[R-SIG-Mac] Cannot open PDF Vignettes on Ventura

Kevin Thorpe kev|n@thorpe @end|ng |rom utoronto@c@
Tue Feb 7 15:17:58 CET 2023 

Thanks Marc.

I have now confirmed that this is not a MAC only issue. Tested on my windows box just now.

Thanks again to everyone who helped.

Kevin

-- 
Kevin E. Thorpe
Head of Biostatistics,  Applied Health Research Centre (AHRC)
Li Ka Shing Knowledge Institute of St. Michael’s Hospital
Assistant Professor, Dalla Lana School of Public Health
University of Toronto
email: kevin.thorpe using utoronto.ca  Tel: 416.864.5776  Fax: 416.864.3016

> On Feb 7, 2023, at 8:02 AM, Marc Schwartz <marc_schwartz using me.com> wrote:
> 
> Hi,
> 
> Just as an FYI, without getting too far OT, if you are not familiar with Electron (https://www.electronjs.org), beyond being "free", it is cross-platform (Windows, macOS, and Linux), which is why a notable number of application developers, including "for profit" ones, are shifting to it. You can get a sense for that here:
> 
>   https://www.electronjs.org/apps
>    
> That being said, as with most such things, there are pros and cons to using that framework, in the latter case, notably the material memory overhead and that you lose the OS specific UI/UX as apps take on a more generic web-like esthetic across each platform. Some have also raised security issues with the framework.
> 
> I don't use RStudio, but it sounds like there is bug with RStudio's new version, which should be reported to them. It looks like they are in the midst of some structural changes to their web site given the recent corporate change from RStudio to Posit, but here is a link to the current community support page:
> 
>   https://community.rstudio.com
> 
> Regards,
> 
> Marc Schwartz
> 
> 
> On February 7, 2023 at 7:28:23 AM, Kevin Thorpe (kevin.thorpe using utoronto.ca (mailto:kevin.thorpe using utoronto.ca)) wrote:
> 
>> Thanks for that Ken.
>> 
>> I downloaded the “non-Electron” version from the link you posted and PDFs now open properly. Naturally, RStudio now wants to update but I assume an update will fetch the broken Electron version.
>> 
>> Thanks for all the help troubleshooting.
>> 
>> Kevin
>> 
>> --
>> Kevin E. Thorpe
>> Head of Biostatistics, Applied Health Research Centre (AHRC)
>> Li Ka Shing Knowledge Institute of St. Michael’s Hospital
>> Assistant Professor, Dalla Lana School of Public Health
>> University of Toronto
>> email: kevin.thorpe using utoronto.ca Tel: 416.864.5776 Fax: 416.864.3016
>> 
>>> On Feb 7, 2023, at 2:45 AM, Ken Beath wrote:
>>> 
>>> The problem seems to be with the Electron framework they switched to in the current version.
>>> 
>>> From https://dailies.rstudio.com/version/2022.07.1+554.pro3/ the previous version works, but not the Electron version. For those that are interested Electron is a newer framework that has the advantage of being completely free, and is what is now used by RStudio rather than Qt.
>>> 
>>> Ken
>>> 
>>>> On 7 Feb 2023, at 2:49 pm, Kevin Thorpe wrote:
>>>> 
>>>> Thanks Simon and Duncan.
>>>> 
>>>> I found the same plugins and removed them. It works correctly in the R.app.
>>>> 
>>>> RStudio still directs me to a browser window at the localhost address 127.0.0.1 and nothing loads. I know RStudio is not R and this list is for R so will probably have to search elsewhere for that solution unless anyone here happens to have an idea.
>>>> 
>>>> Kevin
>>>> 
>>>> --
>>>> Kevin E. Thorpe
>>>> Head of Biostatistics, Applied Health Research Centre (AHRC)
>>>> Li Ka Shing Knowledge Institute of St. Michael’s Hospital
>>>> Assistant Professor, Dalla Lana School of Public Health
>>>> University of Toronto
>>>> email: kevin.thorpe using utoronto.ca Tel: 416.864.5776 Fax: 416.864.3016
>>>> 
>>>>> On Feb 6, 2023, at 7:53 PM, Duncan Murdoch wrote:
>>>>> 
>>>>> That worked for me. I deleted two plugins from the global /Library/Internet\ Plug-Ins folder named
>>>>> 
>>>>> AdobePDFViewer.plugin
>>>>> AdobePDFViewerNPAPI.plugin
>>>>> 
>>>>> and dated from 2020. Now things are fine.
