[R-SIG-Mac] Error creating Reference Manual for R-packages with MacTeX

cstrato cstrato at aon.at
Fri May 7 19:34:19 CEST 2010 

Dear all,

After a fresh installation of Snow Leopard I have installed the smaller 
distribution of MacTeX (BasicTeX.dmg and MacTeX-Additions-2009.mpkg) 
from: http://www.tug.org/mactex/2009/morepackages.html

While this version of MacTeX is able to create pdf-files for the 
vignettes R CMD check fails to create pdf-files for the Reference 
Manuals. To make sure that this is not a problem of my package only I 
have tested this with the following packages:
DynDoc_1.26.0.tar.gz
externalVector_1.14.0.tar.gz
gpls_1.20.0.tar.gz
Icens_1.20.0.tar.gz
preprocessCore_1.10.0.tar.gz
xps_1.9.0.tar.gz

As the different Rdlatex.log reveal, the problem is always the same:
kpathsea: Running mktexmf pcrr8t
! I can't find file `pcrr8t'.

For example the relevant output of "R CMD check DynDoc_1.26.0.tar.gz" is:

* checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Font T1/pcr/m/n/10=pcrr8t at 10.0pt not loadable: Metric (TFM) file 
not found
.
<to be read again>
                    relax
l.23 \email{bioconductor at stat.math.ethz.ch}}
! Font T1/phv/m/n/14.4=phvr8t at 14.4pt not loadable: Metric (TFM) file 
not fou
nd.
<to be read again>
                    relax
l.30 \Rdcontents{\R{} topics documented:}
! Font T1/pcr/m/n/9=pcrr8t at 9.0pt not loadable: Metric (TFM) file not 
found.
<to be read again>
                    relax
l.109 \begin{ExampleCode}

* checking PDF version of manual without index ... ERROR


Below I attach the complete output of Rdlatex.log for R CMD check DynDoc.

Since doing a Google search did not reveal any helpful information my 
question is:

Is there any file missing from BasicTeX which I need to install?
(According to the web-site "BasicTeX contains all of the standard tools 
needed to write TeX documents...")

Thank you in advance.
Best regards
Christian
_._._._._._._._._._._._._._._._._._
C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
V.i.e.n.n.a           A.u.s.t.r.i.a
e.m.a.i.l:        cstrato at aon.at
_._._._._._._._._._._._._._._._._._


Here is the complete output of Rdlatex.log for R CMD check DynDoc:

Hmm ... looks like a package
Creating pdf output from LaTeX ...
This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009)
entering extended mode
(./Rd2.tex
LaTeX2e <2009/09/24>
Babel <v3.8l> and hyphenation patterns for english, usenglishmax, 
dumylang, noh
yphenation, basque, danish, dutch, finnish, french, german, ngerman, 
hungarian,
  italian, bokmal, nynorsk, polish, portuguese, spanish, swedish, 
ukenglish, loa
ded.

