[R-SIG-Mac] latex errors, Rd problems
Prof Brian Ripley
ripley at stats.ox.ac.uk
Sat Mar 21 20:18:28 CET 2015
On 21/03/2015 19:10, boB Rudis wrote:
> I noticed that there's an obvious hard-coding of /usr/local/bin when
> running the command. I had to symlink it from /usr/bin to /usr/local/bin
> to get it to go.
It is not hard-coded! It is set when R is configured: if this was a
binary distribution of R, using the expected layout. If you want to
override it, set the environment variable R_TEXI2DVICMD . For all such
variables see /Library/Frameworks/R.framework/Resources/etc/Renviron
(and the R manuals).
Do follow the posting guide and *not send HTML*.
>
> I'm pretty sure the OS X Rd build errors are more MacTex related than
> R-related at this point.
>
> On Sat, Mar 21, 2015 at 3:02 PM, Adrian Dușa <dusa.adrian at unibuc.ro
> <mailto:dusa.adrian at unibuc.ro>> wrote:
>
> On Sat, Mar 21, 2015 at 3:09 PM, Prof Brian Ripley
> <ripley at stats.ox.ac.uk <mailto:ripley at stats.ox.ac.uk>>
> wrote:
>
> > On 21/03/2015 12:38, Adrian Dușa wrote:
> >
> >> [...]
> >
> >
> > So the next step is to run R CMD Rd2pdf --no-clean on the unpacked package
> > sources and look at the logs in its check directory. You may need to run
> > texi2dvi -D --pdf on the .tex file produced there.
>
>
> Already tried that (in my first post), and I get:
>
> ###
> Adrians-MBP:~ dusadrian$ R CMD Rd2pdf --no-clean DDIwR/
> Hmm ... looks like a package
> Converting Rd files to LaTeX
> Creating pdf output from LaTeX ...
> Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet =
> quiet, :
> Running 'texi2dvi' on 'Rd2.tex' failed.
> Messages:
> sh: /usr/local/bin/texi2dvi: No such file or directory
> Output:
>
> Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet =
> quiet, :
> Running 'texi2dvi' on 'Rd2.tex' failed.
> Messages:
> sh: /usr/local/bin/texi2dvi: No such file or directory
> Output:
>
> Error in running tools::texi2pdf()
> You may want to clean up by 'rm -rf .Rd2pdf19534'
> ###
>
>
> My search for this problem boiled down to texi2dvi which doesn't
> seem to be
> found, despite a full reinstall of a fresh MacTeX-2014.
> As far as I read, texi2dvi <should> be found, so my next guess was a
> path
> issue, which gives:
>
> Adrians-MBP:~ dusadrian$ $PATH
> -bash:
> /usr/local/mysql/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/usr/local/MacGPG2/bin:/usr/texbin:
> No such file or directory
>
> "No such file or directory" (probably for /usr/texbin)... and this
> is where
> I got stuck.
>
> Curiously, there <is> a .tex file in the DDIwR.Rcheck directory, and
> running texi2dvi (although it previously complained it could not
> find it)
> gives:
>
> ###
> Adrians-MBP:~ dusadrian$ texi2dvi -D --pdf DDIwR.Rcheck/DDIwR-manual.tex
> + for command_line_filename in '${1+"$@"}'
> + false 'Processing DDIwR.Rcheck/DDIwR-manual.tex ...'
> + echo DDIwR.Rcheck/DDIwR-manual.tex
> + egrep '^(/|[A-z]:/)'
> + command_line_filename=./DDIwR.Rcheck/DDIwR-manual.tex
> + test '!' -r ./DDIwR.Rcheck/DDIwR-manual.tex
> ++ sed 's!/[^/]*$!!;s!^$!.!'
