Re: [Bioc-devel] EXTERNAL: permanent link to package

[Turaga, Nitesh]

I think, http://bioconductor.org/packages/CAMTHC should be fine. 

This link is permanent, but the 10.18129/B9.bioc.CAMTHC link isn’t a bad idea 
as well. This DOI link just resolves to the original link ( 
http://bioconductor.org/packages/CAMTHC) anyway.

Take a look a this too, https://support.bioconductor.org/p/99617/. 


Best,

Nitesh 


> On Jul 31, 2018, at 12:34 PM, Lulu Chen  wrote:
> 
> Dear Bioc Team,
> 
> My package is still in the develop version.  But I need to add a permanent
> URL link in my paper. Which option is better:
> http://bioconductor.org/packages/CAMTHC  or  10.18129/B9.bioc.CAMTHC
> 
> 
> Thanks,
> Lulu
> 
>   [[alternative HTML version deleted]]
> 
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[Bioc-devel] permanent link to package

[Lulu Chen]

 Dear Bioc Team,

My package is still in the develop version.  But I need to add a permanent
URL link in my paper. Which option is better:
http://bioconductor.org/packages/CAMTHC  or  10.18129/B9.bioc.CAMTHC


Thanks,
Lulu

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Re: [Bioc-devel] EXTERNAL: introducing BiocManager in devel package pages?

[Shepherd, Lori]

We assume most users are using release not devel.  So this page is appropriate 
for the majority users using release 3.7.  This page is scheduled to be updated 
when the next release happens and BiocManager goes live in the Bioc3.8 release.


It has been pointed out and we have it as a task to update the useDevel page 
asap http://www.bioconductor.org/developers/how-to/useDevel/as this should 
be updated now for BiocManager.



Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: James W. MacDonald 
Sent: Tuesday, July 31, 2018 11:24:32 AM
To: Shepherd, Lori
Cc: Tim Triche, Jr.; bioc-devel
Subject: Re: [Bioc-devel] EXTERNAL: introducing BiocManager in devel package 
pages?

Well, there's this:

Package Archives

Follow 
Installation 
instructions to use this package in your R session.

And the link for the Installation instructions directs you to the page that 
says to use biocLite.

Jim



On Tue, Jul 31, 2018 at 10:59 AM, Shepherd, Lori 
mailto:lori.sheph...@roswellpark.org>> wrote:
Yes DropletUtils has a release and a devel page; as most of the Bioconductor 
package do. The devel pages have been updated for the BiocManager while the 
release still are BiocInstaller.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Tim Triche, Jr. mailto:tim.tri...@gmail.com>>
Sent: Tuesday, July 31, 2018 10:26:31 AM
To: Shepherd, Lori
Cc: bioc-devel
Subject: Re: EXTERNAL: [Bioc-devel] introducing BiocManager in devel package 
pages?

Now I am wondering about my sanity... it seems like perhaps DropletUtils has a 
release package page too?  In any event, looks like things are all set.

thanks!

--t


On Tue, Jul 31, 2018 at 9:21 AM Shepherd, Lori 
mailto:lori.sheph...@roswellpark.org>>>
 wrote:

Where exactly did you see this?  It will be up to the package maintainers to 
update their package documentation (vignettes and such).  We have updated the 
devel package landing pages to include the new BiocManager instructions already:


https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html



Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel 
mailto:bioc-devel-boun...@r-project.org>>>
 on behalf of Tim Triche, Jr. 
mailto:tim.tri...@gmail.com>>>
Sent: Tuesday, July 31, 2018 9:14:24 AM
To: bioc-devel
Subject: EXTERNAL: [Bioc-devel] introducing BiocManager in devel package pages?

So I was looking at DropletUtils and stumbled on this:

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R;)
biocLite("DropletUtils")


It seems like maybe devel might be a sensible place to start migrating
users to BiocManager::install(...).  Thoughts?

--t

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--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and 

Re: [Bioc-devel] EXTERNAL: introducing BiocManager in devel package pages?

[Shepherd, Lori]

Yes DropletUtils has a release and a devel page; as most of the Bioconductor 
package do. The devel pages have been updated for the BiocManager while the 
release still are BiocInstaller.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Tim Triche, Jr. 
Sent: Tuesday, July 31, 2018 10:26:31 AM
To: Shepherd, Lori
Cc: bioc-devel
Subject: Re: EXTERNAL: [Bioc-devel] introducing BiocManager in devel package 
pages?

