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
Problem viewing overview pdf's
12 messages · Zak, David Winsemius, Simon Urbanek +2 more
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. 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. 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 > > _______________________________________________ > R-SIG-Mac mailing list > R-SIG-Mac at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
On Feb 9, 2009, at 20:59 , Zak wrote:
Just installed the latest (3.8.1)
Cool - do you have a time machine ? ;)
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!
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 ... Also vignettes are accessible via Help -> Vignettes which is much better than using vignettes() [which is a function in R, not Bioconductor AFAICS]. Thanks, S
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
_______________________________________________ R-SIG-Mac mailing list R-SIG-Mac at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
_______________________________________________ R-SIG-Mac mailing list R-SIG-Mac at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
An embedded and charset-unspecified text was scrubbed... Name: not available URL: <https://stat.ethz.ch/pipermail/r-sig-mac/attachments/20090210/af372603/attachment.pl>
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
_______________________________________________ R-SIG-Mac mailing list R-SIG-Mac at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
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
_______________________________________________ R-SIG-Mac mailing list R-SIG-Mac at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
An embedded and charset-unspecified text was scrubbed... Name: not available URL: <https://stat.ethz.ch/pipermail/r-sig-mac/attachments/20090210/f874ed9c/attachment.pl>
On Feb 10, 2009, at 10:41 AM, Simon Urbanek wrote:
On Feb 9, 2009, at 20:59 , Zak wrote:
Just installed the latest (3.8.1)
Cool - do you have a time machine ? ;)
Ah, sorry, I should not have revealed my spatiotemporal capabilities. But let me assure you, 3.8.1 looks great! Particularly enjoyed the "pay-the-programmer-with-food" package.
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!
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 ... Also vignettes are accessible via Help -> Vignettes which is much better than using vignettes() [which is a function in R, not Bioconductor AFAICS].
OK, it happens for all pdfs in all packages but here is an example from AffyCompatible (mac screen shots) -------------- next part -------------- A non-text attachment was scrubbed... Name: pastedGraphic.tiff Type: image/tiff Size: 132546 bytes Desc: not available URL: <https://stat.ethz.ch/pipermail/r-sig-mac/attachments/20090210/0bbc2a75/attachment-0003.tiff> -------------- next part -------------- -------------- next part -------------- A non-text attachment was scrubbed... Name: pastedGraphic.tiff Type: image/tiff Size: 77810 bytes Desc: not available URL: <https://stat.ethz.ch/pipermail/r-sig-mac/attachments/20090210/0bbc2a75/attachment-0004.tiff> -------------- next part --------------
-------------- next part -------------- A non-text attachment was scrubbed... Name: pastedGraphic.tiff Type: image/tiff Size: 66730 bytes Desc: not available URL: <https://stat.ethz.ch/pipermail/r-sig-mac/attachments/20090210/0bbc2a75/attachment-0005.tiff> -------------- next part --------------
Thanks, S
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
_______________________________________________ R-SIG-Mac mailing list R-SIG-Mac at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
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
_______________________________________________ R-SIG-Mac mailing list R-SIG-Mac at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
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
_______________________________________________ R-SIG-Mac mailing list R-SIG-Mac at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
-------------- next part -------------- An HTML attachment was scrubbed... URL: <https://stat.ethz.ch/pipermail/r-sig-mac/attachments/20090211/51423fbb/attachment-0001.html> -------------- next part -------------- A non-text attachment was scrubbed... Name: Picture 2.png Type: image/png Size: 10020 bytes Desc: not available URL: <https://stat.ethz.ch/pipermail/r-sig-mac/attachments/20090211/51423fbb/attachment-0001.png>