Cannot open PDF Vignettes on Ventura

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 at utoronto.ca  Tel: 416.864.5776  Fax: 416.864.3016

> On Feb 6, 2023, at 2:45 PM, Simon Urbanek <simon.urbanek at R-project.org> wrote:
> 
> Kevin,
> 
> this looks like a problem with your Adobe installation - you seem to have the stub installed, but not an actual Adobe viewer. Perhaps look for uninstallation instructions for Adobe, reinstall it or ask their support? After upgrades it is often necessary to re-install 3rd party software.
> 
> Cheers,
> Simon
> 
> 
>> On Feb 7, 2023, at 5:14 AM, Kevin Thorpe <kevin.thorpe at utoronto.ca> wrote:
>> 
>> I noticed today that I can no longer open PDF vignettes from the help system in Ventura. I first noticed it in RStudio. Previously PDFs would open in Preview but now they try to open in a web page. So, I tried in native R (outside RStudio). I started the help system and went to the survival package vignettes and tried to open one. I eventually got a Finder window with the message, "AdobePDFViewer cannot find a compatible Adobe Acrobat or Adobe Reader to view this PDF. Please select one.? At the top of it.
>> 
>> Besides Preview I do also have Adobe Acrobat Reader installed (but it is not set as the default viewer for PDFs).
>> 
>> Additionally, the following error appeared in the Console when I tried to view a PDF vignette (for the sake of reproducibility I tried to load the survival.pdf vignette).
>> 
>> 2023-02-06 11:10:56.198 R[52961:4981916] CFURLResourceIsReachable failed because it was passed a URL which has no scheme
>> 
>> Has anyone else encountered this?
>> 
>> Here is my sessionInfo()
>> 
>>> sessionInfo()
>> R version 4.2.2 (2022-10-31)
>> Platform: x86_64-apple-darwin17.0 (64-bit)
>> Running under: macOS Ventura 13.1
>> 
>> Matrix products: default
>> BLAS:   /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
>> LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
>> 
>> locale:
>> [1] en_CA.UTF-8
>> 
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base     
>> 
>> other attached packages:
>> [1] knitr_1.42
>> 
>> loaded via a namespace (and not attached):
>> [1] compiler_4.2.2 tools_4.2.2    xfun_0.37     
>> 
>> 
>> 
>> -- 
>> 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 at utoronto.ca  Tel: 416.864.5776  Fax: 416.864.3016
>> 
>> _______________________________________________
>> R-SIG-Mac mailing list
>> R-SIG-Mac at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>

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 at utoronto.ca  Tel: 416.864.5776  Fax: 416.864.3016

> On Feb 6, 2023, at 3:01 PM, Kevin Thorpe <kevin.thorpe at utoronto.ca> wrote:
> 
> Thanks for the reply Simon.
> 
> As near as I can tell I have a working Adobe reader. I checked for updates and have the current version, it is just not set as my default viewer for PDF. Why has it stopped working with the Mac Preview app? Is it related to the loss of PS/EPS support?
> 
> I would prefer not to have to set Adobe Reader as my default. I could try removing and re-installing and see what happens.
> 
> 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 at utoronto.ca  Tel: 416.864.5776  Fax: 416.864.3016
> 
>> On Feb 6, 2023, at 2:45 PM, Simon Urbanek <simon.urbanek at R-project.org> wrote:
>> 
>> Kevin,
>> 
>> this looks like a problem with your Adobe installation - you seem to have the stub installed, but not an actual Adobe viewer. Perhaps look for uninstallation instructions for Adobe, reinstall it or ask their support? After upgrades it is often necessary to re-install 3rd party software.
>> 
>> Cheers,
>> Simon
>> 
>> 
>>> On Feb 7, 2023, at 5:14 AM, Kevin Thorpe <kevin.thorpe at utoronto.ca> wrote:
>>> 
>>> I noticed today that I can no longer open PDF vignettes from the help system in Ventura. I first noticed it in RStudio. Previously PDFs would open in Preview but now they try to open in a web page. So, I tried in native R (outside RStudio). I started the help system and went to the survival package vignettes and tried to open one. I eventually got a Finder window with the message, "AdobePDFViewer cannot find a compatible Adobe Acrobat or Adobe Reader to view this PDF. Please select one.? At the top of it.
>>> 
>>> Besides Preview I do also have Adobe Acrobat Reader installed (but it is not set as the default viewer for PDFs).
>>> 
>>> Additionally, the following error appeared in the Console when I tried to view a PDF vignette (for the sake of reproducibility I tried to load the survival.pdf vignette).
>>> 
>>> 2023-02-06 11:10:56.198 R[52961:4981916] CFURLResourceIsReachable failed because it was passed a URL which has no scheme
>>> 
>>> Has anyone else encountered this?
>>> 
>>> Here is my sessionInfo()
>>> 
>>>> sessionInfo()
>>> R version 4.2.2 (2022-10-31)
>>> Platform: x86_64-apple-darwin17.0 (64-bit)
>>> Running under: macOS Ventura 13.1
>>> 
>>> Matrix products: default
>>> BLAS:   /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
>>> LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
>>> 
>>> locale:
>>> [1] en_CA.UTF-8
>>> 
>>> attached base packages:
>>> [1] stats     graphics  grDevices utils     datasets  methods   base     
>>> 
>>> other attached packages:
>>> [1] knitr_1.42
>>> 
>>> loaded via a namespace (and not attached):
>>> [1] compiler_4.2.2 tools_4.2.2    xfun_0.37     
>>> 
>>> 
>>> 
>>> -- 
>>> 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 at utoronto.ca  Tel: 416.864.5776  Fax: 416.864.3016
>>> 
>>> _______________________________________________
>>> R-SIG-Mac mailing list
>>> R-SIG-Mac at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>> 
> 
> _______________________________________________
> R-SIG-Mac mailing list
> R-SIG-Mac at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac

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 at utoronto.ca  Tel: 416.864.5776  Fax: 416.864.3016

> On Feb 6, 2023, at 3:25 PM, Simon Urbanek <simon.urbanek at R-project.org> wrote:
> 
> Kevin,
> 
> no this is an Adobe issue - it seems to hijack the PDF support. R simply uses "open" so it doesn't care who handles it - that is a system setting, it has nothing to do with R. Did you try setting Preview as your system viewer?
> 
> Cheers,
> Simon
> 
> 
>> On Feb 7, 2023, at 9:01 AM, Kevin Thorpe <kevin.thorpe at utoronto.ca> wrote:
>> 
>> Thanks for the reply Simon.
>> 
>> As near as I can tell I have a working Adobe reader. I checked for updates and have the current version, it is just not set as my default viewer for PDF. Why has it stopped working with the Mac Preview app? Is it related to the loss of PS/EPS support?
>> 
>> I would prefer not to have to set Adobe Reader as my default. I could try removing and re-installing and see what happens.
>> 
>> 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 at utoronto.ca  Tel: 416.864.5776  Fax: 416.864.3016
>> 
>>> On Feb 6, 2023, at 2:45 PM, Simon Urbanek <simon.urbanek at R-project.org> wrote:
>>> 
>>> Kevin,
>>> 
>>> this looks like a problem with your Adobe installation - you seem to have the stub installed, but not an actual Adobe viewer. Perhaps look for uninstallation instructions for Adobe, reinstall it or ask their support? After upgrades it is often necessary to re-install 3rd party software.
>>> 
>>> Cheers,
>>> Simon
>>> 
>>> 
>>>> On Feb 7, 2023, at 5:14 AM, Kevin Thorpe <kevin.thorpe at utoronto.ca> wrote:
>>>> 
>>>> I noticed today that I can no longer open PDF vignettes from the help system in Ventura. I first noticed it in RStudio. Previously PDFs would open in Preview but now they try to open in a web page. So, I tried in native R (outside RStudio). I started the help system and went to the survival package vignettes and tried to open one. I eventually got a Finder window with the message, "AdobePDFViewer cannot find a compatible Adobe Acrobat or Adobe Reader to view this PDF. Please select one.? At the top of it.
>>>> 
>>>> Besides Preview I do also have Adobe Acrobat Reader installed (but it is not set as the default viewer for PDFs).
>>>> 
>>>> Additionally, the following error appeared in the Console when I tried to view a PDF vignette (for the sake of reproducibility I tried to load the survival.pdf vignette).
>>>> 
>>>> 2023-02-06 11:10:56.198 R[52961:4981916] CFURLResourceIsReachable failed because it was passed a URL which has no scheme
>>>> 
>>>> Has anyone else encountered this?
>>>> 
>>>> Here is my sessionInfo()
>>>> 
>>>>> sessionInfo()
>>>> R version 4.2.2 (2022-10-31)
>>>> Platform: x86_64-apple-darwin17.0 (64-bit)
>>>> Running under: macOS Ventura 13.1
>>>> 
>>>> Matrix products: default
>>>> BLAS:   /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
>>>> LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
>>>> 
>>>> locale:
>>>> [1] en_CA.UTF-8
>>>> 
>>>> attached base packages:
>>>> [1] stats     graphics  grDevices utils     datasets  methods   base     
>>>> 
>>>> other attached packages:
>>>> [1] knitr_1.42
>>>> 
>>>> loaded via a namespace (and not attached):
>>>> [1] compiler_4.2.2 tools_4.2.2    xfun_0.37     
>>>> 
>>>> 
>>>> 
>>>> -- 
>>>> 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 at utoronto.ca  Tel: 416.864.5776  Fax: 416.864.3016
>>>> 
>>>> _______________________________________________
>>>> R-SIG-Mac mailing list
>>>> R-SIG-Mac at r-project.org
>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>> 
>> 
>

