From csardi.gabor at gmail.com  Thu Jan  8 23:18:27 2015
From: csardi.gabor at gmail.com (=?UTF-8?B?R8OhYm9yIENzw6FyZGk=?=)
Date: Thu, 8 Jan 2015 17:18:27 -0500
Subject: [Rd] latex warning
Message-ID: <CABtg=KmoDFv87r+drDsPwvXW+=p+Ern6QpqD7iG8ommHNm9HKg@mail.gmail.com>

Dear all,

I am getting an R CMD check warning about the PDF manual. I am having a
hard time finding out what is wrong, here is the log of the Rd2pdf call.

The full check (and other) log is at
https://api.travis-ci.org/jobs/46373922/log.txt?deansi=true if anybody is
interested, and the package itself is here:
https://github.com/metacran/r-builder/tree/bintex/rbuildertest

Thanks, Best,
Gabor


+cat ./rbuildertest.Rcheck/Rdlatex.log
Hmm ... looks like a package
This is pdfTeX, Version 3.14159265-2.6-1.40.15 (TeX Live 2014) (preloaded
format=pdflatex)
 restricted \write18 enabled.

kpathsea: Running mktexfmt pdflatex.fmt
fmtutil: running `pdftex -ini   -jobname=pdflatex -progname=pdflatex
-translate-file=cp227.tcx *pdflatex.ini' ...
This is pdfTeX, Version 3.14159265-2.6-1.40.15 (TeX Live 2014) (INITEX)
 restricted \write18 enabled.
 (/home/travis/R-bin/texlive/texmf-dist/web2c/cp227.tcx)
entering extended mode
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/latexconfig/pdflatex.ini
(/home/travis/R-bin/texlive/texmf-config/tex/generic/config/pdftexconfig.tex)
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/base/latex.ltx
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/base/texsys.cfg)
./texsys.aux found


\@currdir set to: ./.


Assuming \openin and \input
have the same search path.


Defining UNIX/DOS style filename parser.

catcodes, registers, compatibility for TeX 2,  parameters,
LaTeX2e <2014/05/01>
hacks, control, par, spacing, files, font encodings, lengths,
====================================

Local config file fonttext.cfg used

====================================
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/base/fonttext.cfg
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/base/fonttext.ltx
=== Don't modify this file, use a .cfg file instead ===

(/home/travis/R-bin/texlive/texmf-dist/tex/latex/base/omlenc.def)
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/base/t1enc.def)
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/base/ot1enc.def)
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/base/omsenc.def)
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/base/t1cmr.fd)
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/base/ot1cmr.fd)
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/base/ot1cmss.fd)
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/base/ot1cmtt.fd)))
====================================

Local config file fontmath.cfg used

====================================
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/base/fontmath.cfg
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/base/fontmath.ltx
=== Don't modify this file, use a .cfg file instead ===

(/home/travis/R-bin/texlive/texmf-dist/tex/latex/base/omlcmm.fd)
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/base/omscmsy.fd)
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/base/omxcmex.fd)
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/base/ucmr.fd)))
====================================

Local config file preload.cfg used

=====================================
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/base/preload.cfg
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/base/preload.ltx)) page
nos.,
x-ref, environments, center, verbatim, math definitions, boxes, title,
sectioning, contents, floats, footnotes, index, bibliography, output,
===========================================
Local configuration file hyphen.cfg used
===========================================
(/home/travis/R-bin/texlive/texmf-dist/tex/generic/babel/hyphen.cfg
(/home/travis/R-bin/texlive/texmf-dist/tex/generic/babel/switch.def)
(/home/travis/R-bin/texlive/texmf-dist/tex/generic/hyphen/hyphen.tex)
(/home/travis/R-bin/texlive/texmf-dist/tex/generic/hyphen/dumyhyph.tex)
(/home/travis/R-bin/texlive/texmf-dist/tex/generic/hyphen/zerohyph.tex))
=================================
Applying patch file ltpatch.ltx
=================================
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/base/ltpatch.ltx)
 ) )
Beginning to dump on file pdflatex.fmt
 (preloaded format=pdflatex 2015.1.8)
4976 strings of total length 68991
45099 memory locations dumped; current usage is 144&43215
3320 multiletter control sequences
\font\nullfont=nullfont
\font\OMX/cmex/m/n/10=cmex10
\font\tenln=line10
\font\tenlnw=linew10
\font\tencirc=lcircle10
\font\tencircw=lcirclew10
\font\OT1/cmr/m/n/5=cmr5
\font\OT1/cmr/m/n/7=cmr7
\font\OT1/cmr/m/n/10=cmr10
\font\OML/cmm/m/it/5=cmmi5
\font\OML/cmm/m/it/7=cmmi7
\font\OML/cmm/m/it/10=cmmi10
\font\OMS/cmsy/m/n/5=cmsy5
\font\OMS/cmsy/m/n/7=cmsy7
\font\OMS/cmsy/m/n/10=cmsy10
3633 words of font info for 14 preloaded fonts
14 hyphenation exceptions
Hyphenation trie of length 6081 has 183 ops out of 35111
  2 for language 1
  181 for language 0
0 words of pdfTeX memory
0 indirect objects
No pages of output.
Transcript written on pdflatex.log.
fmtutil: /home/travis/.texlive2014/texmf-var/web2c/pdftex/pdflatex.fmt
installed.
fmtutil: No errors, exiting successfully.
entering extended mode
(./Rd2.tex
LaTeX2e <2014/05/01>
Babel <3.9l> and hyphenation patterns for 2 languages loaded.

