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The warning mentioned in the title occurs only if luaotfload is loaded. The txr.vf + txr.tfm files are OK: other TeX engines or dvips etc. don't have problem, tftopl and vftovp show that the checksum is the same, the clean new TeXlive 2013 or 2014 pretest distribution is used.

here is a minimal file:

\input luaotfload.sty
\font\f=txr \f a\end

Process it by luatex. The terminal or log says:

checksum mismatch in font txr.vf ignored  [1{/.../tl2013/texmf-var/fonts/m
ap/pdftex/updmap/pdftex.map}] ){/.../tl2013/texmf-dist/fonts/enc/dvips/bas
e/8r.enc}</.../tl2013/texmf-dist/fonts/type1/public/amsfonts/cm/cmr10.pfb>
</.../tl2013/texmf-dist/fonts/type1/urw/times/utmr8a.pfb>
Output written on pok.pdf (1 page, 12634 bytes).
Transcript written on pok.log.

The ``more minimal'' file is:

\input luafonts
\font\f=txr \f a\end

The file luafonts.tex does the same as luaotfload.sty, it means that it reinstalls the \font primitive in order to the OTF fonts can be loaded. The only difference is that luafonts.tex doesn't input next 42 external files.

If we comment out the line \input luaotfload.sty or luafonts then the curious warning doesn't appear. The txr font is normal tfm+vf font, no OTF. Other fonts are without this problem. It seems that the warning is a bug in luaotfload code. Is it true?

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    The checksum is compared when a pair <name>.tfm and <name>.vf is found, which should ensure they were both produced by the same run of vptovf (or other program). In the case where <name> is txr, the checksum is 32212676346 (octal) for both, so my feeling is that luaotfload does the wrong comparison. – egreg May 21 '14 at 13:19
  • The problem has been discussed some time ago comments.gmane.org/gmane.comp.tex.live/30992 but imho never really been investigated (it doesn't make much sense to use such fonts with lualatex). You could open a bug report at https://github.com/lualatex/luaotfload/issues?state=open – Ulrike Fischer May 21 '14 at 13:29
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    Also the checksum for the mapped fonts coincide, in my TeX distribution, but with luafonts the warning appears nonetheless. I tried recreating the .vf and .tfm files after removing the checksum information in the .vpl file. The recreated files show the same information as before, because the checksums are taken from the referenced fonts. But the warning remains. – egreg May 21 '14 at 13:30
  • @UlrikeFischer: (it doesn't make much sense to use such fonts with lualatex) -- with lualatex may be but the font is set as default for math in csplain format when Times-like font family is selected. I.e. it is used with luatex. Regardles of the usage of this font it is not good new that the TeX engine we are using includes a bug. – wilik May 21 '14 at 13:57
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    I only wanted to explain why nobody really pressed to solve the problem: is only a (harmless) message you don't get often. And you should be aware that luatex and luaotfload certainly contains more (and more serious) bugs. The best you can do is to report them so that they can be solved. – Ulrike Fischer May 21 '14 at 14:02
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The problem has been discussed some time ago http://comments.gmane.org/gmane.comp.tex.live/30992 but imho never really been investigated (it doesn't make much sense to use such fonts with lualatex and so there is not much pressure in resolving a rather harmless warning).

You could open a bug report at https://github.com/lualatex/luaotfload/issues?state=open

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