[Bioc-devel] AnnotationHubServer requires AnnotationHubData of a particular vintage

[Dan Tenenbaum]

On Tue, Jun 25, 2013 at 9:30 AM, Tim Triche, Jr. <tim.triche at gmail.com> wrote:
> I've been having this problem for a while with the package:
>
> tim at tim-ThinkPad-T420s:~/bioc-devel$ more
> /home/tim/bioc-devel/AnnotationHubServer.Rcheck/00install.out
> * installing *source* package ‘AnnotationHubServer’ ...
> ** R
> ** inst
> ** preparing package for lazy loading
> Error in match.fun(FUN) : node stack overflow
> ERROR: lazy loading failed for package ‘AnnotationHubServer’
> * removing
> ‘/home/tim/bioc-devel/AnnotationHubServer.Rcheck/AnnotationHubServer’
>
> This morning it dawned on me that perhaps installing AnnotationHubData was
> a prerequisite, so I gave it a shot:
>
> [1] Creating log directory /home/tim/.AnnotationHubData
> * DONE (AnnotationHubData)
> tim at tim-ThinkPad-T420s:~/bioc-devel$ R CMD INSTALL AnnotationHubServer/*
> installing to library ‘/usr/lib64/R/library’
> * installing *source* package ‘AnnotationHubServer’ ...
> ** R
> ** inst
> ** preparing package for lazy loading
> rmongodb package (mongo-r-driver) loaded
> Use 'help("mongo")' to get started.
>
> ** help
> *** installing help indices
> ** building package indices
> ** installing vignettes
> ** testing if installed package can be loaded
> rmongodb package (mongo-r-driver) loaded
> Use 'help("mongo")' to get started.
>
> * DONE (AnnotationHubServer)
>
>
> So perhaps that should go in the DESCRIPTION file for the latter, along
> with a revision number?  It would seem that I must have had
> AnnotationHubData from an older vintage installed, but said older vintage
> was not satisfactory, thus, error.
>
> Anyways.  Just in case anyone else has the same issue, here it is.
>


Thanks, I've committed the following change to devel:

 svn diff
Index: DESCRIPTION
===================================================================
--- DESCRIPTION (revision 77902)
+++ DESCRIPTION (working copy)
@@ -1,10 +1,10 @@
 Package: AnnotationHubServer
 Title: AnnotationHub Server component
-Version: 0.1.3
+Version: 0.1.4
 Author: Dan Tenenbaum
 Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>
 Description: AnnotationHub Server component
-Depends: AnnotationHubData
+Depends: AnnotationHubData (>= 0.0.37)
 Imports: FastRWeb, methods, rmongodb, rjson, IRanges, parallel,
     futile.logger, knitr, parallel
 Suggests: RUnit, BiocGenerics, knitr


Dan


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