Hi,
Tooltips that appear while hovering over selected links are easy to
miss. This alone will likely not be clear enough. We should convey the
information that the entire website presents a different version of the
package.
The idea of a notification box that can be made visible by the
Seems like there are two problems, first that the release and devel pages look
similar, but more importantly that people are downloading and installing from
the package pages when they should be using biocLite().
I am open to the suggestions for making the release/devel pages look more
Given that we have an ongoing problem with people inadvisedly clicking
and installing things, is there a good rationale for allowing them to do
so?
Perhaps the landing page for each package should be stripped of links
and replaced with some indication of the availability for each package
on
- Original Message -
From: James W. MacDonald jmac...@uw.edu
To: Dan Tenenbaum dtene...@fhcrc.org, Julian Gehring
julian.gehr...@embl.de
Cc: Michael Lawrence lawrence.mich...@gene.com, bioc-devel@r-project.org
Sent: Tuesday, July 22, 2014 9:26:13 AM
Subject: Re: [Bioc-devel]
Hi all,
I think having links is useful, e.g. for someone who uses BioC release
but wants to install by hand a particular package from the devel
branch.
Distinct colors between release and devel make sense only if one
understands their meaning, which in the end might prove not to be very
useful.
Agreed. Disabling the links is a good idea. There's really no good reason
for someone to install packages manually. If a user really wants to mix
release/devel, it is still technically possible but this change would
strongly discourage it.
For ensuring the user notices that a page is for the
- Original Message -
From: Andrzej Oleś andrzej.o...@gmail.com
To: James W. MacDonald jmac...@uw.edu
Cc: Dan Tenenbaum dtene...@fhcrc.org, Julian Gehring
julian.gehr...@embl.de, Michael Lawrence
lawrence.mich...@gene.com, bioc-devel@r-project.org
Sent: Tuesday, July 22, 2014
- Original Message -
From: Matthew McCall mcca...@gmail.com
To: Michael Lawrence lawrence.mich...@gene.com
Cc: bioc-devel@r-project.org
Sent: Tuesday, July 22, 2014 10:49:39 AM
Subject: Re: [Bioc-devel] Distinction between release and devel package
websites
I hope the
Just check out from svn to get the source... way easier to keep up to date,
and if you notice an issue, easier to make a patch.
On Tue, Jul 22, 2014 at 10:49 AM, Matthew McCall mcca...@gmail.com wrote:
I hope the package source link is not on the proposed list of links to
remove. I often
The current link to the source tarball is called Package Source hence the
quotes. Yes, I could check out the package using svn, but when browsing
through a Bioconductor workflow, there are these handy links to the package
pages that let me download and browse the source tarball without having to
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
hi,
after updating to the last devel version of all packages I cannot load
one of the packages I develop, VariantFiltering, in MacOS (Snow Leopard)
while the same version loads smoothly in LInux.
This is the error I get:
library(VariantFiltering)
No methods found in IRanges for requests:
Thanks everyone for the input.
We'll make some changes (over the next day or so), and then iterate on those as
needed. Specifically
1. text after the package title indicating when the user is on the 'developer'
page, with link to a 'stable release version'.
2. more prominent Installation
Hi Andrzej,
On 07/22/2014 10:14 AM, Andrzej Oleś wrote:
Hi all,
I think having links is useful, e.g. for someone who uses BioC release
but wants to install by hand a particular package from the devel
branch.
Distinct colors between release and devel make sense only if one
understands their
Dear Dan, James, Michael, Matt,
thank you, I see your point but I'm afraid I must disagree with you.
I've had this situation numerous times that I have added/fixed
something in the devel branch of a package and had to advice the users
to use this latest version. Needless to say, they were
Hi Andrzej,
- Original Message -
From: Andrzej Oleś andrzej.o...@gmail.com
To: Dan Tenenbaum dtene...@fhcrc.org
Cc: James W. MacDonald jmac...@uw.edu, Julian Gehring
julian.gehr...@embl.de, Michael Lawrence
lawrence.mich...@gene.com, bioc-devel@r-project.org
Sent: Tuesday, July 22,
Andrzej,
If you have the an important enough bugfix the correct procedure is to
commit it to the release branch. Then users would simply update the package
via biocLite.
Note that this should be fixes ONLY. No new features. Regardless of how
much the users want them, those belong in dev.
~G
While mixing release and devel may work in specific cases, enabling it in
the specific case means also enabling it in general. And in general, it
will break and cause frustration and hardship for both users and developers.
The other way to access source code is through R itself.
On Tue, Jul 22,
Hi Hervé,
thank you for the demo! Yes, this is definitely much more clear than
just a different color. Maybe we could first implement this idea on
the build/check report websites and see how the uptake will be? I
always keep getting confused by the colors which keep changing with
every release
Hi Martin,
thank you!
On Tue, Jul 22, 2014 at 9:01 PM, Martin Morgan mtmor...@fhcrc.org wrote:
We might tell google not to index devel packages (but then packages added
during a particular release cycle aren't indexed until the next release).
This adds to the complexity and I'm not sure how
Hi Dan, Michael, Julian,
Thank's for keeping the links to the tarballs!
I don't argue that mixing release and devel is a good idea in general.
Rather, that for some users this might be the best compromise between
the following two objectives:
1. a stable working environment
2. the possibility to
hi Dan,
I re-installed R, getting the newer 3.1.1 over the 3.1.0 I had but did
not make a difference because I had the devel packages into a specific
devel folder which was still available to the installation. However,
when I removed it and made a completely new fresh installation of
On 7/22/2014 4:27 PM, Robert Castelo wrote:
hi Dan,
I re-installed R, getting the newer 3.1.1 over the 3.1.0 I had but did not make
a difference because I had the devel packages into a specific devel folder which
was still available to the installation. However, when I removed it and made a
On Tue, Jul 22, 2014 at 7:10 PM, Andrzej OleÅ andrzej.o...@gmail.com
wrote:
Hi Dan, Michael, Julian,
Thank's for keeping the links to the tarballs!
I don't argue that mixing release and devel is a good idea in general.
Rather, that for some users this might be the best compromise between
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