[R-SIG-Mac] R-SIG-Mac Digest, Vol 239, Issue 4
John H Maindonald
jhm@|ndon@|d @end|ng |rom gm@||@com
Tue Feb 7 00:32:41 CET 2023
An ‘interesting’ aside is that in Monterey (12.6.2), a blank window
appears when I click on ‘PDF’ from within the RStudio help system.
Within the R GUI, there is not a problem. In either case, typing
vignette('concordance', package='survival’)
in the command line window works fine. Kevin, does this work
for you?
John Maindonald.
> On 7/02/2023, at 12:01, r-sig-mac-request using r-project.org wrote:
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> Today's Topics:
>
> 1. Re: Cannot open PDF Vignettes on Ventura (Duncan Murdoch)
> 2. Re: Cannot open PDF Vignettes on Ventura (Kevin Thorpe)
> 3. Re: Cannot open PDF Vignettes on Ventura (Simon Urbanek)
> 4. Re: Cannot open PDF Vignettes on Ventura (Kevin Thorpe)
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 6 Feb 2023 15:56:16 -0500
> From: Duncan Murdoch <murdoch.duncan using gmail.com>
> To: Kevin Thorpe <kevin.thorpe using utoronto.ca>, Simon Urbanek
> <simon.urbanek using R-project.org>
> Cc: "r-sig-mac using r-project.org" <r-sig-mac using r-project.org>
> Subject: Re: [R-SIG-Mac] Cannot open PDF Vignettes on Ventura
> Message-ID: <05a096f4-7590-ea0e-c7fc-a22c9fdf1620 using gmail.com>
> Content-Type: text/plain; charset="utf-8"; Format="flowed"
>
> 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
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 6 Feb 2023 20:58:17 +0000
> From: Kevin Thorpe <kevin.thorpe using utoronto.ca>
> To: Duncan Murdoch <murdoch.duncan using gmail.com>
> Cc: Simon Urbanek <simon.urbanek using R-project.org>,
> "r-sig-mac using r-project.org" <r-sig-mac using r-project.org>
> Subject: Re: [R-SIG-Mac] Cannot open PDF Vignettes on Ventura
> Message-ID: <4B85F1EB-A812-4CEF-AA1F-D0B2023C6BDF using utoronto.ca>
> Content-Type: text/plain; charset="utf-8"
>
> 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 <murdoch.duncan using 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
>
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 7 Feb 2023 10:58:16 +1300
> From: Simon Urbanek <simon.urbanek using R-project.org>
> To: Kevin Thorpe <kevin.thorpe using utoronto.ca>
> Cc: Duncan Murdoch <murdoch.duncan using gmail.com>,
> "r-sig-mac using r-project.org" <r-sig-mac using r-project.org>
> Subject: Re: [R-SIG-Mac] Cannot open PDF Vignettes on Ventura
> Message-ID: <DEF57CF1-8973-4D26-8B52-6ED142F3C459 using R-project.org>
> Content-Type: text/plain; charset="utf-8"
>
> 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 using 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 using utoronto.ca Tel: 416.864.5776 Fax: 416.864.3016
>>
>>> On Feb 6, 2023, at 3:56 PM, Duncan Murdoch <murdoch.duncan using 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
>>
>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Mon, 6 Feb 2023 23:01:19 +0000
> From: Kevin Thorpe <kevin.thorpe using utoronto.ca>
> To: Simon Urbanek <simon.urbanek using R-project.org>
> Cc: Duncan Murdoch <murdoch.duncan using gmail.com>,
> "r-sig-mac using r-project.org" <r-sig-mac using r-project.org>
> Subject: Re: [R-SIG-Mac] Cannot open PDF Vignettes on Ventura
> Message-ID: <043E8348-FC53-4BF0-977D-05633FEC4B32 using utoronto.ca>
> Content-Type: text/plain; charset="utf-8"
>
> 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 <simon.urbanek using 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 using 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 using utoronto.ca Tel: 416.864.5776 Fax: 416.864.3016
>>>
>>>> On Feb 6, 2023, at 3:56 PM, Duncan Murdoch <murdoch.duncan using 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
>>>
>>
>
>
>
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>
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