(/home/travis/R-bin/texlive/texmf-dist/tex/latex/base/book.cls
Document Class: book 2014/09/29 v1.4h Standard LaTeX document class
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/base/bk10.clo))
(/home/travis/R-bin/R-3.0.3/lib/R/share/texmf/tex/latex/Rd.sty
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/base/ifthen.sty)
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/tools/longtable.sty)
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/tools/bm.sty)
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/tools/verbatim.sty)
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/url/url.sty)
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/base/textcomp.sty
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/base/ts1enc.def))
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/base/t1enc.def))
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/psnfss/times.sty))
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/base/inputenc.sty
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/base/utf8.def
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/base/t1enc.dfu)
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/base/ot1enc.dfu)
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/base/omsenc.dfu)
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/base/ts1enc.dfu))
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/base/latin1.def))
No file Rd2.aux.
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/base/ts1cmr.fd)
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd)
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd)
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)
No file Rd2.toc.
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/base/utf8.def)
[1{/home/travis
/R-bin/texlive/texmf-var/fonts/map/pdftex/updmap/pdftex.map}] (./Rd2.aux)
){/ho
me/travis/R-bin/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc}</home/travis/R-
bin/texlive/texmf-dist/fonts/type1/urw/courier/ucrr8a.pfb></home/travis/R-bin/t
exlive/texmf-dist/fonts/type1/urw/helvetic/uhvr8a.pfb></home/travis/R-bin/texli
ve/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></home/travis/R-bin/texlive/texm
f-dist/fonts/type1/urw/times/utmr8a.pfb></home/travis/R-bin/texlive/texmf-dist/
fonts/type1/urw/times/utmri8a.pfb>
Output written on Rd2.pdf (1 page, 46322 bytes).
Transcript written on Rd2.log.
This is pdfTeX, Version 3.14159265-2.6-1.40.15 (TeX Live 2014) (preloaded
format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./Rd2.tex
LaTeX2e <2014/05/01>
Babel <3.9l> and hyphenation patterns for 2 languages loaded.

(/home/travis/R-bin/texlive/texmf-dist/tex/latex/base/book.cls
Document Class: book 2014/09/29 v1.4h Standard LaTeX document class
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/base/bk10.clo))
(/home/travis/R-bin/R-3.0.3/lib/R/share/texmf/tex/latex/Rd.sty
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/base/ifthen.sty)
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/tools/longtable.sty)
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/tools/bm.sty)
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/tools/verbatim.sty)
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/url/url.sty)
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/base/textcomp.sty
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/base/ts1enc.def))
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/base/t1enc.def))
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/psnfss/times.sty))
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/base/inputenc.sty
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/base/utf8.def
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/base/t1enc.dfu)
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/base/ot1enc.dfu)
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/base/omsenc.dfu)
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/base/ts1enc.dfu))
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/base/latin1.def))
(./Rd2.aux)
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/base/ts1cmr.fd)
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd)
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd)
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)
(./Rd2.toc)
(/home/travis/R-bin/texlive/texmf-dist/tex/latex/base/utf8.def)
[1{/home/travis
/R-bin/texlive/texmf-var/fonts/map/pdftex/updmap/pdftex.map}] [2]
(./Rd2.aux) )
{/home/travis/R-bin/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc}</home/travi
s/R-bin/texlive/texmf-dist/fonts/type1/urw/courier/ucrr8a.pfb></home/travis/R-b
in/texlive/texmf-dist/fonts/type1/urw/helvetic/uhvr8a.pfb></home/travis/R-bin/t
exlive/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></home/travis/R-bin/texlive/
texmf-dist/fonts/type1/urw/times/utmr8a.pfb></home/travis/R-bin/texlive/texmf-d
ist/fonts/type1/urw/times/utmr8a.pfb></home/travis/R-bin/texlive/texmf-dist/fon
ts/type1/urw/times/utmri8a.pfb>
Output written on Rd2.pdf (2 pages, 54276 bytes).
Transcript written on Rd2.log.
Saving output to 'rbuildertest-manual.pdf' ...
Done
You may want to clean up by 'rm -rf /tmp/RtmppU5OjJ/Rd2pdf10671bb8dd18'

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[Rd] latex warning
=?UTF-8?B?R8OhYm9yIENzw6FyZGk=?=