From @pencer@gr@ve@ @ending from prod@y@e@com  Thu Sep  6 15:29:51 2018
From: @pencer@gr@ve@ @ending from prod@y@e@com (Spencer Graves)
Date: Thu, 6 Sep 2018 08:29:51 -0500
Subject: [Rd] svg ignores cex.axis in R3.5.1 on macOS
In-Reply-To: <b3b2fc46-f072-bf1e-73f3-1d0f1fa1b9b9@stats.ox.ac.uk>
References: <ac8f9908-f064-d723-61a8-7e8ca085dd43@prodsyse.com>
 <c506e0f9-bf78-cab1-3d38-ef8b0b1dd850@prodsyse.com>
 <02422C33-8D62-41AA-9064-EE4FADD33F2D@llnl.gov>
 <E0DF64F8-672E-4634-AB2D-7C2EE2EF83A1@gmail.com>
 <b3b2fc46-f072-bf1e-73f3-1d0f1fa1b9b9@stats.ox.ac.uk>
Message-ID: <7ddf8356-811b-da56-342a-9afc44cbf0ea@prodsyse.com>



On 2018-09-06 05:17, Prof Brian Ripley wrote:
> On 06/09/2018 10:47, peter dalgaard wrote:
>> I think this needs to be taken off the bug repository and continued 
>> here. By now it seems pretty clear that this is not an R bug, but a 
>> local problem on Spencer's machine, likely connected to font 
>> configurations.
>
> Or even on R-sig-Mac.
>
>> I poked around a bit on the three Macs that I can access, and found 
>> that fc-match does different things, including throwing warnings, 
>> hanging and even crashing my old MB Air...
>>
>> One possible reason is that it can apparently be installed in 
>> multiple locations, for reasons lost in the mists of time:
>>
>> Peters-iMac:BUILD-dist pd$ ls -l /opt/local/bin/fc-*
>> -rwxr-xr-x? 1 root? wheel? 44072 Apr? 5? 2014 /opt/local/bin/fc-cache
>> -rwxr-xr-x? 1 root? wheel? 43444 Apr? 5? 2014 /opt/local/bin/fc-cat
>> -rwxr-xr-x? 1 root? wheel? 34480 Apr? 5? 2014 /opt/local/bin/fc-list
>> -rwxr-xr-x? 1 root? wheel? 34928 Apr? 5? 2014 /opt/local/bin/fc-match
>> -rwxr-xr-x? 1 root? wheel? 34480 Apr? 5? 2014 /opt/local/bin/fc-pattern
>> -rwxr-xr-x? 1 root? wheel? 34008 Apr? 5? 2014 /opt/local/bin/fc-query
>> -rwxr-xr-x? 1 root? wheel? 34448 Apr? 5? 2014 /opt/local/bin/fc-scan
>> -rwxr-xr-x? 1 root? wheel? 38780 Apr? 5? 2014 /opt/local/bin/fc-validate
>> Peters-iMac:BUILD-dist pd$ ls -l /opt/X11/bin/fc-*
