[Bioc-devel] session info of Single Package Builder Machines

Dan Tenenbaum dtenenba at fhcrc.org
Wed Aug 7 20:43:33 CEST 2013

On Wed, Aug 7, 2013 at 11:11 AM, hettling <j.hettling at vu.nl> wrote:
> Dear all,
> I try to resubmit my package in the file submit tracker after completing
> the package revisions. I tested my package on various machines with R
> 3.0.1 and Bioc 2.13, build and check proceed without any errors or
> warnings.
> However, the built with the "Single Package Builder fails" on the
> machines parceval and zin1 on upload. I checked all versions etc. and
> cannot see what the problem is, I even run the same ubuntu version as on
> zin1.
> It makes it almost impossible for me to debug since on my machines
> everything works fine. I only spam the submission system when
> re-uploading and thinking I got it fixed each time.
> My question is: Is it possible to get the sessionInfo() of the machines
> after the build fails? I want to make sure that any loaded and attached
> packages on my machines conform with the versions installed on the
> Single Package Builder computers.

Here is the sessionInfo() on zin1:

Error in edgeNodeDir[[end]] : subscript out of bounds
> traceback()
4: stop(msg, err, call. = FALSE)
3: RweaveTryStop(err, options)
2: driver$runcode(drobj, chunk, chunkopts)
1: Sweave("BiGGR.Rnw")
> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-unknown-linux-gnu (64-bit)

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [7] LC_PAPER=C                 LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C

attached base packages:
[1] grid      parallel  stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] BiGGR_0.99.0       LIM_1.4.4          diagram_1.6.1      shape_1.4.0
 [5] limSolve_1.5.5     hyperdraw_1.13.1   Rgraphviz_2.5.4    hypergraph_1.33.0
 [9] graph_1.39.3       rsbml_2.19.1       BiocGenerics_0.7.3

loaded via a namespace (and not attached):
[1] lpSolve_5.6.7  MASS_7.3-28    quadprog_1.5-5 stats4_3.0.1   tools_3.0.1

I'll try to figure out what is going on here.

> Many thanks in advance,
> Hannes
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