> ++ echo ./DDIwR.Rcheck/DDIwR-manual.tex
> + filename_dir=./DDIwR.Rcheck
> ++ cd ./DDIwR.Rcheck
> ++ pwd
> + filename_dir=/Users/dusadrian/DDIwR.Rcheck
> ++ basename ./DDIwR.Rcheck/DDIwR-manual.tex
> + filename_ext=DDIwR-manual.tex
> ++ echo DDIwR-manual.tex
> ++ sed 's/\.[^.]*$//'
> + filename_noext=DDIwR-manual
> ++ echo DDIwR-manual.tex
> ++ sed 's/^.*\.//'
> + ext=tex
> +
> tmpdir_src=/var/folders/wl/xtd1693n1jsfff4c_zl06vgw0000gn/T//t2d19553/src
> +
> filename_src=/var/folders/wl/xtd1693n1jsfff4c_zl06vgw0000gn/T//t2d19553/src/DDIwR-manual.tex
> +
> tmpdir_xtr=/var/folders/wl/xtd1693n1jsfff4c_zl06vgw0000gn/T//t2d19553/xtr
> +
> filename_xtr=/var/folders/wl/xtd1693n1jsfff4c_zl06vgw0000gn/T//t2d19553/xtr/DDIwR-manual.tex
> +
> tmpdir_rcd=/var/folders/wl/xtd1693n1jsfff4c_zl06vgw0000gn/T//t2d19553/rcd
> +
> filename_rcd=/var/folders/wl/xtd1693n1jsfff4c_zl06vgw0000gn/T//t2d19553/rcd/DDIwR-manual.tex
> +
> tmpdir_bak=/var/folders/wl/xtd1693n1jsfff4c_zl06vgw0000gn/T//t2d19553/bak
> + mkdir /var/folders/wl/xtd1693n1jsfff4c_zl06vgw0000gn/T//t2d19553/src
> /var/folders/wl/xtd1693n1jsfff4c_zl06vgw0000gn/T//t2d19553/xtr
> /var/folders/wl/xtd1693n1jsfff4c_zl06vgw0000gn/T//t2d19553/rcd
> /var/folders/wl/xtd1693n1jsfff4c_zl06vgw0000gn/T//t2d19553/bak
> + common=/Users/dusadrian:/Users/dusadrian/DDIwR.Rcheck:
> + for var in '$tex_envvars'
> + eval 'BIBINPUTS=$common$BIBINPUTS_orig'
> ++ BIBINPUTS=/Users/dusadrian:/Users/dusadrian/DDIwR.Rcheck:
> + export BIBINPUTS
> + for var in '$tex_envvars'
> + eval 'BSTINPUTS=$common$BSTINPUTS_orig'
> ++ BSTINPUTS=/Users/dusadrian:/Users/dusadrian/DDIwR.Rcheck:
> + export BSTINPUTS
> + for var in '$tex_envvars'
> + eval 'INDEXSTYLE=$common$INDEXSTYLE_orig'
> ++ INDEXSTYLE=/Users/dusadrian:/Users/dusadrian/DDIwR.Rcheck:
> + export INDEXSTYLE
> + for var in '$tex_envvars'
> + eval 'TEXINPUTS=$common$TEXINPUTS_orig'
> ++ TEXINPUTS=/Users/dusadrian:/Users/dusadrian/DDIwR.Rcheck:
> + export TEXINPUTS
> + replace_empty='-e '\''s/^:/EMPTY:/g'\'' -e
> '\''s/:$/:EMPTY/g'\'' -e '\''s/::/:EMPTY:/g'\'''
> ++ echo /Users/dusadrian:/Users/dusadrian/DDIwR.Rcheck:
> ++ eval sed -e ''\''s/^:/EMPTY:/g'\''' -e ''\''s/:$/:EMPTY/g'\''' -e
> ''\''s/::/:EMPTY:/g'\'''
> +++ sed -e 's/^:/EMPTY:/g' -e 's/:$/:EMPTY/g' -e s/::/:EMPTY:/g
> + TEXINPUTS=/Users/dusadrian:/Users/dusadrian/DDIwR.Rcheck:EMPTY
> ++ echo /Users/dusadrian:/Users/dusadrian/DDIwR.Rcheck:
> ++ eval sed -e ''\''s/^:/EMPTY:/g'\''' -e ''\''s/:$/:EMPTY/g'\''' -e
> ''\''s/::/:EMPTY:/g'\'''
> +++ sed -e 's/^:/EMPTY:/g' -e 's/:$/:EMPTY/g' -e s/::/:EMPTY:/g
> + INDEXSTYLE=/Users/dusadrian:/Users/dusadrian/DDIwR.Rcheck:EMPTY
> + save_IFS='
> '
> + IFS=:
> + set x /Users/dusadrian /Users/dusadrian/DDIwR.Rcheck EMPTY
> + shift
> + TEXINPUTS=.
> + for dir in '"$@"'
> + case $dir in
> + TEXINPUTS=.:/Users/dusadrian
> + for dir in '"$@"'
> + case $dir in
> + TEXINPUTS=.:/Users/dusadrian:/Users/dusadrian/DDIwR.Rcheck
> + for dir in '"$@"'
> + case $dir in
> + TEXINPUTS=.:/Users/dusadrian:/Users/dusadrian/DDIwR.Rcheck:
> + set x /Users/dusadrian /Users/dusadrian/DDIwR.Rcheck EMPTY
> + shift
> + INDEXSTYLE=.