>> -rwxr-xr-x? 1 root? wheel? 58128 Oct 26? 2016 /opt/X11/bin/fc-cache
>> -rwxr-xr-x? 1 root? wheel? 57600 Oct 26? 2016 /opt/X11/bin/fc-cat
>> -rwxr-xr-x? 1 root? wheel? 48384 Oct 26? 2016 /opt/X11/bin/fc-list
>> -rwxr-xr-x? 1 root? wheel? 48992 Oct 26? 2016 /opt/X11/bin/fc-match
>> -rwxr-xr-x? 1 root? wheel? 44256 Oct 26? 2016 /opt/X11/bin/fc-pattern
>> -rwxr-xr-x? 1 root? wheel? 44000 Oct 26? 2016 /opt/X11/bin/fc-query
>> -rwxr-xr-x? 1 root? wheel? 44288 Oct 26? 2016 /opt/X11/bin/fc-scan
>> -rwxr-xr-x? 1 root? wheel? 48608 Oct 26? 2016 /opt/X11/bin/fc-validate
>> Peters-iMac:BUILD-dist pd$ ls -l /usr/local/bin/fc-*
>> -rwxr-xr-x@ 1 root? wheel? 1463900 Oct 21? 2008 /usr/local/bin/fc-cache
>> -rwxr-xr-x@ 1 root? wheel? 1459780 Oct 21? 2008 /usr/local/bin/fc-cat
>> -rwxr-xr-x@ 1 root? wheel? 1455628 Oct 21? 2008 /usr/local/bin/fc-list
>> -rwxr-xr-x@ 1 root? wheel? 1476560 Oct 21? 2008 /usr/local/bin/fc-match
>>
>> Notice that these are all different, no links. I guess that the ones 
>> you want are in /opt/X11, presumably installed by XQuartz.
>
> Yes, for the device compiled into the CRAN binary R package. (Other 
> builds may differ.)? On that, the cairo-based devices such as svg() 
> are linked to (current versions on my machine)
>
> ????/usr/lib/libz.1.dylib (compatibility version 1.0.0, current 
> version 1.2.5)
> ????/opt/X11/lib/libcairo.2.dylib (compatibility version 11403.0.0, 
> current version 11403.6.0)
> ????/opt/X11/lib/libpixman-1.0.dylib (compatibility version 35.0.0, 
> current version 35.0.0)
> ????/opt/X11/lib/libfontconfig.1.dylib (compatibility version 11.0.0, 
> current version 11.2.0)
> ...
>
>
>> So, going out on a limb, I have two ideas:
>>
>> (A) Rebuild the font cache with
>>
>> /opt/X11/bin/fc-cache -vf
>>
>> (B) Check that XQuartz is up to date (possibly reinstall it, even if 
>> it is)
>
> (B) is expected to do (A).? My advice was going to be to reinstall 
> xquartz: macOS updates can partially break it.


