Re: [Bioc-devel] CINdex package build error in Linux

2018-01-19 Thread Yuriy Gusev 
Great news!

Thanks Valerie

Best Regards
Yuriy


On Fri, Jan 19, 2018 at 11:40 AM, Obenchain, Valerie <
valerie.obench...@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
>
>   [[alternative HTML version deleted]]
>
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-- 
Yuriy Gusev, Ph.D., Associate Professor
Innovation Center for Biomedical Informatics (ICBI)
Georgetown University Medical Center
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Tel. (202) 687-5094; Fax (202) 687-5011
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Re: [Bioc-devel] CINdex package build error in Linux

2018-01-19 Thread Obenchain, Valerie 
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

[[alternative HTML version deleted]]

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This email message may contain legally privileged and/or confidential 
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recipient(s), you are hereby notified that any disclosure, copying, 
distribution, or use of this email message is prohibited.  If you have received 
this message in error, please notify the sender immediately by e-mail and 
delete this email message from your computer. Thank you.
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[Bioc-devel] CINdex package build error in Linux

2018-01-18 Thread Krithika Bhuvaneshwar 
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

[[alternative HTML version deleted]]

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