(/usr/local/texlive/2009basic/texmf-dist/tex/latex/base/book.cls
Document Class: book 2007/10/19 v1.4h Standard LaTeX document class
(/usr/local/texlive/2009basic/texmf-dist/tex/latex/base/bk10.clo))
(/Library/Frameworks/R.framework/Resources/share/texmf/Rd.sty
(/usr/local/texlive/2009basic/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/local/texlive/2009basic/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/local/texlive/2009basic/texmf-dist/tex/latex/tools/bm.sty)
(/usr/local/texlive/2009basic/texmf-dist/tex/latex/base/alltt.sty)
(/usr/local/texlive/2009basic/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/local/texlive/2009basic/texmf-dist/tex/latex/ltxmisc/url.sty)
(/Library/Frameworks/R.framework/Resources/share/texmf/upquote.sty
(/usr/local/texlive/2009basic/texmf-dist/tex/latex/base/textcomp.sty
(/usr/local/texlive/2009basic/texmf-dist/tex/latex/base/ts1enc.def)))
NOT loading ae
(/usr/local/texlive/2009basic/texmf-dist/tex/latex/base/fontenc.sty
(/usr/local/texlive/2009basic/texmf-dist/tex/latex/base/t1enc.def))
(/usr/local/texlive/2009basic/texmf-dist/tex/latex/psnfss/times.sty)
NOT loading lmodern
(/usr/local/texlive/2009basic/texmf-dist/tex/latex/graphics/color.sty
(/usr/local/texlive/2009basic/texmf-dist/tex/latex/latexconfig/color.cfg)
(/usr/local/texlive/2009basic/texmf-dist/tex/latex/pdftex-def/pdftex.def))
(/usr/local/texlive/2009basic/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/local/texlive/2009basic/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/local/texlive/2009basic/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty
(/usr/local/texlive/2009basic/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/local/texlive/2009basic/texmf-dist/tex/generic/oberdiek/etexcmds.sty))
(/usr/local/texlive/2009basic/texmf-dist/tex/generic/oberdiek/pdfescape.sty
(/usr/local/texlive/2009basic/texmf-dist/tex/generic/oberdiek/pdftexcmds.sty
(/usr/local/texlive/2009basic/texmf-dist/tex/generic/oberdiek/ifluatex.sty)
(/usr/local/texlive/2009basic/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)))
(/usr/local/texlive/2009basic/texmf-dist/tex/generic/oberdiek/ifpdf.sty)
(/usr/local/texlive/2009basic/texmf-dist/tex/generic/oberdiek/ifvtex.sty)
(/usr/local/texlive/2009basic/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/local/texlive/2009basic/texmf-dist/tex/latex/oberdiek/hycolor.sty
(/usr/local/texlive/2009basic/texmf-dist/tex/latex/oberdiek/xcolor-patch.sty))
(/usr/local/texlive/2009basic/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/local/texlive/2009basic/texmf-dist/tex/generic/oberdiek/intcalc.sty)
(/usr/local/texlive/2009basic/texmf-dist/tex/latex/latexconfig/hyperref.cfg)
(/usr/local/texlive/2009basic/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
Implicit mode ON; LaTeX internals redefined
(/usr/local/texlive/2009basic/texmf-dist/tex/generic/oberdiek/bitset.sty
(/usr/local/texlive/2009basic/texmf-dist/tex/generic/oberdiek/bigintcalc.sty))
(/usr/local/texlive/2009basic/texmf-dist/tex/generic/oberdiek/atbegshi.sty))
*hyperref using default driver hpdftex*
(/usr/local/texlive/2009basic/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/local/texlive/2009basic/texmf-dist/tex/generic/oberdiek/atveryend.sty)
(/usr/local/texlive/2009basic/texmf-dist/tex/generic/oberdiek/rerunfilecheck.st
y
(/usr/local/texlive/2009basic/texmf-dist/tex/generic/oberdiek/uniquecounter.sty
)))

Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref)                setting the option has no effect on input line 
327.


Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref)                setting the option has no effect on input line 
327.

) (/usr/local/texlive/2009basic/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/local/texlive/2009basic/texmf-dist/tex/latex/base/inputenc.sty
(/usr/local/texlive/2009basic/texmf-dist/tex/latex/base/utf8.def
(/usr/local/texlive/2009basic/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/local/texlive/2009basic/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/local/texlive/2009basic/texmf-dist/tex/latex/base/omsenc.dfu)
(/usr/local/texlive/2009basic/texmf-dist/tex/latex/base/ts1enc.dfu))
(/usr/local/texlive/2009basic/texmf-dist/tex/latex/base/latin1.def))
Writing index file Rd2.idx
No file Rd2.aux.
(/usr/local/texlive/2009basic/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/local/texlive/2009basic/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/local/texlive/2009basic/texmf-dist/tex/context/base/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/local/texlive/2009basic/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/local/texlive/2009basic/texmf-dist/tex/latex/oberdiek/refcount.sty)
(/usr/local/texlive/2009basic/texmf-dist/tex/generic/oberdiek/gettitlestring.st
y)) (/usr/local/texlive/2009basic/texmf-dist/tex/latex/psnfss/t1pcr.fd)
kpathsea: Running mktextfm pcrr8t
mktextfm: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1; 
nonstopmode; input pcrr8t
This is METAFONT, Version 2.718281 (TeX Live 2009)

kpathsea: Running mktexmf pcrr8t

! I can't find file `pcrr8t'.
<*> ...:=ljfour; mag:=1; nonstopmode; input pcrr8t

Please type another input file name
! Emergency stop.
<*> ...:=ljfour; mag:=1; nonstopmode; input pcrr8t

Transcript written on mfput.log.
grep: pcrr8t.log: No such file or directory
mktextfm: `mf-nowin -progname=mf \mode:=ljfour; mag:=1; nonstopmode; 
input pcrr8t' failed to make pcrr8t.tfm.
kpathsea: Appending font creation commands to missfont.log.

