[Bioc-devel] BiocCheck error

[Pages, Herve]

On 8/21/19 18:51, Zhezhen Wang wrote:
> 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?

But then isn't it going to be somewhat painful to keep the 2 repos in 
sync? Sounds like using some kind of alias or redirect mechanism would 
be better but you would need to ask the Git or GitHub experts on how to 
do this.

H.

> 
> 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
>> 
>> 
>>              [[alternative HTML version deleted]]
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>> 
> 
> -- 
> Hervé Pagès
> 
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
> 
> E-mail: hpages using fredhutch.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages using fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319