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 at utoronto.ca  Tel: 416.864.5776  Fax: 416.864.3016

> On Feb 6, 2023, at 3:56 PM, Duncan Murdoch <murdoch.duncan at gmail.com> 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

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 at utoronto.ca  Tel: 416.864.5776  Fax: 416.864.3016

> On Feb 6, 2023, at 4:58 PM, Simon Urbanek <simon.urbanek at R-project.org> 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 <kevin.thorpe at utoronto.ca> 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 at utoronto.ca  Tel: 416.864.5776  Fax: 416.864.3016
>> 
>>> On Feb 6, 2023, at 3:56 PM, Duncan Murdoch <murdoch.duncan at gmail.com> 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
>> 
>

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 at utoronto.ca  Tel: 416.864.5776  Fax: 416.864.3016

> On Feb 6, 2023, at 7:53 PM, Duncan Murdoch <murdoch.duncan at gmail.com> 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 <kevin.thorpe at utoronto.ca> 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 at utoronto.ca  Tel: 416.864.5776  Fax: 416.864.3016
>>> 
>>>> On Feb 6, 2023, at 4:58 PM, Simon Urbanek <simon.urbanek at R-project.org> 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 <kevin.thorpe at utoronto.ca> 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 at utoronto.ca  Tel: 416.864.5776  Fax: 416.864.3016
>>>>> 
>>>>>> On Feb 6, 2023, at 3:56 PM, Duncan Murdoch <murdoch.duncan at gmail.com> 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
>>>>> 
>>>> 
>>> 
>

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 at utoronto.ca  Tel: 416.864.5776  Fax: 416.864.3016

> On Feb 7, 2023, at 2:45 AM, Ken Beath <ken at kjbeath.com.au> 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 <kevin.thorpe at utoronto.ca> 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 at utoronto.ca  Tel: 416.864.5776  Fax: 416.864.3016
>> 
>>> On Feb 6, 2023, at 7:53 PM, Duncan Murdoch <murdoch.duncan at gmail.com> 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 <kevin.thorpe at utoronto.ca> 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 at utoronto.ca  Tel: 416.864.5776  Fax: 416.864.3016
>>>>> 
>>>>>> On Feb 6, 2023, at 4:58 PM, Simon Urbanek <simon.urbanek at R-project.org> 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 <kevin.thorpe at utoronto.ca> 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 at utoronto.ca  Tel: 416.864.5776  Fax: 416.864.3016
>>>>>>> 
>>>>>>>> On Feb 6, 2023, at 3:56 PM, Duncan Murdoch <murdoch.duncan at gmail.com> 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
>>>>>>> 
>>>>>> 
>>>>> 
>>> 
>> 
>> _______________________________________________
>> R-SIG-Mac mailing list
>> R-SIG-Mac at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>

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 at utoronto.ca  Tel: 416.864.5776  Fax: 416.864.3016

> On Feb 7, 2023, at 8:02 AM, Marc Schwartz <marc_schwartz at 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 at utoronto.ca (mailto:kevin.thorpe at 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 at 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 at 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 at 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 at 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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>> 
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