[Bioc-devel] notify out-dated branches

Mon Jun 13 11:31:16 CEST 2016

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 <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
>>>>
>>>
>>>
>>> --
>>
>
>
>

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