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

Hi Valarie
OK , thanks for your detailed reply.
I thought we had cleared all errors before commit (another colleague has actually been doing it, not me) but obviously we missed the namespaceExport issue somehow, so apologies for wasting your time.
We'll get that cleared and do a new commit.
Thanks
Glyn


-----Original Message-----
From: Obenchain, Valerie [mailto:Valerie.Obenchain at RoswellPark.org]
Sent: 16 March 2016 13:46
To: Glyn Bradley; bioc-devel at r-project.org
Subject: Re: [Bioc-devel] Issues uploading our updated package (CausalR)

Hi Glyn,

On 03/16/2016 03:20 AM, Glyn Bradley 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.

The package is deprecated in both release and devel. There is no devel landing page because the package has never successfully build in devel.

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)

The builds start ~2pm PST each day. If the commit was done after this the changes won't be picked up until the next build. It looks like your commit just missed the pick up:

------------------------------------------------------------------------
r114806 | s.barrett | 2016-03-15 14:03:31 -0700 (Tue, 15 Mar 2016) | 1 line

Bug fixes for igraph update responsible for breaking package.

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?

Yes, you should always keep an eye on the build of your package in both
release:

  http://www.bioconductor.org/checkResults/release/bioc-LATEST/

and devel:

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

These are separate repositories. For instructions on working on release branch (ie, the url you need to check out the release version of the
package) see this page:

  http://www.bioconductor.org/developers/how-to/source-control/

Kasper already mentioned this link - is it not clear how to check out of release? Let us know what doesn't make sense.



Please don't remove the 'PackageStatus' line from DESCRIPTION. The deprecated status will stay with the package until we have a clean build and check on the build system. I have added that line back and bumped the version to 1.1.2. When I tried to build the package I got this error:


~/sandbox >R-dev CMD build CausalR/
* checking for file 'CausalR/DESCRIPTION' ... OK
* preparing 'CausalR':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
      -----------------------------------
* installing *source* package 'CausalR' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded Error in namespaceExport(ns, exports) :
  undefined exports: MakePredictionsFromCG, WriteExplainedNodesToSifFile
Error: loading failed
Execution halted
ERROR: loading failed
* removing '/tmp/RtmpAN17YO/Rinstbb0375dc637/CausalR'
      -----------------------------------
ERROR: package installation failed

Did you run R CMD build and R CMD check before your commit?

Valerie

Many thanks. Feel free to email me directly if this isn't a suitable discussion for the mailing list.
Glyn

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.