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

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List:       bioc-devel
Subject:    Re: [Bioc-devel] Issues uploading our updated package (CausalR)
From:       Dan Tenenbaum <dtenenba () fredhutch ! org>
Date:       2016-03-22 18:53:11
Message-ID: 1949510134.3577689.1458672791488.JavaMail.zimbra () fredhutch ! org
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----- Original Message -----
> From: "Martin Morgan" <martin.morgan@roswellpark.org>
> To: "Glyn Bradley" <glyn.x.bradley@gsk.com>, "bioc-devel" \
>                 <bioc-devel@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@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@gmail.com]
> > Sent: 16 March 2016 13:20
> > To: Glyn Bradley
> > Cc: bioc-devel@r-project.org<mailto:bioc-devel@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@gsk.com<mailto:glyn.x.bradley@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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