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

Tue Mar 22 19:53:11 CET 2016

----- Original Message -----
> From: "Martin Morgan" <martin.morgan at roswellpark.org>
> To: "Glyn Bradley" <glyn.x.bradley at gsk.com>, "bioc-devel" <bioc-devel at r-project.org>
> Sent: Tuesday, March 22, 2016 6:03:56 AM
> Subject: Re: [Bioc-devel] Issues uploading our updated package (CausalR)

> 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.
> 

This is a bit puzzling as the tag was removed from both release and devel on 3/18.
Perhaps there is an installed version of the package on one or more build machines that is still marked as deprecated. I will take a look.
Dan

> 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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