[Bioc-devel] session info of Single Package Builder Machines
j.hettling at vu.nl
Wed Aug 7 23:43:24 CEST 2013
My sessionInfo() gave the same versions for all packages compared to the ones on zin1.
I still do not know why it build without problems on my machines and threw an error on zin.
However, since you indicated where things went wrong:
> So it's a problem in the plot method of the hyperdraw package.
> Specifically in drawHyperEdge() in draw.R line 258, it tries to access
> edgeNodeDir[[end]]. end is set to "R_HEX1" and edgeNodeDir is
> R_HEX1:0.4 R_PGI:0.4 R_PFK:0.4 R_FBA:0.4 R_TPI:0.4 R_GAPD:0.8 R_PGK:-0.8
> -1.5707963 -1.5707963 -1.5707963 -2.0031933 -0.8577054 -1.5707963 -1.5707963
> R_PGM:-0.8 R_ENO:0.8 R_PYK:0.8
> -1.5707963 -1.5707963 -1.5707963
I was able to fix the problem: Originally I changed edge labels in a hyperdraw graph after creating the object, and did not
update "end". Now I found a way to assign all edge labels beforehand which is much cleaner.
I uploaded the package and just got the email that everything build without errors.
Thanks a lot for your help!
From: dandante at gmail.com [dandante at gmail.com] on behalf of Dan Tenenbaum [dtenenba at fhcrc.org]
Sent: 07 August 2013 20:55
To: Hettling, J.
Subject: Re: [Bioc-devel] session info of Single Package Builder Machines
On Wed, Aug 7, 2013 at 11:43 AM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
> 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
>> 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
>> 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
> 4: stop(msg, err, call. = FALSE)
> 3: RweaveTryStop(err, options)
> 2: driver$runcode(drobj, chunk, chunkopts)
> 1: Sweave("BiGGR.Rnw")
> R version 3.0.1 (2013-05-16)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>  LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>  LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
>  LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
>  LC_PAPER=C LC_NAME=C
>  LC_ADDRESS=C LC_TELEPHONE=C
>  LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> attached base packages:
>  grid parallel stats graphics grDevices utils datasets
>  methods base
> other attached packages:
>  BiGGR_0.99.0 LIM_1.4.4 diagram_1.6.1 shape_1.4.0
>  limSolve_1.5.5 hyperdraw_1.13.1 Rgraphviz_2.5.4 hypergraph_1.33.0
>  graph_1.39.3 rsbml_2.19.1 BiocGenerics_0.7.3
> loaded via a namespace (and not attached):
>  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.
More specifically, the error is at this line in the vignette in the
So it's a problem in the plot method of the hyperdraw package.
Specifically in drawHyperEdge() in draw.R line 258, it tries to access
edgeNodeDir[[end]]. end is set to "R_HEX1" and edgeNodeDir is
R_HEX1:0.4 R_PGI:0.4 R_PFK:0.4 R_FBA:0.4 R_TPI:0.4 R_GAPD:0.8 R_PGK:-0.8
-1.5707963 -1.5707963 -1.5707963 -2.0031933 -0.8577054 -1.5707963 -1.5707963
R_PGM:-0.8 R_ENO:0.8 R_PYK:0.8
-1.5707963 -1.5707963 -1.5707963
>> Many thanks in advance,
>> Bioc-devel at r-project.org mailing list
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