Now I am wondering about my sanity... it seems like perhaps DropletUtils has a 
release package page too?  In any event, looks like things are all set.

thanks!

--t


On Tue, Jul 31, 2018 at 9:21 AM Shepherd, Lori 
mailto:lori.sheph...@roswellpark.org>> wrote:

Where exactly did you see this?  It will be up to the package maintainers to 
update their package documentation (vignettes and such).  We have updated the 
devel package landing pages to include the new BiocManager instructions already:


https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html



Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel 
mailto:bioc-devel-boun...@r-project.org>> on 
behalf of Tim Triche, Jr. mailto:tim.tri...@gmail.com>>
Sent: Tuesday, July 31, 2018 9:14:24 AM
To: bioc-devel
Subject: EXTERNAL: [Bioc-devel] introducing BiocManager in devel package pages?

So I was looking at DropletUtils and stumbled on this:

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R;)
biocLite("DropletUtils")


It seems like maybe devel might be a sensible place to start migrating
users to BiocManager::install(...).  Thoughts?

--t

[[alternative HTML version deleted]]

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email message is prohibited. If you have received this message in error, please 
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Re: [Bioc-devel] EXTERNAL: introducing BiocManager in devel package pages?

[Tim Triche, Jr.]

Now I am wondering about my sanity... it seems like perhaps DropletUtils
has a release package page too?  In any event, looks like things are all
set.

thanks!

--t


On Tue, Jul 31, 2018 at 9:21 AM Shepherd, Lori <
lori.sheph...@roswellpark.org> wrote:

> Where exactly did you see this?  It will be up to the package maintainers
> to update their package documentation (vignettes and such).  We have
> updated the devel package landing pages to include the new BiocManager
> instructions already:
>
>
> https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> --
> *From:* Bioc-devel  on behalf of Tim
> Triche, Jr. 
> *Sent:* Tuesday, July 31, 2018 9:14:24 AM
> *To:* bioc-devel
> *Subject:* EXTERNAL: [Bioc-devel] introducing BiocManager in devel
> package pages?
>
> So I was looking at DropletUtils and stumbled on this:
>
> To install this package, start R and enter:
>
> ## try http:// if https:// URLs are not supported
> source("https://bioconductor.org/biocLite.R;)
> biocLite("DropletUtils")
>
>
> It seems like maybe devel might be a sensible place to start migrating
> users to BiocManager::install(...).  Thoughts?
>
> --t
>
> [[alternative HTML version deleted]]
>
> ___
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>
> This email message may contain legally privileged and/or confidential
> information. If you are not the intended recipient(s), or the employee or
> agent responsible for the delivery of this message to the intended
> recipient(s), you are hereby notified that any disclosure, copying,
> distribution, or use of this email message is prohibited. If you have
> received this message in error, please notify the sender immediately by
> e-mail and delete this email message from your computer. Thank you.

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Re: [Bioc-devel] EXTERNAL: introducing BiocManager in devel package pages?

[Shepherd, Lori]

Where exactly did you see this?  It will be up to the package maintainers to 
update their package documentation (vignettes and such).  We have updated the 
devel package landing pages to include the new BiocManager instructions already:


https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html



Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Tim Triche, 
Jr. 
Sent: Tuesday, July 31, 2018 9:14:24 AM
To: bioc-devel
Subject: EXTERNAL: [Bioc-devel] introducing BiocManager in devel package pages?

So I was looking at DropletUtils and stumbled on this:

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R;)
biocLite("DropletUtils")


It seems like maybe devel might be a sensible place to start migrating
users to BiocManager::install(...).  Thoughts?

--t

[[alternative HTML version deleted]]

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[Bioc-devel] introducing BiocManager in devel package pages?

[Tim Triche, Jr.]

So I was looking at DropletUtils and stumbled on this:

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R;)
biocLite("DropletUtils")


It seems like maybe devel might be a sensible place to start migrating
users to BiocManager::install(...).  Thoughts?

--t

[[alternative HTML version deleted]]

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