[Bioc-devel] question regarding timeout

[Obenchain, Valerie]

Hi,

I'm not sure what's going on here. It looks there haven't been any
changes to the vignette and the package doesn't have the timeout in devel.

I went on the release builder and was able to build the vignette which
confirms that the vignette doesn't hang, it just takes a long time.

When I ran the vignette I did notice one example took a long time. This
is the output -

Chr: 1
1  2  3  4  5  6  7  8  9  10  11  12  13  14  15  16  17  18  19  20 
21  22  23  24  25  26  27  28  29  30  31  32  3
3  34  35  36  37  38  39  40  41  42  43  44  45  46  47  48  49  50 
51  52  53  54  55  56  57  58  59  60  61  62  6
3
Chr: 2
1  2  3  4  5  6  7  8  9  10  11  12  13  14  15  16  17  18  19  20 
21  22  23  24  25  26  27  28  29  30  31  32  3
3  34  35  36  37  38  39  40  41  42  43  44  45  46  47  48  49  50 
51  52  53  54  55  56  57  58  59  60  61  62
Chr: 3
1  2  3  4  5  6  7  8  9  10  11  12  13  14  15  16  17  18  19  20 
21  22  23  24  25  26  27  28  29  30  31  32  3
3  34  35  36  37  38  39  40  41  42  43  44  45  46  47  48  49  50 
51  52  53  54  55  56  57  58  59  60  61  62
Chr: 4
1  2  3  4  5  6  7  8  9  10  11  12  13  14  15  16  17  18  19  20 
21  22  23  24  25  26  27  28  29  30  31  32  3
3  34  35  36  37  38  39  40  41  42  43  44  45  46  47
...

I would recommend shortening that example to use just a few chromosomes
instead of all 22. On the windows machines packages are built on both 32
and 64 bit architecture so it can take twice as long as the other
builders. This isn't really a satisfying answer because the package
doesn't timeout in devel.

Not sure what else to suggest except let's keep an eye on it.

Valerie


On 06/08/2017 06:51 AM, Krithika Bhuvaneshwar wrote:
> Hello,
>
> We are the maintainers of the CINdex package.
>
> I believe when the upgrade to the new Bioconductor version happened,
> the package times out in Windows environment during build.
>
> https://bioconductor.org/packages/release/bioc/html/CINdex.html
>
> Could you please let us know if we need to do anything from our end  ?
>
> Thanks,
> Krithika
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>



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