[Bioc-devel] ndexr fails on vignette build on windows

Thu Oct 24 15:29:48 CEST 2019

Thanks for this.  I will try with the upcoming curl from github....

On Thu, Oct 24, 2019 at 7:21 AM Florian J. Auer <
florian.auer using informatik.uni-augsburg.de> wrote:

> Hi Vincent,
>
> For me the sollution was quite simple: I just put the protocol to the url,
> i.e. replaced www.ndexbio.org with http://www.ndexbio.org.
>
> I guess providing the protocol would be good practice anyways.
>
> In general, the issue was in curl, which should be fixed in the current
> devel release. For more information see also the curl issue:
>
> https://github.com/jeroen/curl/issues/209#issuecomment-542127937
>
> and the discussion in the httr issue:
>
> https://github.com/r-lib/httr/issues/619
>
> It seems, that this issue still exists in windows:
> *jeroen <https://github.com/jeroen> *commented 8 days ago
> <https://github.com/jeroen/curl/issues/209#issuecomment-542758288> •
> edited
>
> On Windows you have to wait for the next release of the r package
>
> https://github.com/jeroen/curl/issues/209#issuecomment-542758288
>
> Greetings
>
> Florian
> Am 23.10.19 um 21:23 schrieb Vincent Carey:
>
> May I ask what is the resolution here?  I have updated curl and httr on my
> windows box and continue
> to see errors unique to windows when requests lack the protocol in the URL.
>
> On Wed, Oct 23, 2019 at 7:28 AM Shepherd, Lori <
> Lori.Shepherd using roswellpark.org> wrote:
>
>> Thank you for the update.
>>
>>
>> Lori Shepherd
>>
>> Bioconductor Core Team
>>
>> Roswell Park Comprehensive Cancer Center
>>
>> Department of Biostatistics & Bioinformatics
>>
>> Elm & Carlton Streets
>>
>> Buffalo, New York 14263
>>
>> ________________________________
>> From: Florian J. Auer <florian.auer using informatik.uni-augsburg.de>
>> Sent: Wednesday, October 23, 2019 7:25 AM
>> To: Shepherd, Lori <Lori.Shepherd using RoswellPark.org>
>> <Lori.Shepherd using RoswellPark.org>; bioc-devel using r-project.org <
>> bioc-devel using r-project.org>
>> Subject: Re: [Bioc-devel] ndexr fails on vignette build on windows
>>
>>
>> Hi Lori,
>>
>> Thanks a lot, that really helped!
>>
>> It seems, that the error is caused by httr, and curl in the end.
>>
>>
>> https://github.com/r-lib/httr/issues/619
>>
>>
>> Greetings
>>
>> Florian
>>
>>
>>
>> Am 09.10.19 um 17:37 schrieb Shepherd, Lori:
>> I did a little digging and here is what I've found...
>>
>>
>> I R CMD Stangle the vignette and then sourced the code:
>>
>>
>> > source("ndexr-vignette.R", echo=TRUE)
>>
>> > ## ----
>> eval=FALSE---------------------------------------------------------
>> > ## if (!requireNamespace("BiocManager", quietly=TRUE))
>> > ##     instal .... [TRUNCATED]
>>
>> > ## ----
>> eval=FALSE---------------------------------------------------------
>> > ## ## login to the NDEx server
>> > ## ndexcon = ndex_connect("username", .... [TRUNCATED]
>> Error in if (is_http) { : argument is of length zero
>> > traceback()
>> 8: request_perform(req, hu$handle$handle)
>> 7: httr::GET(url = url, config = auth_param) at ndex_helper.r#149
>> 6: ndex_helper_httpResponseHandler(httr::GET(url = url, config =
>> auth_param),
>>        log_txt, verbose) at ndex_connect.r#84
>> 5: ndex_connect() at ndexr-vignette.R#24
>> 4: eval(ei, envir)
>> 3: eval(ei, envir)
>> 2: withVisible(eval(ei, envir))
>> 1: source("ndexr-vignette.R", echo = TRUE)
>>
>>
>> If I then did a
>> debug(httr:::request_perform)
>>
