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

[Hettling, J.]

Hi,

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!

Hannes


________________________________________
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
>> 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)
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=C                 LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=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.


More specifically, the error is at this line in the vignette in the
'figure1' chunk:

plot(hd)

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

HTH
Dan




> Dan
>
>
>> Many thanks in advance,
>>
>> Hannes
>>
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