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

[Shepherd, Lori]

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>; 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


This email message may contain legally privileged and/or confidential information.  If you are not the intended recipient(s), or the employee or agent responsible for the 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 and delete this email message from your computer. Thank you.
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