R-SIG-Mac Digest, Vol 239, Issue 4

2 messages · John Maindonald, Kevin E. Thorpe

Original

John Maindonald

Mon, Feb 6, 2023 3:32 PM #

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.

	https://stat.ethz.ch/mailman/listinfo/r-sig-mac
or, via email, send a message with subject or body 'help' to
	r-sig-mac-request at r-project.org

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When replying, please edit your Subject line so it is more specific
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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 at gmail.com>
To: Kevin Thorpe <kevin.thorpe at utoronto.ca>, Simon Urbanek
	<simon.urbanek at R-project.org>
Cc: "r-sig-mac at r-project.org" <r-sig-mac at r-project.org>
Subject: Re: [R-SIG-Mac] Cannot open PDF Vignettes on Ventura
Message-ID: <05a096f4-7590-ea0e-c7fc-a22c9fdf1620 at 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 at utoronto.ca>
To: Duncan Murdoch <murdoch.duncan at gmail.com>
Cc: Simon Urbanek <simon.urbanek at R-project.org>,
	"r-sig-mac at r-project.org" <r-sig-mac at r-project.org>
Subject: Re: [R-SIG-Mac] Cannot open PDF Vignettes on Ventura
Message-ID: <4B85F1EB-A812-4CEF-AA1F-D0B2023C6BDF at 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 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



------------------------------

Message: 3
Date: Tue, 7 Feb 2023 10:58:16 +1300
From: Simon Urbanek <simon.urbanek at R-project.org>
To: Kevin Thorpe <kevin.thorpe at utoronto.ca>
Cc: Duncan Murdoch <murdoch.duncan at gmail.com>,
	"r-sig-mac at r-project.org" <r-sig-mac at r-project.org>
Subject: Re: [R-SIG-Mac] Cannot open PDF Vignettes on Ventura
Message-ID: <DEF57CF1-8973-4D26-8B52-6ED142F3C459 at 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 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





------------------------------

Message: 4
Date: Mon, 6 Feb 2023 23:01:19 +0000
From: Kevin Thorpe <kevin.thorpe at utoronto.ca>
To: Simon Urbanek <simon.urbanek at R-project.org>
Cc: Duncan Murdoch <murdoch.duncan at gmail.com>,
	"r-sig-mac at r-project.org" <r-sig-mac at r-project.org>
Subject: Re: [R-SIG-Mac] Cannot open PDF Vignettes on Ventura
Message-ID: <043E8348-FC53-4BF0-977D-05633FEC4B32 at 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 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





------------------------------

Subject: Digest Footer

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------------------------------

End of R-SIG-Mac Digest, Vol 239, Issue 4
*****************************************

Kevin E. Thorpe

Tue, Feb 7, 2023 4:21 AM #

Thanks John.

Yes, that does work. I see that Ken Beath posted about a potential problem with a new framework. I am going to try a different build.

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 6:32 PM, John H Maindonald <jhmaindonald at gmail.com> wrote:
> 
> 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 at r-project.org wrote:
>> 
>> Send R-SIG-Mac mailing list submissions to
>> r-sig-mac at r-project.org
>> 
>> To subscribe or unsubscribe via the World Wide Web, visit
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>> or, via email, send a message with subject or body 'help' to
>> r-sig-mac-request at r-project.org
>> 
>> You can reach the person managing the list at
>> r-sig-mac-owner at r-project.org
>> 
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of R-SIG-Mac digest..."
>> 
>> 
>> 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 at gmail.com>
>> To: Kevin Thorpe <kevin.thorpe at utoronto.ca>, Simon Urbanek
>> <simon.urbanek at R-project.org>
>> Cc: "r-sig-mac at r-project.org" <r-sig-mac at r-project.org>
>> Subject: Re: [R-SIG-Mac] Cannot open PDF Vignettes on Ventura
>> Message-ID: <05a096f4-7590-ea0e-c7fc-a22c9fdf1620 at 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 at utoronto.ca>
>> To: Duncan Murdoch <murdoch.duncan at gmail.com>
>> Cc: Simon Urbanek <simon.urbanek at R-project.org>,
>> "r-sig-mac at r-project.org" <r-sig-mac at r-project.org>
>> Subject: Re: [R-SIG-Mac] Cannot open PDF Vignettes on Ventura
>> Message-ID: <4B85F1EB-A812-4CEF-AA1F-D0B2023C6BDF at 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 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
>> 
>> 
>> 
>> ------------------------------
>> 
>> Message: 3
>> Date: Tue, 7 Feb 2023 10:58:16 +1300
>> From: Simon Urbanek <simon.urbanek at R-project.org>
>> To: Kevin Thorpe <kevin.thorpe at utoronto.ca>
>> Cc: Duncan Murdoch <murdoch.duncan at gmail.com>,
>> "r-sig-mac at r-project.org" <r-sig-mac at r-project.org>
>> Subject: Re: [R-SIG-Mac] Cannot open PDF Vignettes on Ventura
>> Message-ID: <DEF57CF1-8973-4D26-8B52-6ED142F3C459 at 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 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
>>> 
>> 
>> 
>> 
>> 
>> ------------------------------
>> 
>> Message: 4
>> Date: Mon, 6 Feb 2023 23:01:19 +0000
>> From: Kevin Thorpe <kevin.thorpe at utoronto.ca>
>> To: Simon Urbanek <simon.urbanek at R-project.org>
>> Cc: Duncan Murdoch <murdoch.duncan at gmail.com>,
>> "r-sig-mac at r-project.org" <r-sig-mac at r-project.org>
>> Subject: Re: [R-SIG-Mac] Cannot open PDF Vignettes on Ventura
>> Message-ID: <043E8348-FC53-4BF0-977D-05633FEC4B32 at 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 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
>>>> 
>>> 
>> 
>> 
>> 
>> ------------------------------
>> 
>> Subject: Digest Footer
>> 
>> _______________________________________________
>> R-SIG-Mac mailing list
>> R-SIG-Mac at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>> 
>> 
>> ------------------------------
>> 
>> End of R-SIG-Mac Digest, Vol 239, Issue 4
>> *****************************************
> 
> _______________________________________________
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