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.a...@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.sheph...@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.a...@informatik.uni-augsburg.de> >> Sent: Wednesday, October 23, 2019 7:25 AM >> To: Shepherd, Lori <lori.sheph...@roswellpark.org> >> <lori.sheph...@roswellpark.org>; bioc-devel@r-project.org < >> bioc-devel@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-boun...@r-project.org><mailto: >> bioc-devel-boun...@r-project.org> on behalf of Florian J. Auer < >> florian.a...@informatik.uni-augsburg.de><mailto: >> florian.a...@informatik.uni-augsburg.de> >> Sent: Thursday, September 26, 2019 7:52 AM >> To: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> < >> bioc-devel@r-project.org><mailto:bioc-devel@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.a...@informatik.uni-augsburg.de<mailto: >> florian.a...@informatik.uni-augsburg.de> >> phone: (+49) 0821- 598 - 3748 >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> >> This email message may contain legally privileged and/or confidential >> information. 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If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > -- > 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.a...@informatik.uni-augsburg.de > phone: (+49) 0821- 598 - 3748 > > -- The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline <http://www.partners.org/complianceline> . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. 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