[R-SIG-Mac] latex errors, Rd problems

[Simon Urbanek]

On Mar 21, 2015, at 3:10 PM, boB Rudis <bob at rudis.net> 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.
> 


Bad idea - OS X comes with an ancient texinfo version (over 10 years old, presumably for licensing reasons), but R requires a more recent version. That's why you have to use the more recent one which is what CRAN R does. As Brian pointed out if you don't want to use the one we provide you can set R_TEXI2DVICMD to whichever you prefer.

Cheers,
Simon



> 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> wrote:
> 
>> On Sat, Mar 21, 2015 at 3:09 PM, Prof Brian Ripley <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.'
>> + 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
>> 
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>> 
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> 
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