> + for dir in '"$@"'
> + case $dir in
> + INDEXSTYLE=.:/Users/dusadrian
> + for dir in '"$@"'
> + case $dir in
> + INDEXSTYLE=.:/Users/dusadrian:/Users/dusadrian/DDIwR.Rcheck
> + for dir in '"$@"'
> + case $dir in
> + INDEXSTYLE=.:/Users/dusadrian:/Users/dusadrian/DDIwR.Rcheck:
> + IFS='
> '
> + test -n ''
> + sed 1q ./DDIwR.Rcheck/DDIwR-manual.tex
> + grep 'input texinfo'
> + language=
> + case ${language:-$filename_ext} in
> + language=latex
> + bibtex=bibtex
> + makeinfo=
> + texindex=makeindex
> + textra_cmd=1i
> + test pdf = dvi
> + tex=pdflatex
> + thumbpdf=thumbpdf
> ++ cd /var/folders/wl/xtd1693n1jsfff4c_zl06vgw0000gn/T//t2d19553
> ++ pdflatex --help
> + tex_help='Usage: pdftex [OPTION]... [TEXNAME[.tex]] [COMMANDS]
> or: pdftex [OPTION]... \FIRST-LINE
> or: pdftex [OPTION]... &FMT ARGS
> Run pdfTeX on TEXNAME, usually creating TEXNAME.pdf.
> Any remaining COMMANDS are processed as pdfTeX input, after
> TEXNAME is
> read.
> If the first line of TEXNAME is %&FMT, and FMT is an existing
> .fmt file,
> use it. Else use `NAME.fmt'\'', where NAME is the program invocation
> name,
> most commonly `pdftex'\''.
>
> Alternatively, if the first non-option argument begins with a
> backslash,
> interpret all non-option arguments as a line of pdfTeX input.
>
> Alternatively, if the first non-option argument begins with a &, the
> next word is taken as the FMT to read, overriding all else. Any
> remaining arguments are processed as above.
>
> If no arguments or options are specified, prompt for input.
>
> -draftmode switch on draft mode (generates no output PDF)
> -enc enable encTeX extensions such as \mubyte
> -etex enable e-TeX extensions
> [-no]-file-line-error disable/enable file:line:error style messages
> -fmt=FMTNAME use FMTNAME instead of program name or a %& line
> -halt-on-error stop processing at the first error
> -ini be pdfinitex, for dumping formats; this is
> implicitly
> true if the program name is `pdfinitex'\''
> -interaction=STRING set interaction mode
> (STRING=batchmode/nonstopmode/
> scrollmode/errorstopmode)
> -ipc send DVI output to a socket as well as the usual
> output file
> -ipc-start as -ipc, and also start the server at the
> other end
> -jobname=STRING set the job name to STRING
> -kpathsea-debug=NUMBER set path searching debugging flags according to
> the bits of NUMBER
> [-no]-mktex=FMT disable/enable mktexFMT generation
> (FMT=tex/tfm/pk)
> -mltex enable MLTeX extensions such as \charsubdef
> -output-comment=STRING use STRING for DVI file comment instead of date
> (no effect for PDF)
> -output-directory=DIR use existing DIR as the directory to write
> files in
> -output-format=FORMAT use FORMAT for job output; FORMAT is `dvi'\'' or
> `pdf'\''
> [-no]-parse-first-line disable/enable parsing of first line of
> input file
> -progname=STRING set program (and fmt) name to STRING
> -recorder enable filename recorder
> [-no]-shell-escape disable/enable \write18{SHELL COMMAND}
> -shell-restricted enable restricted \write18
> -src-specials insert source specials into the DVI file
> -src-specials=WHERE insert source specials in certain places of
> the DVI file. WHERE is a comma-separated
> value
> list: cr display hbox math par parend vbox
> -synctex=NUMBER generate SyncTeX data for previewers if nonzero
> -translate-file=TCXNAME use the TCX file TCXNAME
> -8bit make all characters printable by default
> -help display this help and exit
> -version output version information and exit
>
> Email bug reports to pdftex at tug.org <mailto:pdftex at tug.org>.'
> + tex_args=
> + case $tex_help in
> + tex_args=' --file-line-error'
> + false
> + test -n ''
> + test 0 -ne 0
> + test '!' -r
> /var/folders/wl/xtd1693n1jsfff4c_zl06vgw0000gn/T//t2d19553/src/DDIwR-manual.tex
> + false 'Reverting to ./DDIwR.Rcheck/DDIwR-manual.tex ...'
