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

[Florian J. Auer]

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"
>
>
> #
> # on windows
> #
>
> Browse[2]> resp
> $url
> [1] "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> on behalf of
> Florian J. Auer <florian.auer using informatik.uni-augsburg.de>
> *Sent:* Thursday, September 26, 2019 7:52 AM
> *To:* bioc-devel using r-project.org <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
> 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
phone: (+49) 0821- 598 - 3748


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