more in Hervé's wheelhouse ;-).
--t
> On Mar 4, 2016, at 7:17 AM, Lyle Burgoon wrote:
>
> Also keep in mind US copyright rules for data are different from European. We
> ran into this recently when wanting to
There are a number of variables defined. You could check to see if the variable
BBS_HOME is defined (it does not matter what the value is in your case, just
whether it is defined or not).
Dan
- Original Message -
> From: "Thomas Dybdal Pedersen"
> To: "bioc-devel"
> Sent: Friday, Mar
Are you using R-devel on your computer?
- Original Message -
> From: "Wolfgang Kaisers"
> To: "bioc-devel"
> Sent: Friday, March 4, 2016 12:41:30 AM
> Subject: [Bioc-devel] spliceSites Vignette build error
> Dear All,
>
> the package check on bioc-LATEST return an error during the vig
Also keep in mind US copyright rules for data are different from European.
We ran into this recently when wanting to publish european data from a web
database.
On Mar 4, 2016 10:05 AM, "Tim Triche, Jr." wrote:
> Data (facts) are not copyright worthy, but databases (collections of
> facts) can be.
Data (facts) are not copyright worthy, but databases (collections of facts) can
be. See Feist v Rural for precedent; in short, there must be an inobvious and
creative aspect to the database for it to be elevated to copyrightable status.
I doubt that a collection of datasets would clear this ba
I am pretty sure in general "data" is not copyrightable per se (
http://www.lib.umich.edu/copyright/facts-and-data), so while I might
contact the original authors as a courtesy, if the data has been released
into any public database, then you should be free to do with it as you
please. Providing th
For data packages, which does not contain any code, it seems weird to use a
software license such as GPL or GPL-2. It seems better to use something
like Artistic-2.0 or one of the CC licenses.
On Thu, Mar 3, 2016 at 5:15 PM, davide risso wrote:
> Hi Hervé and Sean,
>
> thanks for your help. It
Hi,
this is just to clarify the relation between the two github repos
https://github.com/Bioconductor-mirror/BiocStyle and
https://github.com/Bioconductor/BiocStyle mentioned by Martin: actually,
these two are perfectly in sync right now. The "This branch is 3 commits
ahead, 3 commits behind Biocon
One thing about accessing the html versions locally (e.g., via ? with
options(help_type="html")] or help.start() or Rstudio) is that you get the
version relevant to your R / Bioconductor, rather than whatever is at the top
of google; I guess the same applies to the pdf versions, and the reason t
Hi
Are there any environment variables set on the bloc build machines that unique
identify them as such? The reason I ask is that I’m planning to create a
testthat PR that adds a skip_on_bioc (similar to skip_on_cran) function. While
I know you generally shouldn’t skip unit tests on build machi
Dear All,
the package check on bioc-LATEST return an error during the vignette
build.
A broken dependency to another package of mine in CRAN seems to be the
reason.
The check using the last version available on CRAN is OK on my computer
and I added a dependency "refGenome (>= 1.5.8)" into t
Dear all,
Thanks a lot for your help. I managed to commit the new version of the
package to the release branch.
Many thanks again for your replies.
Best,
Sandro
On 3 Mar 2016 16:28, "Dan Tenenbaum" wrote:
> You can merge from devel into release (as long as it's only bug fixes),
> but make sure yo
20 matches
Mail list logo
