[Bioc-devel] notify out-dated branches

[Yu, Guangchuang]

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
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
>
>
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.

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.

Best wishes,
Guangchuang


On Mon, Jun 13, 2016 at 11:10 AM, Dan Tenenbaum <dtenenba at fredhutch.org>
wrote:

>
>
> ----- Original Message -----
> > From: "Yinming Jiao" <20907099 at zju.edu.cn>
> > To: "Dan Tenenbaum" <dtenenba at fredhutch.org>
> > Cc: "Yu, Guangchuang" <gcyu at connect.hku.hk>, "bioc-devel" <
> bioc-devel at 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" <dtenenba at fredhutch.org>
> >> 发送时间: 2016年6月13日 星期一
> >> 收件人: "Yu, Guangchuang" <gcyu at connect.hku.hk>
> >> 抄送: bioc-devel <bioc-devel at r-project.org>
> >> 主题: Re: [Bioc-devel] notify out-dated branches
> >>
> >>
> >>
> >> ----- Original Message -----
> >> > From: "Yu, Guangchuang" <gcyu at connect.hku.hk>
> >> > To: "bioc-devel" <bioc-devel at 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 at r-project.org mailing list
> >> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>
> >> _______________________________________________
> >> Bioc-devel at r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>
> >
> >
> > --
>



-- 
--~--~---------~--~----~------------~-------~--~----~
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
-~----------~----~----~----~------~----~------~--~---

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