Re: [R-SIG-Mac] Cannot open PDF Vignettes on Ventura
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.tho...@utoronto.ca Tel: 416.864.5776 Fax: 416.864.3016
> On Feb 7, 2023, at 8:02 AM, Marc Schwartz 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.tho...@utoronto.ca
> (mailto:kevin.tho...@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.tho...@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.tho...@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
Re: [R-SIG-Mac] Cannot open PDF Vignettes on Ventura
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.tho...@utoronto.ca
(mailto:kevin.tho...@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.tho...@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.tho...@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.
> >
>
Re: [R-SIG-Mac] Cannot open PDF Vignettes on Ventura
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.tho...@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.tho...@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.tho...@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.tho...@utoronto.ca Tel:
Re: [R-SIG-Mac] Cannot open PDF Vignettes on Ventura
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.tho...@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.tho...@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.tho...@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
Re: [R-SIG-Mac] Cannot open PDF Vignettes on Ventura
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.tho...@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.tho...@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.tho...@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
>
>>>
>
___
R-SIG-Mac mailing list
R-SIG-Mac@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Cannot open PDF Vignettes on Ventura
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.tho...@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.tho...@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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Re: [R-SIG-Mac] Cannot open PDF Vignettes on Ventura
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.tho...@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.tho...@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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Re: [R-SIG-Mac] Cannot open PDF Vignettes on Ventura
On 06/02/2023 6:01 p.m., 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 I don't have Ventura installed (I'm still on Monterey 12.6.3), and following the procedure you describe I get similar results. On the other hand, if I choose Help | Vignettes I get a preview in the R.app vignette window, then if I double click on it, it opens in Acrobat reader (which is the default PDF viewer on my system). Duncan ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Cannot open PDF Vignettes on Ventura
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.tho...@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.tho...@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 >> > ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Cannot open PDF Vignettes on Ventura
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.tho...@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 > ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Cannot open PDF Vignettes on Ventura
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.tho...@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 ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Cannot open PDF Vignettes on Ventura
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@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Cannot open PDF Vignettes on Ventura
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 -- 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.tho...@utoronto.ca Tel: 416.864.5776 Fax: 416.864.3016 > On Feb 6, 2023, at 3:25 PM, Simon Urbanek 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 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.tho...@utoronto.ca Tel: 416.864.5776 Fax: 416.864.3016 >> >>> On Feb 6, 2023, at 2:45 PM, Simon Urbanek >>> 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 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_4.2.2xfun_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.tho...@utoronto.ca Tel: 416.864.5776 Fax: 416.864.3016 ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac >>> >> > ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Cannot open PDF Vignettes on Ventura
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 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.tho...@utoronto.ca Tel: 416.864.5776 Fax: 416.864.3016 > >> On Feb 6, 2023, at 2:45 PM, Simon Urbanek >> 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 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_4.2.2xfun_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.tho...@utoronto.ca Tel: 416.864.5776 Fax: 416.864.3016 >>> >>> ___ >>> R-SIG-Mac mailing list >>> R-SIG-Mac@r-project.org >>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >> > ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Cannot open PDF Vignettes on Ventura
I removed and re-installed Acrobat Reader. The error persists. I even let Reader be my default for PDFs and still no success. 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.tho...@utoronto.ca Tel: 416.864.5776 Fax: 416.864.3016 > On Feb 6, 2023, at 3:01 PM, Kevin Thorpe 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.tho...@utoronto.ca Tel: 416.864.5776 Fax: 416.864.3016 > >> On Feb 6, 2023, at 2:45 PM, Simon Urbanek >> 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 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_4.2.2xfun_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.tho...@utoronto.ca Tel: 416.864.5776 Fax: 416.864.3016 >>> >>> ___ >>> R-SIG-Mac mailing list >>> R-SIG-Mac@r-project.org >>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >> > > ___ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Cannot open PDF Vignettes on Ventura
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.tho...@utoronto.ca Tel: 416.864.5776 Fax: 416.864.3016 > On Feb 6, 2023, at 2:45 PM, Simon Urbanek 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 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_4.2.2xfun_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.tho...@utoronto.ca Tel: 416.864.5776 Fax: 416.864.3016 >> >> ___ >> R-SIG-Mac mailing list >> R-SIG-Mac@r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac > ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Cannot open PDF Vignettes on Ventura
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 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_4.2.2xfun_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.tho...@utoronto.ca Tel: 416.864.5776 Fax: 416.864.3016 > > ___ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
[R-SIG-Mac] Cannot open PDF Vignettes on Ventura
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_4.2.2xfun_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.tho...@utoronto.ca Tel: 416.864.5776 Fax: 416.864.3016 ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