>> httr:::request_fetch results in different output on windows than on
>> mac/linux
>>
>>
>>
>> #
>> # on linux and mac
>> #
>>
>> Browse[2]> resp
>> $url
>> [1] "HTTP://www.ndexbio.org/v2/admin/status"<
>> HTTP://www.ndexbio.org/v2/admin/status>
>>
>>
>> #
>> # on windows
>> #
>>
>> Browse[2]> resp
>> $url
>> [1] "www.ndexbio.org/v2/admin/status<
>> http://www.ndexbio.org/v2/admin/status>"
>>
>> This causes the eventual error.
>>
>>
>> You might try to come up with a small reproducible example and report as
>> a bug to httr.
>>
>>
>>
>>
>> Lori Shepherd
>>
>> Bioconductor Core Team
>>
>> Roswell Park Comprehensive Cancer Center
>>
>> Department of Biostatistics & Bioinformatics
>>
>> Elm & Carlton Streets
>>
>> Buffalo, New York 14263
>>
>> ________________________________
>> From: Bioc-devel <bioc-devel-bounces using r-project.org><mailto:
>> bioc-devel-bounces using r-project.org> on behalf of Florian J. Auer <
>> florian.auer using informatik.uni-augsburg.de><mailto:
>> florian.auer using informatik.uni-augsburg.de>
>> Sent: Thursday, September 26, 2019 7:52 AM
>> To: bioc-devel using r-project.org<mailto:bioc-devel using r-project.org> <
>> bioc-devel using r-project.org><mailto:bioc-devel using r-project.org>
>> Subject: [Bioc-devel] ndexr fails on vignette build on windows
>>
>> Hi everyone,
>>
>> my package ndexr produces some errors while building the vignette, but
>> only in the Windows build.
>>
>> In particular, the error message shows:
>>
>> Quitting from lines 76-78 (ndexr-vignette.Rmd)
>> Error: processing vignette 'ndexr-vignette.Rmd' failed with diagnostics:
>> argument is of length zero
>> --- failed re-building 'ndexr-vignette.Rmd'
>>
>> Seems like it's occurring in the following lines:
>>
>> ```{r, echo=FALSE, results='hide', message=FALSE}
>> ## login to the NDEx server
>> ndexcon = ndex_connect()
>> ```
>>
>> Is there some different behavior in Windows of how the code blocks are
>> treated? Or is the error occurring within the code?
>>
>> Have there been some changes on the build server, since the error only
>> occurred recently without any changes in the package?
>>
>> I'm grateful for any feedback!
>>
>> Greetings
>>
>> Florian
>>
>> --
>> Dipl.Bioinf. Florian Auer
>> IT Infrastructure for Translational Medical Research
>> Faculty of Applied Computer Science
>> Faculty of Medicine
>> University of Augsburg
>> Alter Postweg 101
>> 86159 Augsburg
>>
>> email: Florian.Auer using informatik.uni-augsburg.de<mailto:
>> Florian.Auer using informatik.uni-augsburg.de>
>> phone: (+49) 0821- 598 - 3748
>>
>>
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>> --
>> Dipl.Bioinf. Florian Auer
>> IT Infrastructure for Translational Medical Research
>> Faculty of Applied Computer Science
>> Faculty of Medicine
>> University of Augsburg
>> Alter Postweg 101
>> 86159 Augsburg
>>
>> email: Florian.Auer using informatik.uni-augsburg.de<mailto:
>> Florian.Auer using informatik.uni-augsburg.de>
>> phone: (+49) 0821- 598 - 3748
>>
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>> This email message may contain legally privileged and/or confidential
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> --
> Dipl.Bioinf. Florian Auer
> IT Infrastructure for Translational Medical Research
> Faculty of Applied Computer Science
> Faculty of Medicine
> University of Augsburg
> Alter Postweg 101
> 86159 Augsburg
>
> email: Florian.Auer using informatik.uni-augsburg.de
> phone: (+49) 0821- 598 - 3748
>
>

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