Re: [Bioc-devel] Writing examples for accessing web API

Thank you Martin for the response, it was very helpful. I am facing difficulties to write code examples, unit tests and vignettes for accessing web APIs. I understand that the use of \dontrun{} is not the best solution for examples. I am using testthat::skip_on_bioc() to avoid time consuming and

Re: [Bioc-devel] Writing examples for accessing web API

Thank you Nan Xiao, I think it is a good solution for my case. I will put the definition of host outside the \dontrun{}. Welliton Em ter, 7 de mar de 2017 16:27, Nan Xiao escreveu: > - this check can be bypassed by > writing "partially working" examples, > for instance: >

Re: [Bioc-devel] Writing examples for accessing web API

- this check can be bypassed by writing "partially working" examples, for instance: #' token = "foo" #' \dontrun{ #' api(..., token)} Best, -Nan On Tue, Mar 7, 2017 at 2:13 PM, Welliton Souza wrote: > Hi Sean, > > It doesn't require authentication. I've been using this

Re: [Bioc-devel] Writing examples for accessing web API

Hi Sean, It doesn't require authentication. I've been using this server ( http://1kgenomes.ga4gh.org) to provide working examples and do unit tests but I am not responsible for this server. However the package was developed to access any server endpoint that use the same API. There are many web

Re: [Bioc-devel] Writing examples for accessing web API

Hi, Welliton. Great question. Just out of curiosity, what are the internet connection requirements that preclude running examples? Is authentication required? Or are you connecting to a server that runs only intermittently? Sean On Tue, Mar 7, 2017 at 1:57 PM, Welliton Souza

[Bioc-devel] Writing examples for accessing web API

Hi, I am developing a package that access web API endpoints. I wrote the examples within \dontrun{} due to internet connection requirements. However, the BiocCheck reports that I should provide at least 80 % of running examples. What I should do? The package is mainly focused on accessing web API

Re: [Bioc-devel] build report with error

Thanks very much Andrea From: Obenchain, Valerie Sent: 07 March 2017 17:39:58 To: Rodriguez Martinez, Andrea; bioc-devel@r-project.org Subject: Re: [Bioc-devel] build report with error Hi Andrea, Our emails just crossed:

Re: [Bioc-devel] build report with error

Hi Andrea, Our emails just crossed: https://stat.ethz.ch/pipermail/bioc-devel/2017-March/010543.html Anytime you see the same error across many (in this case hundreds of) packages it's safe to assume it's a build system error. I'll try to keep everyone informed of known failures by posting to

Re: [Bioc-devel] problems with master.bioconductor.org

Access was restored after about 30 minutes of downtime - the machine is back to normal. I haven't found any insights in the logs as to why this happened. Valerie On 03/07/2017 08:27 AM, Obenchain, Valerie wrote: > We are having some problems with the machine that serves the web site > and is

[Bioc-devel] devel builds: windows and mac

The devel build report for March 6 had 336 install failures on Windows (tokay2). The common error message was 'Biobase' not available ... which is ironic since Biobase is 'green' on the build report. We aren't 100% certain what happens in this case but think it's related to the Single Package

[Bioc-devel] build report with error

Hi, I just noticed that my packages MetaboSignal and MWASTools have a build report with error for Windows in the devel branch. I wonder if there is something I can do about this. See the specific error messages below: -For MetaboSignal it says: ## ### Running command: ### ### chmod a+r

[Bioc-devel] problems with master.bioconductor.org

We are having some problems with the machine that serves the web site and is the end point for downloading packages with biocLite(). We'll try to get this fixed and back to normal as soon as possible. Valerie This email message may contain legally privileged and/or confidential information.

Re: [Bioc-devel] GitHub mirror not synced for GenomicTuples

Hello, I have the same issue for the DRIMSeq package. The Bioconductor git mirror is not synchronized with the svn. Is there a way I could fix that or somebody from the core team has to do that? I will use the squashing approach for the next time but if this happens again, should I write it