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

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.

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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