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

Obenchain, Valerie Valerie.Obenchain at roswellpark.org
Wed Mar 16 14:46:28 CET 2016

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


and devel:


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:


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?


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