To use some module for ReportLab I need some Adobe fonts, which I believe are already placed on my Gentoo box. A zip file provided by author of the package at http://bioinf.scri.ac.uk/lp/programs.php#genomediagram points to http://bioinf.scri.ac.uk/lp/downloads/programs/genomediagram/linfonts.zip, containing: $ unzip -t ~mmokrejs/tmp/linfonts.zip Archive: /home/mmokrejs/tmp/linfonts.zip testing: usr/lib/python2.3/site-packages/reportlab/fonts/AdobeSansMM.MMM.pfb OK testing: usr/lib/python2.3/site-packages/reportlab/fonts/AdobeSansMM.pfb OK testing: usr/lib/python2.3/site-packages/reportlab/fonts/AdobeSerifMM.MMM.pfb OK testing: usr/lib/python2.3/site-packages/reportlab/fonts/AdobeSerifMM.pfb OK testing: usr/lib/python2.3/site-packages/reportlab/fonts/Arial-BoldItalic.pfb OK testing: usr/lib/python2.3/site-packages/reportlab/fonts/Arial-Bold.pfb OK testing: usr/lib/python2.3/site-packages/reportlab/fonts/Arial-Italic.pfb OK testing: usr/lib/python2.3/site-packages/reportlab/fonts/Arial.pfb OK testing: usr/lib/python2.3/site-packages/reportlab/fonts/Courier-BoldOblique.pfb OK testing: usr/lib/python2.3/site-packages/reportlab/fonts/Courier-Bold.pfb OK testing: usr/lib/python2.3/site-packages/reportlab/fonts/Courier-Oblique.pfb OK testing: usr/lib/python2.3/site-packages/reportlab/fonts/Courier.pfb OK testing: usr/lib/python2.3/site-packages/reportlab/fonts/Symbol.pfb OK testing: usr/lib/python2.3/site-packages/reportlab/fonts/TimesNewRoman-BoldItalic.pfb OK testing: usr/lib/python2.3/site-packages/reportlab/fonts/TimesNewRoman-Bold.pfb OK testing: usr/lib/python2.3/site-packages/reportlab/fonts/TimesNewRoman-Italic.pfb OK testing: usr/lib/python2.3/site-packages/reportlab/fonts/TimesNewRoman.pfb OK testing: usr/lib/python2.3/site-packages/reportlab/fonts/ZapfDingbats.pfb OK $ The program itself gives: $ python generate_image_from_genbank.py /usr/lib/python2.4/site-packages/GenomeDiagram/GDLinearDrawer.py:347: DeprecationWarning: integer argument expected, got float for marker in range(self.start, self.end, fragment_step): /usr/lib/python2.4/site-packages/GenomeDiagram/GDLinearDrawer.py:529: DeprecationWarning: integer argument expected, got float smallticks = range(self.start, self.end, smallinterval) Warn: Can't find .pfb for face 'Times-Roman' Traceback (most recent call last): File "generate_image_from_genbank.py", line 23, in ? gdd.write('example1.png', 'PNG') File "/usr/lib/python2.4/site-packages/GenomeDiagram/GDDiagram.py", line 351, in write drawmethod.drawToFile(self.drawing, filename, output, dpi=dpi) File "/usr/lib/python2.4/site-packages/reportlab/graphics/renderPM.py", line 591, in drawToFile c = drawToPMCanvas(d, dpi=dpi, bg=bg, configPIL=configPIL, showBoundary=showBoundary) File "/usr/lib/python2.4/site-packages/reportlab/graphics/renderPM.py", line 577, in drawToPMCanvas draw(d, c, 0, 0, showBoundary=showBoundary) File "/usr/lib/python2.4/site-packages/reportlab/graphics/renderPM.py", line 49, in draw R.draw(renderScaledDrawing(drawing), canvas, x, y, showBoundary=showBoundary) File "/usr/lib/python2.4/site-packages/reportlab/graphics/renderbase.py", line 200, in draw self.initState(x,y) #this is the push() File "/usr/lib/python2.4/site-packages/reportlab/graphics/renderPM.py", line 86, in initState self.applyState() File "/usr/lib/python2.4/site-packages/reportlab/graphics/renderPM.py", line 80, in applyState self._canvas.setFont(s['fontName'], s['fontSize']) File "/usr/lib/python2.4/site-packages/reportlab/graphics/renderPM.py", line 358, in setFont _setFont(self._gs,fontName,fontSize) File "/usr/lib/python2.4/site-packages/reportlab/graphics/renderPM.py", line 238, in _setFont raise RenderPMError, "Can't setFont(%s) missing the T1 files?\nOriginally %s: %s" % (fontName,s1,s2) reportlab.graphics.renderPM.RenderPMError: Can't setFont(Times-Roman) missing the T1 files? Originally exceptions.TypeError: makeT1Font() argument 2 must be string, not None $
Created attachment 123190 [details] fonts.txt I have installed all kinds of font packages I have found in portage, here is the list of the files on my system. Still, no Times-Roman available? Maybe that is a configuration issue, but how can I know? Sorry. # find /usr/ -name *.pfb > fonts.txt
