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 <[email protected] <mailto:[email protected]>> wrote: On Sat, Mar 21, 2015 at 3:09 PM, Prof Brian Ripley <[email protected] <mailto:[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] <mailto:[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] <mailto:[email protected]> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
-- Brian D. Ripley, [email protected] Emeritus Professor of Applied Statistics, University of Oxford 1 South Parks Road, Oxford OX1 3TG, UK _______________________________________________ R-SIG-Mac mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-mac
