[Bioc-devel] ndexr fails on vignette build on windows
Florian J. Auer
||or|@n@@uer @end|ng |rom |n|orm@t|k@un|-@ug@burg@de
Thu Oct 24 13:21:09 CEST 2019
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 <mailto: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
> <mailto:florian.auer using informatik.uni-augsburg.de>>
> Sent: Wednesday, October 23, 2019 7:25 AM
> To: Shepherd, Lori <Lori.Shepherd using RoswellPark.org>;
> 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: 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><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>><mailto: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>><mailto: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><mailto: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>><mailto: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><mailto:Florian.Auer using informatik.uni-augsburg.de
> <mailto:Florian.Auer using informatik.uni-augsburg.de>>
> phone: (+49) 0821- 598 - 3748
>
>
> [[alternative HTML version deleted]]
>
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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><mailto:Florian.Auer using informatik.uni-augsburg.de
> <mailto:Florian.Auer using informatik.uni-augsburg.de>>
> phone: (+49) 0821- 598 - 3748
>
>
> This email message may contain legally privileged and/or
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> delivery of this message to the intended 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
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