 ????? I was going to try that, but I rebooted (again), and now it's 
working.


 ????? I rebooted before I first reported the problem, and I've rebooted 
a couple of times since without success.? This time was different, I 
don't know why.? Before I rebooted this time, I saw "XQuartz" on my 
taskbar / "Dock", switched to it, then clicked on the XQuartz icon in 
upper left and selected "About X11".? This said "XQuartz 2.7.11 
(xorg-server 1.18.4)."? Then I rebooted and restarted RStudio then tried 
svg again with cex.axis=2, and it worked.? Moreover, a web search took 
me to "https://xquartz.en.softonic.com/mac", which says that the current 
XQuartz for Mac is 2.6.1.? Since I now have 2.7.11 and it's working, I 
think I should leave it alone.


 ????? If anyone wants me to try something further to add to this 
record, I will.? Otherwise, I'll wait:? If the problem recurs, I'll try 
reinstalling XQuartz again, as Professors Dalgaard and Ripley 
suggested.? And if I have another problem with svg and need further 
help, I will consider R-sig-Mac.


 ????? Thanks also to Paul Murrell, who provided several responses to my 
(non)-bug report.


 ????? Spencer Graves
>
>>
>> -pd
>>
>>> On 5 Sep 2018, at 21:13 , MacQueen, Don via R-devel 
>>> <r-devel at r-project.org> wrote:
>>>
>>> Seems ok on my system. Axis label size changes when cex.axis does.
>>>
>>> ## tested in the middle of another long session, so many additional 
>>> packages are attached, including some personal packages not 
>>> available elsewhere
>>>
>>>> sessionInfo()
>>> R version 3.5.1 (2018-07-02)
>>> Platform: x86_64-apple-darwin15.6.0 (64-bit)
>>> Running under: macOS High Sierra 10.13.6
>>>
>>> Matrix products: default
>>> BLAS: 
>>> /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
>>> LAPACK: 
>>> /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
>>>
>>> locale:
>>> [1] C
>>>
>>> attached base packages:
>>> [1] stats???? graphics? grDevices utils???? datasets methods?? base
>>>
>>> other attached packages:
>>> [1] survival_2.42-3 ROracle_1.3-1?? DBI_1.0.0 bookdown_0.7??? 
>>> knitr_1.20????? rmarkdown_1.10 wdr_3.2???????? taurus_3.2-4??? 
>>> xlsx_0.6.1
>>> [10] rmacq_1.3-8
>>>
>>> loaded via a namespace (and not attached):
>>> [1] Rcpp_0.12.17??? magrittr_1.5??? splines_3.5.1 lattice_0.20-35 
>>> highr_0.7?????? stringr_1.3.1 tools_3.5.1???? grid_3.5.1????? xfun_0.3
>>> [10] tinytex_0.6???? htmltools_0.3.6 yaml_2.1.19 rprojroot_1.3-2 
>>> digest_0.6.15?? zip_1.0.0 Matrix_1.2-14?? rJava_0.9-10??? 
>>> xlsxjars_0.6.1
>>> [19] evaluate_0.10.1 openxlsx_4.1.0? stringi_1.2.3 compiler_3.5.1? 
>>> backports_1.1.2
>>>
>>> -- 
>>> Don MacQueen
>>> Lawrence Livermore National Laboratory
>>> 7000 East Ave., L-627
>>> Livermore, CA 94550
>>> 925-423-1062
>>> Lab cell 925-724-7509
>>>
>>>
>>>
>>> ?On 8/31/18, 1:02 PM, "R-devel on behalf of Spencer Graves" 
>>> <r-devel-bounces at r-project.org on behalf of 
>>> spencer.graves at prodsyse.com> wrote:
>>>
>>>
>>>
>>> ??? On 2018-08-31 14:21, Spencer Graves wrote:
>>>> Plots produced using svg in R 3.5.1 under macOS 10.13.6 ignores
>>>> cex.axis=2.? Consider the following:
>>>>
>>>>
>>>>> plot(1:2, cex.axis=2)
>>>>> svg('svg_ignores_cex.axis.svg')
>>>>> plot(1:2, cex.axis=2)
>>>>> dev.off()
>>>>> sessionInfo()
>>>> R version 3.5.1 (2018-07-02)
>>>> Platform: x86_64-apple-darwin15.6.0 (64-bit)
>>>> Running under: macOS High Sierra 10.13.6
>>>>
>>>> Matrix products: default
>>>> BLAS:
>>>> /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib 
>>>>
>>>> LAPACK:
>>>> /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib 
>>>>
>>>>
>>>> locale:
>>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>>>
>>>> attached base packages:
>>>> [1] stats???? graphics? grDevices utils???? datasets methods base
>>>>
>>>> loaded via a namespace (and not attached):
>>>> [1] compiler_3.5.1
>>>>
>>>>
>>>> ????? ** The axis labels are appropriately expanded with the first
>>>> "plot(1:2, cex.axis=2)".? However, when I wrote that to an svg file
>>>> and opened it in other applications (GIMP and Safari), the cex.axis
>>>> request was ignored.? This also occurred inside RStudio on my Mac. It
>>>> worked properly using R 3.2.1 under Windows 7.
>>>
>>>
>>> ??? I just confirmed that when I created a file like this under 
>>> Windows 7
>>> ??? and brought it back to my Mac, it displayed fine.? I have not 
>>> tried this
>>> ??? with the current version of R under Windows 7 nor an old version 
>>> of R on
>>> ??? my Mac.? Thanks.? Spencer
>>>>
>>>>
>>>> ????? Thanks,
>>>> ????? Spencer Graves
>


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[Rd] svg ignores cex.axis in R3.5.1 on macOS
Spencer Graves