[Bioc-devel] BiocCheck error

[Zhezhen Wang]

Thank you so much for that remainder. The thing is the NPS linkage is already included in our grant submission, but then we found that there already is a package called NPS so we decided to change it BioTIP. Is making another copy and rename that to BioTIP the best way to solve my situation?

Zhezhen
________________________________
From: Pages, Herve <hpages using fredhutch.org>
Sent: Wednesday, August 21, 2019 7:47 PM
To: Zhezhen Wang <zhezhen using uchicago.edu>; Martin Morgan <mtmorgan.bioc using gmail.com>; Vincent Carey <stvjc using channing.harvard.edu>
Cc: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] BiocCheck error

Note that the name of the package (BioTIP) differs from the name of the
GitHub repo (NPS). They will need to match if you intend to submit to
Bioconductor. Thanks!

H.


On 8/20/19 09:20, Zhezhen Wang wrote:
> I see, thank you Martin!
> Zhezhen
> ________________________________
> From: Martin Morgan <mtmorgan.bioc using gmail.com>
> Sent: Tuesday, August 20, 2019 11:15 AM
> To: Zhezhen Wang <zhezhen using uchicago.edu>; Vincent Carey <stvjc using channing.harvard.edu>
> Cc: bioc-devel using r-project.org <bioc-devel using r-project.org>
> Subject: Re: [Bioc-devel] BiocCheck error
>
> I think this is from BiocCheck, needing access to CRAN / Bioconductor to look at package status. Likely there are issues accessing these sites (BiocManager::repositories()) from your computer. It seems not to be an issue that you as developer need to worry about, provided you are confident that you are using current packages.
>
> Martin
>
> On 8/20/19, 12:04 PM, "Bioc-devel on behalf of Zhezhen Wang" <bioc-devel-bounces using r-project.org on behalf of zhezhen using uchicago.edu> wrote:
>
>      The github repo is https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_xyang2uchicago_NPS&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=DsHb4fuqI94H_l8UosIRZgMvGezo2wlah7MV9lZVBuw&s=XROazf2UylAST2t8NvzZfcr0Sv-Y4RL6G3WloKc-yVo&e=
>
>
>      ________________________________
>      From: Vincent Carey <stvjc using channing.harvard.edu>
>      Sent: Tuesday, August 20, 2019 10:52 AM
>      To: Zhezhen Wang <zhezhen using uchicago.edu>
>      Cc: bioc-devel using r-project.org <bioc-devel using r-project.org>
>      Subject: Re: [Bioc-devel] BiocCheck error
>
>      If your package that generates the error is in a github repo, please give the details.
>      If it is already in Bioconductor please give the name of the package and ensure we can
>      get access to the code that is generating the error.  In general it is very hard to help unless
>      we can reproduce the error you report.
>
>      On Tue, Aug 20, 2019 at 11:38 AM Zhezhen Wang <zhezhen using uchicago.edu<mailto:zhezhen using uchicago.edu>> wrote:
>      Hi I am running BiocCheck on my new package and I get the following error message
>
>        *   Checking for deprecated package usage... Warning in readLines(file, skipNul = TRUE) : InternetOpenUrl failed: 'The server name or address could not be resolved' Error in readLines(file, skipNul = TRUE) : cannot open the connection
>
>      May I know what this error message means and how I can correct it?
>
>      Zhezhen
>
>
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--
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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