Bug #1011

Updated by Sebastien Jacquot over 4 years ago

Reported by JCD on Mac OS X 10.9.4: R graphics (WordCloud or CAH) labels are "pixelized".

*Diagnostic 1 - TXM graphics*:
* Question: Can we reproduce the bug?
* Test: produce a CAH from TXM with the following configurations:
** Mac OS X 10.6 + Java 6, 0.65 = no bug
** Mac OS X 10.9 + Java 7, 0.60 + xQuartz 2.7.6 = no bug
** Mac OS X 10.9 + Java 7, 0.67 + xQuartz 2.7.6 = no bug
** Mac OS X 10.9 + Java 7, 0.67 + xQuartz 2.7.7 = no bug
** Remark: Mac OS X 10.9 + Java 7, 0.67 - xQuartz = FAILS, no graphic is displayed. This is expected
* Conclusion: Impossible to reproduce the bug (MD + SJ) -> JCD must help us to diagnose the bug.

*Diagnostic 2 - JCD R script graphics*:
* Question: Is native R buggy for graphics?
* Test: Run the "bfmprogression.R" script directly from R = no bug
* *Conclusion: ask to set graphic device to 'svg'*

*Diagnostic 3 - JCD TXM SVG graphics*:
* Question: Is the SVG file generated corrupted?
* Test: Get the SVG file generated in the "results" directory then check if it opens well in external editor and in TXM Batik SVG Editor
* Conclusion: nope, the glyphs are just wrong

*Diagnostic 4 - JCD TXM R script graphics*:
* Question: Is TXM R execution for graphics buggy?
* Test: Run "bfmprogression.R" script from TXM
* Conclusion: yes

*Diagnostic 5 - is the bug present in TXM 0.7.5*:
* Question: Has TXM 0.7.6 introduced this bug?
* Test: Reinstall TXM 0.7.5 and compute a CAH graphic
* Conclusion:

*Hypothesis 1*
* see what could go wrong with the 'svg' device of the 'cairo' R package

*WIP*
- define if the bug is only related to the svg() device (SVG device based on cairo graphics) or to all the devices
- to do that, 2 solutions:
1) plot on png, jpg, native window (Quartz) devices in TXM and see if the bug is present
2) plot on svg device in R outside TXM and see if the bug is present
- NOTE: cairo uses X11 on some OS. On Mac OS X 10.9, svg() uses cairo that needs and uses XQuartz
- define if the bug is linked to a font problem
- define if the bug is linked to SVG antialiasing. I got pretty much same results as JCD when setting 'shape-rendering="optimizeSpeed"' attribute of 'svg' tag in an SVG and reopen it in TXM/Batik editor. Be careful, opening the SVG file, in Safari for example, works well. Need the SVG generated by JCD in 'results' directory to confirm that

*NEW TESTS SJ, plotting SVG file from R outside TXM*
** Mac OS X 10.9.4 VM + Java 7 64bit, 0.55 + R version 3.0.1 (2013-05-16) - xQuartz = FAILS to load cairo, as expected
** Mac OS X 10.9.4 VM + Java 7 64bit, 0.55 + R version 3.0.1 (2013-05-16) + xQuartz 2.7.6 = no bug (but two warning messages)
*** NOTE: got theses warnings while plotting: "Fontconfig warning: ignoring UTF-8: not a valid region tag
Fontconfig warning: ignoring UTF-8: not a valid region tag"
** Mac OS X 10.9.4 VM + Java 7 64bit, 0.55 + R version 3.0.1 (2013-05-16) + xQuartz 2.7.7 = no bug (but same warning messages as above)

NOTE: to show current XQuartz version:

<pre>
mdls -name kMDItemVersion /Applications/Utilities/XQuartz.app
</pre>

NOTE: to show current R version, type 'version' in R console

JCD R version : 3.1.0 with RStudio

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