>>>>> 
>>>>> Duncan Murdoch
>>>>> 
>>>>> On 06/02/2023 7:36 p.m., Simon Urbanek wrote:
>>>>>> Kevin,
>>>>>> oh, that's something entirely different - what I was talking about was if you use
>>>>>> vignette("survival")
>>>>>> in R it opens a Preview with the vignette.
>>>>>> What you describe seems like a browser plugin issue, because the help system is just an html page (assuming you are talking about the html help system). So it seems that you may have installed some Adobe browser plugin that doesn't work anymore. The plugins live in ~/Library/Internet\ Plug-Ins/ (user) and /Library/Internet\ Plug-Ins/ (global), so you should remove it from there.
>>>>>> Cheers,
>>>>>> Simon
>>>>>>> On 7/02/2023, at 12:01 PM, Kevin Thorpe wrote:
>>>>>>> 
>>>>>>> When I try to open a PDF vignette (say a vignette from the survival package)from the help system in R it does not open Preview. I cannot actually open any PDF vignettes. All I get is a finder window with the error I previously described. It asks me to select an appropriate viewer. Selecting Preview opens nothing and more errors are thrown to the Console. I could send you and Duncan screenshots off-list, since I know that theses lists are picky about attachments.
>>>>>>> 
>>>>>>> The steps I take are:
>>>>>>> 
>>>>>>> 1. Open the R app.
>>>>>>> 2. Start the Help system.
>>>>>>> 3. Navigate to the survival package vignettes.
>>>>>>> 4. Click the PDF link for the The survival package
>>>>>>> 
>>>>>>> Then the errors happen.
>>>>>>> 
>>>>>>> I will send a screenshot of the result off list.
>>>>>>> 
>>>>>>> Kevin
>>>>>>> 
>>>>>>> --
>>>>>>> Kevin E. Thorpe
>>>>>>> Head of Biostatistics, Applied Health Research Centre (AHRC)
>>>>>>> Li Ka Shing Knowledge Institute of St. Michael’s Hospital
>>>>>>> Assistant Professor, Dalla Lana School of Public Health
>>>>>>> University of Toronto
>>>>>>> email: kevin.thorpe using utoronto.ca Tel: 416.864.5776 Fax: 416.864.3016
>>>>>>> 
>>>>>>>> On Feb 6, 2023, at 4:58 PM, Simon Urbanek wrote:
>>>>>>>> 
>>>>>>>> Kevin,
>>>>>>>> 
>>>>>>>> can you then describe in more detail what you are taking about? If you open a PDF vignette in R, it simply calls "open" so it will open in Preview (as that is your system viewer). And you have confirmed that it is what happens, so are you taking about something else? If so, please describe every step you make to reproduce whatever issue you are having.
>>>>>>>> 
>>>>>>>> Thanks,
>>>>>>>> Simon
>>>>>>>> 
>>>>>>>> 
>>>>>>>> On Feb 7, 2023, at 9:58 AM, Kevin Thorpe wrote:
>>>>>>>>> 
>>>>>>>>> Yes, it does.
>>>>>>>>> 
>>>>>>>>> Kevin
>>>>>>>>> 
>>>>>>>>> --
>>>>>>>>> Kevin E. Thorpe
>>>>>>>>> Head of Biostatistics, Applied Health Research Centre (AHRC)
>>>>>>>>> Li Ka Shing Knowledge Institute of St. Michael’s Hospital
>>>>>>>>> Assistant Professor, Dalla Lana School of Public Health
>>>>>>>>> University of Toronto
>>>>>>>>> email: kevin.thorpe using utoronto.ca Tel: 416.864.5776 Fax: 416.864.3016
>>>>>>>>> 
>>>>>>>>>> On Feb 6, 2023, at 3:56 PM, Duncan Murdoch wrote:
>>>>>>>>>> 
>>>>>>>>>> On 06/02/2023 3:47 p.m., Kevin Thorpe wrote:
>>>>>>>>>>> Simon,
>>>>>>>>>>> Preview is my default viewer. In the finder window that came up I tried selecting Preview as the viewer to use and it still failed. The following errors went to the Console.
>>>>>>>>>>> 2023-02-06 15:43:55.448 R[62964:5174302] +[CATransaction synchronize] called within transaction
>>>>>>>>>>> 2023-02-06 15:43:55.568 R[62964:5174302] +[CATransaction synchronize] called within transaction
>>>>>>>>>>> 2023-02-06 15:44:03.253 R[62964:5174302] +[CATransaction synchronize] called within transaction
>>>>>>>>>>> 2023-02-06 15:44:16.012 R[62964:5174302] +[CATransaction synchronize] called within transaction
>>>>>>>>>>> Kevin
>>>>>>>>>> 
>>>>>>>>>> Hi Kevin.
>>>>>>>>>> 
>>>>>>>>>> If you just run `open some.pdf` in a terminal, does it open properly in Preview?
>>>>>>>>>> 
>>>>>>>>>> Duncan Murdoch
>>>>>>>>> 
>>>>>>>> 
>>>>>>> 
>>>>> 
>>>> 
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