! Font T1/pcr/m/n/10=pcrr8t at 10.0pt not loadable: Metric (TFM) file 
not found
.
<to be read again>
                    relax
l.23 \email{bioconductor at stat.math.ethz.ch}}

(/usr/local/texlive/2009basic/texmf-dist/tex/latex/psnfss/t1phv.fd)
kpathsea: Running mktextfm phvr8t
mktextfm: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1; 
nonstopmode; input phvr8t
This is METAFONT, Version 2.718281 (TeX Live 2009)

kpathsea: Running mktexmf phvr8t

! I can't find file `phvr8t'.
<*> ...:=ljfour; mag:=1; nonstopmode; input phvr8t

Please type another input file name
! Emergency stop.
<*> ...:=ljfour; mag:=1; nonstopmode; input phvr8t

Transcript written on mfput.log.
grep: phvr8t.log: No such file or directory
mktextfm: `mf-nowin -progname=mf \mode:=ljfour; mag:=1; nonstopmode; 
input phvr8t' failed to make phvr8t.tfm.

! Font T1/phv/m/n/14.4=phvr8t at 14.4pt not loadable: Metric (TFM) file 
not fou
nd.
<to be read again>
                    relax
l.30 \Rdcontents{\R{} topics documented:}

(/usr/local/texlive/2009basic/texmf-dist/tex/latex/base/utf8.def) 
[1{/usr/local
/texlive/2009basic/texmf-var/fonts/map/pdftex/updmap/pdftex.map}]
kpathsea: Running mktextfm pcrr8t
mktextfm: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1; 
nonstopmode; input pcrr8t
This is METAFONT, Version 2.718281 (TeX Live 2009)

kpathsea: Running mktexmf pcrr8t

! I can't find file `pcrr8t'.
<*> ...:=ljfour; mag:=1; nonstopmode; input pcrr8t

Please type another input file name
! Emergency stop.
<*> ...:=ljfour; mag:=1; nonstopmode; input pcrr8t

Transcript written on mfput.log.
grep: pcrr8t.log: No such file or directory
mktextfm: `mf-nowin -progname=mf \mode:=ljfour; mag:=1; nonstopmode; 
input pcrr8t' failed to make pcrr8t.tfm.

! Font T1/pcr/m/n/9=pcrr8t at 9.0pt not loadable: Metric (TFM) file not 
found.
<to be read again>
                    relax
l.109 \begin{ExampleCode}

(/usr/local/texlive/2009basic/texmf-dist/tex/latex/base/utf8.def) [2]
(/usr/local/texlive/2009basic/texmf-dist/tex/latex/base/utf8.def) [3]
(/usr/local/texlive/2009basic/texmf-dist/tex/latex/base/utf8.def) [4]
(/usr/local/texlive/2009basic/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2009basic/texmf-dist/tex/latex/base/utf8.def) [5]
(/usr/local/texlive/2009basic/texmf-dist/tex/latex/base/utf8.def) [6]
(/usr/local/texlive/2009basic/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2009basic/texmf-dist/tex/latex/base/utf8.def) [7]
(/usr/local/texlive/2009basic/texmf-dist/tex/latex/base/utf8.def) [8]
(/usr/local/texlive/2009basic/texmf-dist/tex/latex/base/utf8.def) [9]
No file Rd2.ind.
[10] (./Rd2.aux)

Package rerunfilecheck Warning: File `Rd2.out' has changed.
(rerunfilecheck)                Rerun to get outlines right
(rerunfilecheck)                or use package `bookmark'.

  )
(see the transcript file for additional information)pdfTeX warning 
(dest): name
{Rfn.Stangle} has been referenced but does not exist, replaced by a 
fixed one

pdfTeX warning (dest): name{Rfn.vignette} has been referenced but does 
not exis
t, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.Sweave} has been referenced but does not 
exist,
  replaced by a fixed one

{/usr/local/texlive/2009basic/texmf-dist/fonts/enc/dvips/base/8r.enc}</usr/loca
l/texlive/2009basic/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/local/tex
live/2009basic/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/local/texlive/
2009basic/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/local/texlive/2009b
asic/texmf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on Rd2.pdf (10 pages, 103652 bytes).
Transcript written on Rd2.log.
Error in running pdflatex command ('pdflatex')
You may want to clean up by 'rm -rf /Users/rabbitus/temp/Rd2dvi245641692'

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