# find /usr/ -name *.pfb | while read f; do strings $f | grep Times && echo $f; done %!PS-AdobeFont-1.0: QuasiTimes-Italic 1.07 FontDirectory/QuasiTimes-Italic known{/QuasiTimes-Italic findfont dup/UniqueID known{dup /FullName(QuasiTimes-Italic)readonly def /FamilyName(QuasiTimes)readonly def /FontName /QuasiTimes-Italic def /usr/share/texmf/fonts/type1/public/qfonts/qtmri.pfb %!PS-AdobeFont-1.0: QuasiTimes-Regular 1.07 FontDirectory/QuasiTimes-Regular known{/QuasiTimes-Regular findfont dup/UniqueID known{dup /FullName(QuasiTimes-Regular)readonly def /FamilyName(QuasiTimes)readonly def /FontName /QuasiTimes-Regular def /usr/share/texmf/fonts/type1/public/qfonts/qtmr.pfb %!PS-AdobeFont-1.0: QuasiTimes-Bold 1.07 FontDirectory/QuasiTimes-Bold known{/QuasiTimes-Bold findfont dup/UniqueID known{dup /FullName(QuasiTimes-Bold)readonly def /FamilyName(QuasiTimes)readonly def /FontName /QuasiTimes-Bold def /usr/share/texmf/fonts/type1/public/qfonts/qtmb.pfb %!PS-AdobeFont-1.0: QuasiTimes-BoldItalic 1.07 FontDirectory/QuasiTimes-BoldItalic known{/QuasiTimes-BoldItalic findfont dup/UniqueID known{dup /FullName(QuasiTimes-BoldItalic)readonly def /FamilyName(QuasiTimes)readonly def /FontName /QuasiTimes-BoldItalic def /usr/share/texmf/fonts/type1/public/qfonts/qtmbi.pfb #
Hmm this is three years old now. It's a bug about program which is not in Portage. Does not work with dev-python/reportlab-2.3-r1 (needs to install some extension or just simply doesnt work ;) which is oldest version in Portage and description is somewhat vague on "steps to reproduce problem". Maybe it would be OK to close it?
I think GenomeDiagram was donated into biopython, I wonder what the font requirements are then nowadays. I do not have enough time to look into this now, sorry. :( Is probably documented at biopython.org. ;-) I would be happy if the ebuild of reportlab or biopython now checks for some package with Adobe T1 fonts, as shown in the original bug report.
I vote for closing this bug. Reasons: * The bug itself didn't cite the package versions, so we don't know for sure which reportlab version was affected. * No clear steps on how to reproduce it. * Even though tehre were no instructions, I tried to reproduce this bug myself, but everything worked here. I downloaded and extracted the biopython tarball. Then... $ cd biopython-1.53/Tests $ PYTHONPATH=.. python test_GenomeDiagram.py And all 12 tests ran without failure. (using reportlab-2.4) Also, all four test_Graphics*.py ran without problems. (and no other test uses reportlab) Thus, I would close this bug as WORKSFORME. By the way, this bug should NOT block bug 318233.
It looks one needs to be root to have privs to write results of the tests into /usr/share/biopython/Tests/Graphics. :(( At the moment I have installed biopython-1.54. # cd /usr/share/biopython/Tests python run_tests.py test_GenomeDiagram test_GenomeDiagram ... ok ---------------------------------------------------------------------- Ran 1 test in 16.576 seconds # ls -la Graphics/ total 1152 drwxr-xr-x 2 root root 4096 Jun 23 00:04 . drwxr-xr-x 46 root root 16384 Jun 23 00:03 .. -rw-r--r-- 1 root root 31128 Jun 23 00:04 GD_by_meth_circular.pdf -rw-r--r-- 1 root root 9572 Jun 23 00:03 GD_by_meth_linear.pdf -rw-r--r-- 1 root root 651411 Jun 23 00:04 GD_by_obj_circular.pdf -rw-r--r-- 1 root root 24393 Jun 23 00:04 GD_by_obj_linear.pdf -rw-r--r-- 1 root root 18862 Jun 23 00:04 GD_region_circular.pdf -rw-r--r-- 1 root root 49634 Jun 23 00:04 GD_region_circular.svg -rw-r--r-- 1 root root 2830 Jun 23 00:04 GD_region_linear.pdf -rw-r--r-- 1 root root 8333 Jun 23 00:04 GD_region_linear.svg -rw-r--r-- 1 root root 2871 Jun 23 00:04 GD_sigil_arrow_shafts.pdf -rw-r--r-- 1 root root 41854 Jun 23 00:04 GD_sigil_arrow_shafts_c.pdf -rw-r--r-- 1 root root 2922 Jun 23 00:04 GD_sigil_arrows.pdf -rw-r--r-- 1 root root 37548 Jun 23 00:04 GD_sigil_arrows_c.pdf -rw-r--r-- 1 root root 2670 Jun 23 00:04 GD_sigil_arrows_long.pdf -rw-r--r-- 1 root root 50412 Jun 23 00:04 GD_sigil_arrows_long_c.pdf -rw-r--r-- 1 root root 2907 Jun 23 00:04 GD_sigil_arrows_small.pdf -rw-r--r-- 1 root root 31447 Jun 23 00:04 GD_sigil_arrows_small_c.pdf -rw-r--r-- 1 root root 2851 Jun 23 00:04 GD_sigil_labels.pdf -rw-r--r-- 1 root root 97 Jun 13 08:07 README -rw-r--r-- 1 root root 2876 Jun 23 00:04 labels_default.pdf -rw-r--r-- 1 root root 27575 Jun 23 00:04 labels_default_c.pdf -rw-r--r-- 1 root root 43493 Jun 23 00:04 line_graph.pdf -rw-r--r-- 1 root root 50862 Jun 23 00:04 line_graph_c.pdf # The .pdf files look fine, so it works now, thanks.
