[Bioc-devel] CINdex package build error in Linux

Yuriy Gusev yg63 at georgetown.edu
Fri Jan 19 18:08:09 CET 2018


Great news!

Thanks Valerie

Best Regards
Yuriy


On Fri, Jan 19, 2018 at 11:40 AM, Obenchain, Valerie <
Valerie.Obenchain at roswellpark.org> wrote:

> Hi Krithika,
>
> I believe this was related to a problem with getTable() in rtracklayer:
>
>   https://github.com/lawremi/rtracklayer/issues/5
>
> rtracklayer 1.39.5 built successfully today and the error in CINdex has
> cleared up:
>
>   https://bioconductor.org/packages/3.7/bioc/html/CINdex.html
>
> Valerie
>
>
>
> On 01/18/2018 08:19 AM, Krithika Bhuvaneshwar wrote:
>
> Hello Bioconductor team,
>
> We are the creator and maintainers of the CINdex Bioconductor package.
>
> Last few days, we are seeing build errors in our package (See below). The
> package builds fine in Mac OS, but is giving the following error on Ubuntu
> OS.http://bioconductor.org/checkResults/release/bioc-LATEST/CINdex/malbec1-buildsrc.html
>
>
> We have not made any changes to our package, and did not have any errors
> previously.
>
> Is there some action we need to take on our part ? Please advise.
>
> Thanks,
> Krithika
>
> Attaching package: 'Biobase'
>
> The following object is masked from 'package:AnnotationHub':
>
>     cache
>
> ===========================================================================
> Welcome to oligo version 1.42.0
> ===========================================================================
> Loading required package: DBI
> Warning: closing unused connection 5 (hg19ToHg18.over.chain)
> Loading ideogram...
> Quitting from lines 230-240 (PrepareInputData.Rmd)
> Error: processing vignette 'PrepareInputData.Rmd' failed with diagnostics:
> Bad Request
> Execution halted
>
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>
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-- 
Yuriy Gusev, Ph.D., Associate Professor
Innovation Center for Biomedical Informatics (ICBI)
Georgetown University Medical Center
2115 Wisconsin Ave NW, Suite 110
Washington DC 20007
Tel. (202) 687-5094; Fax (202) 687-5011
Email: yg63 at georgetown.edu
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Website:icbi.georgetown.edu/
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