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. <br>
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). <br>
<br>The direct Help/Vignettes route seemingly always works fine no matter what is present. <br><br><br><br><br><br><div class="gmail_quote">On Wed, Feb 11, 2009 at 9:55 AM, isaac Kohane <span dir="ltr"><<a href="mailto:Isaac_Kohane@hms.harvard.edu">Isaac_Kohane@hms.harvard.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Yes, I do have the Adobe plugin installed.<br>
<br>
So, I deleted the following file: /library/Internet Plug-Ins/AdobePDFViewer.plugin<br>
<br>
and presto! the pdf's are now visible. Thanks!<br>
<br>
Again, congratulations on 3.8.1, it's going to be great.<br>
<br>
-Zak<div><div></div><div class="Wj3C7c"><br>
<br>
On Feb 11, 2009, at 9:45 AM, Simon Urbanek wrote:<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
I have tested the exactly same setup and it works for me without<br>
problems.<br>
<br>
One thought - do you happen to have Adobe Acrobat or some other 3rd<br>
party viewer installed as browser plugin for PDF?<br>
<br>
Cheers,<br>
Simon<br>
<br>
<br>
On Feb 10, 2009, at 14:05 , Eric Wooten wrote:<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Sure, sorry to forget about that in the first place:<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
sessionInfo()<br>
</blockquote>
R version 2.8.1 Patched (2009-01-01 r47431)<br>
i386-apple-darwin9.5.0<br>
<br>
locale:<br>
en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8<br>
<br>
attached base packages:<br>
[1] stats graphics grDevices utils datasets methods base<br>
<br>
<br>
Mac OSX 10.5.6<br>
<br>
<br>
<br>
On Tue, Feb 10, 2009 at 1:40 PM, isaac Kohane <<a href="mailto:isaac_kohane@hms.harvard.edu" target="_blank">isaac_kohane@hms.harvard.edu</a><br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
wrote:<br>
</blockquote>
Thanks for asking. Here you go:<br>
<br>
R version 2.8.1 (2008-12-22)<br>
<br>
sessionInfo()<br>
R version 2.8.1 (2008-12-22)<br>
i386-apple-darwin8.11.1<br>
<br>
<br>
locale:<br>
en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8<br>
<br>
attached base packages:<br>
[1] stats graphics grDevices utils datasets methods base<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
</blockquote>
<br>
OX X 10.5.6<br>
<br>
<br>
<br>
On Feb 10, 2009, at 1:29 PM, Simon Urbanek wrote:<br>
<br>
<br>
On Feb 10, 2009, at 1:03 PM, Eric Wooten wrote:<br>
<br>
Can you, please, be more specific - for example why don't you tell<br>
us which package you're looking >at - that would make it much easier<br>
to reproduce ...<br>
<br>
Choose a package. The first one in my listing happens to be ABarray.<br>
Click "Overview." Select either option (the first being<br>
ABarray.pdf:). Get black screen.<br>
<br>
If you'd prefer a more CRAN-based package, try vcd. Select<br>
"Overview"; click "residual shading.pdf"; get black screen.<br>
<br>
<br>
Hm... I cannot replicate this - in 2.8.1 it shows the paper for me<br>
without problems.<br>
Zak, Eric, can you, please, send me your sessionInfo() as well as the<br>
version of the OS X you're running?<br>
<br>
Thanks,<br>
Simon<br>
<br>
<br>
<br>
<br>
On Tue, Feb 10, 2009 at 11:44 AM, Simon Urbanek <<a href="mailto:simon.urbanek@r-project.org" target="_blank">simon.urbanek@r-project.org</a><br>
wrote:<br>
<br>
On Feb 10, 2009, at 10:12 , David Winsemius wrote:<br>
<br>
I'm guessing that it is known, but if not, I can report that it also<br>
happens on my Mac.<br>
<br>
For instance in the 64 bit GUI using the att.research binary R ,<br>
clicking on the doBy line in the Package Manager window brings up a<br>
page with a link to "overview". Clicking on that brings up a black<br>
page in the viewing window.<br>
<br>
The other aspect of the Package Manager that does not appear<br>
finished is the lack of any functionality of the forward and back<br>
buttons. When using the PM for viewing documentation on packages<br>
that are not loaded I need to return to the package index page<br>
because the fwd and back buttons are always greyed out.<br>
<br>
<br>
The usual shortcuts (Cmd+Left/Cmd+Right) still work. It appears that<br>
this was in fact broken by Apple in 10.5 not by us. Anyway, this<br>
should be fixed now.<br>
<br>
Thanks,<br>
<br>
S<br>
<br>
<br>
I just figured that both these were rather minor difficulties, since<br>
the overall capacities of R on the Mac are so vast. I would much<br>
rather that the developers continue as they have been, dealing with<br>
substantive problems like fixing rggobi/Ggobi.<br>
<br>
... um ... I'm losing you here - I don't think that it either<br>
substantive or a problem at least on my end ...<br>
<br>
<br>
<br>
Thank you to all who contributed to that addition. Very kewl. Tried<br>
to break it, er, test it with a big data set but it held up well.<br>
<br>
<br>
<br>
<br>
--<br>
David Winsemius<br>
<br>
sessionInfo and R.Version output follows<br>
<br>
sessionInfo()<br>
R version 2.8.1 Patched (2009-01-07 r47515)<br>
i386-apple-darwin9.6.0<br>
<br>
locale:<br>
en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8<br>
<br>
attached base packages:<br>
[1] splines stats graphics grDevices utils datasets<br>
methods base<br>
<br>
other attached packages:<br>
[1] doBy_3.7 lattice_0.17-20 nlme_3.1-90 Design_2.1-2<br>
survival_2.34-1 Hmisc_3.4-4<br>
<br>
loaded via a namespace (and not attached):<br>
[1] cluster_1.11.12 grid_2.8.1 tools_2.8.1<br>
<br>
R.Version()<br>
$platform<br>
[1] "i386-apple-darwin9.6.0"<br>
<br>
$arch<br>
[1] "i386"<br>
<br>
$os<br>
[1] "darwin9.6.0"<br>
<br>
$system<br>
[1] "i386, darwin9.6.0"<br>
<br>
$status<br>
[1] "Patched"<br>
<br>
$major<br>
[1] "2"<br>
<br>
$minor<br>
[1] "8.1"<br>
<br>
$year<br>
[1] "2009"<br>
<br>
$month<br>
[1] "01"<br>
<br>
$day<br>
[1] "07"<br>
<br>
$`svn rev`<br>
[1] "47515"<br>
<br>
$language<br>
[1] "R"<br>
<br>
$version.string<br>
[1] "R version 2.8.1 Patched (2009-01-07 r47515)"<br>
<br>
<br>
On Feb 9, 2009, at 8:59 PM, Zak wrote:<br>
<br>
Just installed the latest (3.8.1) R for Mac OS X after working for a<br>
year on a much older version. Now, when I use the package manager and<br>
then select a package with an overview that happens to be a pdf then<br>
the pdf does not open up in the lower pane as it used to but only a<br>
black pane appears. The pdf's are definitely there (as I can access<br>
them through the vignette() utility (Bioconductor). Is this a known<br>
bug/feature? Is it something to do with installing over prior<br>
versions? Help!<br>
<br>
Thanks,<br>
<br>
-Zak<br>
<br>
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<br>
<br>
<br>
</blockquote>
<br>
</blockquote>
<br>
</div></div></blockquote></div><br>