[Bioc-devel] Issues uploading our updated package (CausalR)

[Martin Morgan]

On 03/22/2016 07:53 AM, Glyn Bradley wrote:
> Hi,
> We’ve got CausalR back up both in the 3.2 release and devel, but although we committed the same package (with different version number) to both release and devel, the landing pages are showing
> build:OK in release but build:warnings in devel.
>
> Does anyone know why this might be, and more importantly, would the build:warnings in devel affect the release of the package in v3.3?
>

Clicking on the 'build' shield at the top of your package landing page 
takes you to the build report for your package

http://bioconductor.org/checkResults/devel/bioc-LATEST/CausalR/

Clicking on one of the 'WARNING' tags takes you to the build report for 
that platform, and scrolling down we see

* checking whether package ‘CausalR’ can be installed ... [1s/1s] WARNING
Found the following significant warnings:
   Warning: Package 'CausalR' is deprecated and will be removed from 
Bioconductor
See ‘/home/biocbuild/bbs-3.3-bioc/meat/CausalR.Rcheck/00install.out’ for 
details.

Your package was marked for deprecation (usually because there were 
errors that prevented it from building that persisted for a long time, 
leading us to think that the maintainer had abandoned it). Now that the 
package has built, the deprecation tag will be (manually, by 'us') 
removed and the warning will go away. We will remove the deprecation tag.

More generally, bioc-release uses the version of R and other Bioc 
packages that are available to users of the release version of R and 
Bioconductor, whereas bioc-devel uses the version of R and other Bioc 
packages that will be available when the next bioc release occurs. For 
instance, this means that bioc release currently uses R-3.2.4, whereas 
bioc-devel uses R-devel / 3.3.0.

Martin

> Thanks,
> Glyn
>
> From: Glyn Bradley
> Sent: 16 March 2016 13:22
> To: 'Kasper Daniel Hansen'
> Cc: bioc-devel at r-project.org
> Subject: RE: [Bioc-devel] Issues uploading our updated package (CausalR)
>
> Thanks, we’ve already read that.
> I was more hoping for a response from the Bioconductor team
> Glyn
>
> From: Kasper Daniel Hansen [mailto:kasperdanielhansen at gmail.com]
> Sent: 16 March 2016 13:20
> To: Glyn Bradley
> Cc: bioc-devel at r-project.org<mailto:bioc-devel at r-project.org>
> Subject: Re: [Bioc-devel] Issues uploading our updated package (CausalR)
>
> I don't know much about deprecated packages and how to deal with them, but for your svn questions, start by reading the howto:
>
>    https://www.bioconductor.org/developers/source-control/
>
> Kasper
>
> On Wed, Mar 16, 2016 at 6:19 AM, Glyn Bradley <glyn.x.bradley at gsk.com<mailto:glyn.x.bradley at gsk.com>> wrote:
> Hi All,
>
> Our package, CausalR, broke when igraph was updated last year. We have now fixed this, but are having problems uploading the
> new version. The package had become depreciated in devel, but there's still a landing page in release.
>
> We checked out the existing Bioconductor version (via SVN) to a local directory from
> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/CausalR
> The new, fixed, version was uploaded via SVN commit [Revision: 114806*] back to
> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/CausalR
>
> But if you open https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/CausalR in a web browser
> it's still showing old data from Revision: 114827 (we don't understand why our new upload had a revision number lower
> than this)
>
> Also, because CausalR had become depreciated in devel, we were previously told we would have to update the package
> in both the devel and release trunks, but we only have the one url
> (https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/CausalR)
> So separately to the issues above about our update not seeming to stay on the system, could someone please advise how we
> update both trunks?
>
> Many thanks. Feel free to email me directly if this isn't a suitable discussion for the mailing list.
> Glyn
>
>
>
>
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