[Rd] svg ignores cex.axis in R3.5.1 on macOS
Spencer Graves
@pencer@gr@ve@ @ending from prod@y@e@com
Thu Sep 6 15:29:51 CEST 2018
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 using 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 using r-project.org on behalf of
>>> spencer.graves using 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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