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.
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