> + filename_input=/Users/dusadrian/DDIwR.Rcheck/DDIwR-manual.tex
> + test -n ''
> + test latex = texinfo
> + test '' = t
> + :
> ++ get_xref_files DDIwR-manual
> ++ for this_file in '"$1".?o?' '"$1".aux' '"$1".??' '"$1".idx'
> ++ test -s DDIwR-manual.log
> +++ sed -n '1s/^\(.\).*$/\1/p;q' DDIwR-manual.log
> ++ first_character=T
> ++ test xT = 'x\'
> ++ test xT = 'x'\'''
> ++ test xT = x@
> ++ for this_file in '"$1".?o?' '"$1".aux' '"$1".??' '"$1".idx'
> ++ test -s DDIwR-manual.aux
> ++ continue
> ++ for this_file in '"$1".?o?' '"$1".aux' '"$1".??' '"$1".idx'
> ++ test -s 'DDIwR-manual.??'
> ++ continue
> ++ for this_file in '"$1".?o?' '"$1".aux' '"$1".??' '"$1".idx'
> ++ test -s DDIwR-manual.idx
> ++ continue
> ++ echo ''
> + orig_xref_files=
> + test -n ''
> + test -n bibtex
> + test -r DDIwR-manual.aux
> ++ echo ''
> ++ sed 's!.*\.aux!!g;
> s!./DDIwR-manual\.[^ ]o[^ ]!!g;
> s/^[ ]*//;s/[ ]*$//'
> + index_files=
> + test -n makeindex
> + test -n ''
> + cmd='pdflatex --file-line-error'
> + false 'Running pdflatex --file-line-error
> /Users/dusadrian/DDIwR.Rcheck/DDIwR-manual.tex ...'
> + pdflatex --file-line-error
> /Users/dusadrian/DDIwR.Rcheck/DDIwR-manual.tex
> This is pdfTeX, Version 3.14159265-2.6-1.40.15 (TeX Live 2014)
> (preloaded
> format=pdflatex)
> restricted \write18 enabled.
> entering extended mode
> (/Users/dusadrian/DDIwR.Rcheck/DDIwR-manual.tex
> LaTeX2e <2014/05/01>
> Babel <3.9k> and hyphenation patterns for 78 languages loaded.
>
> (/usr/local/texlive/2014/texmf-dist/tex/latex/base/book.cls
> Document Class: book 2007/10/19 v1.4h Standard LaTeX document class
> (/usr/local/texlive/2014/texmf-dist/tex/latex/base/bk10.clo))
>
> ! LaTeX Error: File `Rd.sty' not found.
>
> Type X to quit or <RETURN> to proceed,
> or enter new name. (Default extension: sty)
>
> Enter file name:
> /Users/dusadrian/DDIwR.Rcheck/DDIwR-manual.tex:4: Emergency stop.
> <read *>
>
> l.4 \usepackage
> {makeidx}^^M
> /Users/dusadrian/DDIwR.Rcheck/DDIwR-manual.tex:4: ==> Fatal error
> occurred, no
> output PDF file produced!
> Transcript written on DDIwR-manual.log.
> + echo '/usr/bin/texi2dvi: pdflatex exited with bad status, quitting.'
> /usr/bin/texi2dvi: pdflatex exited with bad status, quitting.
> + echo '/usr/bin/texi2dvi: see DDIwR-manual.log for errors.'
> /usr/bin/texi2dvi: see DDIwR-manual.log for errors.
> + test '' = t
> + exit 1
> ###
>
>
> This sends me to DDIwR-manual.log, which as far as I can see is
> related to
> not being able to \read from terminal in nonstop modes:
>
> ###
> /Users/dusadrian/DDIwR.Rcheck/DDIwR-manual.tex:4: Emergency stop.
> <read *>
>
> l.4 \usepackage
> {makeidx}^^M
> *** (cannot \read from terminal in nonstop modes)
> ###
>
> Any further advice is welcome, thank you very much again,
> Adrian
>
>
> --
> Adrian Dusa
> University of Bucharest
> Romanian Social Data Archive
> Soseaua Panduri nr.90
> 050663 Bucharest sector 5
> Romania
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
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>
--
Brian D. Ripley, ripley at stats.ox.ac.uk
Emeritus Professor of Applied Statistics, University of Oxford
1 South Parks Road, Oxford OX1 3TG, UK
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