On Mar 21, 2015, at 3:10 PM, boB Rudis <[email protected]> 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 <[email protected]> wrote: > >> On Sat, Mar 21, 2015 at 3:09 PM, Prof Brian Ripley <[email protected]> >> 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 [email protected].' >> + 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]] >> >> _______________________________________________ >> R-SIG-Mac mailing list >> [email protected] >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >> > > [[alternative HTML version deleted]] > > _______________________________________________ > R-SIG-Mac mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/r-sig-mac _______________________________________________ R-SIG-Mac mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-mac
