[Bioc-devel] AnnotationHubServer requires AnnotationHubData of a particular vintage
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
-- *A model is a lie that helps you see the truth.* * * Howard Skipper<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf> [[alternative HTML version deleted]]
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