On 06/13/2016 12:32 AM, Yu, Guangchuang wrote:
Dear Dan,
Thanks for the update, this is really helpful.
I think many users are new to R and they just google search their issue and
find out a Bioconductor package may solve their issue. The problem is the
landing page of BioC 3.1 or 3.2 maybe the top hit of google search. Not
check out https://bioconductor.org/robots.txt. google finds /release/
and /devel/ and I see as the top hit for 'ggtree' as
https://bioconductor.org/packages/release/bioc/.../ggtree.ht...
Bioconductor
a phylogenetic tree viewer for different types of tree annotations.
Bioconductor version: Release (3.3). ggtree extends the ggplot2 plotting
system which ...
allow search engines to index old package landing pages is a good idea.
This is the email I received yesterday:
I would like to use ggtree
But everytime I try to install in 3.2
I get this error
Warning message:
In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘ggtree’ had non-zero exit status
using install.packages() would have failed that way in 3.3 also -- it
should be biocLite() as on every package landing page.
Receiving such email is quite often.
The issue is users may only read the vignette and then try to install the
package by using install.packages() without reading the installation guide
in the landing page. They just bug the author without google search it.
Maybe we need to add installation section in vignette too.
refer them to https://bioconductor.org/packages/ggtree and the
installation instructions there. If you add information to your
vignette, make sure that it's accurate -- biocLite("ggtree") and not
install.packages() or installing from github (because then they will mix
package versions across releases -- this only leads to tears down the road).
Another issue is the Bioconductor release policy, Many new users may not
aware of it and they keep asking why they need to upgrade R to install the
latest version. I think it would be great to add a section of `Bioconductor
Release Policy` in the page, https://www.bioconductor.org/install, and add
a link to this page in the installation section of package landing page.
It's described at http://bioconductor.org/install#why-biocLite
Best wishes,
Guangchuang
On Mon, Jun 13, 2016 at 11:10 AM, Dan Tenenbaum <dtene...@fredhutch.org>
wrote:
----- Original Message -----
From: "Yinming Jiao" <20907...@zju.edu.cn>
To: "Dan Tenenbaum" <dtene...@fredhutch.org>
Cc: "Yu, Guangchuang" <g...@connect.hku.hk>, "bioc-devel" <
bioc-devel@r-project.org>
Sent: Sunday, June 12, 2016 7:33:02 PM
Subject: Re: Re: [Bioc-devel] notify out-dated branches
Dear Dan
It's great that we have notification on the package versions. Many
Thanks for
your efforts on the maintanence.
However, I have a question that why so many packages do not support R
3.2, and
this problem is so tough that people have to reinstall other R version
and
roconstruct their pipeline upside down.
Is there some actions to mail the authors and promote the updation of
such
packages?
Which packages do not support R-3.2?
As far as I know the only packages that do not support R-3.2 are those
that were introduced in Bioconductor 3.3 and later, and the supported
solution for those is to upgrade to R-3.3.
This is by design. Each version of Bioconductor is designed to work with a
specific version of R.
Dan
Kind regards
Yinming
-----原始邮件-----
发件人: "Dan Tenenbaum" <dtene...@fredhutch.org>
发送时间: 2016年6月13日 星期一
收件人: "Yu, Guangchuang" <g...@connect.hku.hk>
抄送: bioc-devel <bioc-devel@r-project.org>
主题: Re: [Bioc-devel] notify out-dated branches
----- Original Message -----
From: "Yu, Guangchuang" <g...@connect.hku.hk>
To: "bioc-devel" <bioc-devel@r-project.org>
Sent: Wednesday, June 8, 2016 1:44:12 AM
Subject: [Bioc-devel] notify out-dated branches
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 out-dated branches, just like we have a
message
for devel branch.
For example, for BioC 3.2, a message like:
This is the BioC 3.2 version of XXX_pkg; for the current stable
release
version, see XXX_pkg_url.
would be helpful.
We have implemented your suggestion for package landing pages for old
versions
2.8 through 3.2.
For technical reasons, it will take a little longer to implement this
for
versions prior to 2.8.
We try to make sure that search engines do not index old package
landing pages,
but
people sometimes still link to a particular version of a package
landing page in
publications, etc.
As Martin points out, it's best to use the "short URL" of the package,
for
example:
https://bioconductor.org/packages/a4/
If you click on that page and go to the bottom you will see a line
saying
"Package Short Url". And then if you mouse over the short url it says
"Canonical url for use in publications, etc., will always redirect to
current
release version (or devel if package is not in release yet).".
Thanks,
Dan
Best wishes,
Guangchuang
--
--~--~---------~--~----~------------~-------~--~----~
Guangchuang Yu, PhD Candidate
State Key Laboratory of Emerging Infectious Diseases
School of Public Health
The University of Hong Kong
Hong Kong SAR, China
www: https://guangchuangyu.github.io
-~----------~----~----~----~------~----~------~--~---
[[alternative HTML version deleted]]
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
This email message may contain legally privileged and/or...{{dropped:2}}
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
