[R-SIG-Mac] Problem viewing overview pdf's

Eric Wooten ecwooten at gmail.com
Wed Feb 11 16:27:03 CET 2009 

Removing adobe's pdf plugin does indeed remove the black screen problem, but
also creates a segfault error and attendant forced quits (see attached
screen capture). Occasionally, <Error>: ATSFontFindFromContainer failed:
count = 2. crops up instead.
Turns out I do also have the PDF Browser plugin (for use by Firefox) in my
~/Library/Internet Plugins. Removing that as well seems to fix both black
screen (adobe plugin present) and various memory errors (PDF Browser plugin
present).

The direct Help/Vignettes route seemingly always works fine no matter what
is present.





On Wed, Feb 11, 2009 at 9:55 AM, isaac Kohane
<Isaac_Kohane at hms.harvard.edu>wrote:

> Yes, I do have the Adobe plugin installed.
>
> So, I deleted the following file:  /library/Internet
> Plug-Ins/AdobePDFViewer.plugin
>
> and presto! the pdf's are now visible. Thanks!
>
> Again, congratulations on 3.8.1, it's going to be great.
>
> -Zak
>
>
> On Feb 11, 2009, at 9:45 AM, Simon Urbanek wrote:
>
>  I have tested the exactly same setup and it works for me without
>> problems.
>>
>> One thought - do you happen to have Adobe Acrobat or some other 3rd
>> party viewer installed as browser plugin for PDF?
>>
>> Cheers,
>> Simon
>>
>>
>> On Feb 10, 2009, at 14:05 , Eric Wooten wrote:
>>
>>  Sure, sorry to forget about that in the first place:
>>>
>>>  sessionInfo()
>>>>
>>> R version 2.8.1 Patched (2009-01-01 r47431)
>>> i386-apple-darwin9.5.0
>>>
>>> locale:
>>> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>>>
>>> attached base packages:
>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>
>>>
>>> Mac OSX 10.5.6
>>>
>>>
>>>
>>> On Tue, Feb 10, 2009 at 1:40 PM, isaac Kohane <
>>> isaac_kohane at hms.harvard.edu
>>>
>>>> wrote:
>>>>
>>> Thanks for asking. Here you go:
>>>
>>> R version 2.8.1 (2008-12-22)
>>>
>>> sessionInfo()
>>> R version 2.8.1 (2008-12-22)
>>> i386-apple-darwin8.11.1
>>>
>>>
>>> locale:
>>> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>>>
>>> attached base packages:
>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>
>>>>
>>>>
>>> OX X 10.5.6
>>>
>>>
>>>
>>> On Feb 10, 2009, at 1:29 PM, Simon Urbanek wrote:
>>>
>>>
>>> On Feb 10, 2009, at 1:03 PM, Eric Wooten wrote:
>>>
>>> Can you, please, be more specific - for example why don't you tell
>>> us which package you're looking >at - that would make it much easier
>>> to reproduce ...
>>>
>>> Choose a package. The first one in my listing happens to be ABarray.
>>> Click "Overview." Select either option (the first being
>>> ABarray.pdf:). Get black screen.
>>>
>>> If you'd prefer a more CRAN-based package, try vcd. Select
>>> "Overview"; click "residual shading.pdf"; get black screen.
>>>
>>>
>>> Hm... I cannot replicate this - in 2.8.1 it shows the paper for me
>>> without problems.
>>> Zak, Eric, can you, please, send me your sessionInfo() as well as the
>>> version of the OS X you're running?
>>>
>>> Thanks,
>>> Simon
>>>
>>>
>>>
>>>
>>> On Tue, Feb 10, 2009 at 11:44 AM, Simon Urbanek <
>>> simon.urbanek at r-project.org
>>> wrote:
>>>
>>> On Feb 10, 2009, at 10:12 , David Winsemius wrote:
>>>
>>> I'm guessing that it is known, but if not, I can report that it also
>>> happens on my Mac.
>>>
>>> For instance in the 64 bit GUI using the att.research binary R ,
>>> clicking on the doBy line in the Package Manager window brings up a
>>> page with a link to "overview". Clicking on that brings up a black
>>> page in the viewing window.
>>>
>>> The other aspect of the Package Manager that does not appear
>>> finished is the lack of any functionality of the forward and back
>>> buttons. When using the PM for viewing documentation on packages
>>> that are not loaded I need to return to the package index page
>>> because the fwd and back buttons are always greyed out.
>>>
>>>
>>> The usual shortcuts (Cmd+Left/Cmd+Right) still work. It appears that
>>> this was in fact broken by Apple in 10.5 not by us. Anyway, this
>>> should be fixed now.
>>>
>>> Thanks,
>>>
>>> S
>>>
>>>
>>> I just figured that both these were rather minor difficulties, since
>>> the overall capacities of R on the Mac are so vast. I would much
>>> rather that the developers continue as they have been, dealing with
>>> substantive problems like fixing rggobi/Ggobi.
>>>
>>> ... um ... I'm losing you here - I don't think that it either
>>> substantive or a problem at least on my end ...
>>>
>>>
>>>
>>> Thank you to all who contributed to that addition. Very kewl. Tried
>>> to break it, er, test it with a big data set but it held up well.
>>>
>>>
>>>
>>>
>>> --
>>> David Winsemius
>>>
>>> sessionInfo and R.Version output follows
>>>
>>> sessionInfo()
>>> R version 2.8.1 Patched (2009-01-07 r47515)
>>> i386-apple-darwin9.6.0
>>>
>>> locale:
>>> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>>>
>>> attached base packages:
>>> [1] splines   stats     graphics  grDevices utils     datasets
>>> methods   base
>>>
>>> other attached packages:
>>> [1] doBy_3.7        lattice_0.17-20 nlme_3.1-90     Design_2.1-2
>>> survival_2.34-1 Hmisc_3.4-4
>>>
>>> loaded via a namespace (and not attached):
>>> [1] cluster_1.11.12 grid_2.8.1      tools_2.8.1
>>>
>>> R.Version()
>>> $platform
>>> [1] "i386-apple-darwin9.6.0"
>>>
>>> $arch
>>> [1] "i386"
>>>
>>> $os
>>> [1] "darwin9.6.0"
>>>
>>> $system
>>> [1] "i386, darwin9.6.0"
>>>
>>> $status
>>> [1] "Patched"
>>>
>>> $major
>>> [1] "2"
>>>
>>> $minor
>>> [1] "8.1"
>>>
>>> $year
>>> [1] "2009"
>>>
>>> $month
>>> [1] "01"
>>>
>>> $day
>>> [1] "07"
>>>
>>> $`svn rev`
>>> [1] "47515"
>>>
>>> $language
>>> [1] "R"
>>>
>>> $version.string
>>> [1] "R version 2.8.1 Patched (2009-01-07 r47515)"
>>>
>>>
>>> On Feb 9, 2009, at 8:59 PM, Zak wrote:
>>>
>>> Just installed the latest (3.8.1) R for Mac OS X after working for a
>>> year on a much older version. Now, when I use the package manager and
>>> then select a package with an overview that happens to be a pdf then
>>> the pdf does not open up in the lower pane as it used to but only a
>>> black pane appears. The pdf's are definitely there (as I can access
>>> them through the vignette() utility (Bioconductor). Is this a known
>>> bug/feature? Is it something to do with installing over prior
>>> versions? Help!
>>>
>>> Thanks,
>>>
>>> -Zak
>>>
>>> _______________________________________________
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>>>
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>>>
>>>
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>>>
>>>
>>>
>>>
>>
>
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