Giter Club home page Giter Club logo

Comments (2)

bschilder avatar bschilder commented on June 2, 2024

Got a bit closer! Easiest way to enable TeX on a Macbook was to install mactex via brew (not the suggested methods in the errors above):

brew install --cask mactex

New errors

devtools::build_manual()

Very long series of output errors and warnings related to formatting of documentation. Will need to take some time to comb through each of these and get them in the correct format.

Converting Rd files to LaTeX .............................
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Rd2.tex' failed.
LaTeX errors:
! You can't use `macro parameter character #' in horizontal mode.
l.331 #
       # Not run:
? 
! Emergency stop.
! Emergency stop.
l.331 #
       # Not run:
End of file on the terminal!

!  ==> Fatal error occurred, no output PDF file produced!
Output:
This is pdfTeX, Version 3.14159265-2.6-1.40.21 (TeX Live 2020) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
LaTeX2e <2020-02-02> patch level 5
L3 programming layer <2020-03-06> (./Rd2.tex
(/usr/local/texlive/2020/texmf-dist/tex/latex/base/book.cls
Document Class: book 2019/12/20 v1.4l Standard LaTeX document class
(/usr/local/texlive/2020/texmf-dist/tex/latex/base/bk10.clo))
(/Library/Frameworks/R.framework/Resources/share/texmf/tex/latex/Rd.sty
(/usr/local/texlive/2020/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/tools/bm.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/base/alltt.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/url/url.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/base/textcomp.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/base/fontenc.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/inconsolata/zi4.sty
`inconsolata-zi4' v1.12, 2019/05/17 Text macros for Inconsolata (msharpe)
(/usr/local/texlive/2020/texmf-dist/tex/latex/xkeyval/xkeyval.sty
(/usr/local/texlive/2020/texmf-dist/tex/generic/xkeyval/xkeyval.tex
(/usr/local/texlive/2020/texmf-dist/tex/generic/xkeyval/xkvutils.tex
(/usr/local/texlive/2020/texmf-dist/tex/generic/xkeyval/keyval.tex)))))
(/usr/local/texlive/2020/texmf-dist/tex/latex/graphics/color.sty
(/usr/local/texlive/2020/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/local/texlive/2020/texmf-dist/tex/latex/graphics-def/pdftex.def))
(/usr/local/texlive/2020/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/local/texlive/2020/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty)
(/usr/local/texlive/2020/texmf-dist/tex/generic/iftex/iftex.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/pdftexcmds/pdftexcmds.sty
(/usr/local/texlive/2020/texmf-dist/tex/generic/infwarerr/infwarerr.sty))
(/usr/local/texlive/2020/texmf-dist/tex/generic/kvsetkeys/kvsetkeys.sty)
(/usr/local/texlive/2020/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty)
(/usr/local/texlive/2020/texmf-dist/tex/generic/pdfescape/pdfescape.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/hycolor/hycolor.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/auxhook/auxhook.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/kvoptions/kvoptions.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/local/texlive/2020/texmf-dist/tex/generic/intcalc/intcalc.sty)
(/usr/local/texlive/2020/texmf-dist/tex/generic/etexcmds/etexcmds.sty)
(/usr/local/texlive/2020/texmf-dist/tex/generic/bitset/bitset.sty
(/usr/local/texlive/2020/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty))
(/usr/local/texlive/2020/texmf-dist/tex/generic/atbegshi/atbegshi.sty))
(/usr/local/texlive/2020/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/local/texlive/2020/texmf-dist/tex/latex/atveryend/atveryend.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty

(/usr/local/texlive/2020/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty
)))

Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref)                setting the option has no effect on input line 377.


Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref)                setting the option has no effect on input line 377.

) (/usr/local/texlive/2020/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/base/inputenc.sty)
Writing index file Rd2.idx
(/usr/local/texlive/2020/texmf-dist/tex/latex/l3backend/l3backend-pdfmode.def)
No file Rd2.aux.
(/usr/local/texlive/2020/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/local/texlive/2020/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/local/texlive/2020/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/local/texlive/2020/texmf-dist/tex/latex/refcount/refcount.sty)
(/usr/local/texlive/2020/texmf-dist/tex/generic/gettitlestring/gettitlestring.s
ty)) (/usr/local/texlive/2020/texmf-dist/tex/latex/inconsolata/t1zi4.fd)
[1{/usr/local/texlive/2020/texmf-var/fonts/map/pdftex/updmap/pdftex.map}]
(/usr/local/texlive/2020/texmf-dist/tex/latex/psnfss/t1phv.fd

LaTeX Warning: Font shape declaration has incorrect series value `mc'.
               It should not contain an `m'! Please correct it.
               Found on input line 20.


LaTeX Warning: Font shape declaration has incorrect series value `mc'.
               It should not contain an `m'! Please correct it.
               Found on input line 23.


LaTeX Warning: Font shape declaration has incorrect series value `mc'.
               It should not contain an `m'! Please correct it.
               Found on input line 26.


LaTeX Warning: Font shape declaration has incorrect series value `mc'.
               It should not contain an `m'! Please correct it.
               Found on input line 46.

) [2] (/usr/local/texlive/2020/texmf-dist/tex/latex/psnfss/ts1ptm.fd)
Overfull \hbox (5.4502pt too wide) in paragraph at lines 155--166
[]\T1/ptm/m/n/10 Other an-no-tate: [][]\T1/zi4/m/n/10 ANNOTATE.plot_missense[][
][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SNPs_by_mutation_type[][][]()\T1/ptm/m
/n/10 , [][]\T1/zi4/m/n/10 biomart_geneInfo[][][]()\T1/ptm/m/n/10 ,

Overfull \hbox (65.84094pt too wide) in paragraph at lines 155--166
[][]\T1/zi4/m/n/10 biomart_snp_info[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 
biomart_snps_to_geneInfo[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 epigenetics
_enrichment[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 epigenetics_summary[][][
]()\T1/ptm/m/n/10 ,
[3]
Overfull \hbox (25.4502pt too wide) in paragraph at lines 199--210
[]\T1/ptm/m/n/10 Other an-no-tate: [][]\T1/zi4/m/n/10 ANNOTATE.annotate_missens
e[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SNPs_by_mutation_type[][][]()\T1/p
tm/m/n/10 , [][]\T1/zi4/m/n/10 biomart_geneInfo[][][]()\T1/ptm/m/n/10 ,

Overfull \hbox (65.84094pt too wide) in paragraph at lines 199--210
[][]\T1/zi4/m/n/10 biomart_snp_info[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 
biomart_snps_to_geneInfo[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 epigenetics
_enrichment[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 epigenetics_summary[][][
]()\T1/ptm/m/n/10 ,

Overfull \hbox (0.77168pt too wide) in paragraph at lines 217--217
 []\T1/zi4/m/n/9 gg_missense <- ANNOTATE.plot_missense(merged_DT=merged_DT, snp
_filter="Consensus_SNP==T")[] 
[4] [5]
! You can't use `macro parameter character #' in horizontal mode.
l.331 #
       # Not run:
? 
! Emergency stop.
l.331 #
       # Not run:
!  ==> Fatal error occurred, no output PDF file produced!
Transcript written on Rd2.log.
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Rd2.tex' failed.
LaTeX errors:
! You can't use `macro parameter character #' in horizontal mode.
l.331 #
       # Not run:
? 
! Emergency stop.
! Emergency stop.
l.331 #
       # Not run:
End of file on the terminal!

!  ==> Fatal error occurred, no output PDF file produced!
Output:
This is makeindex, version 2.15 [TeX Live 2020] (kpathsea + Thai support).
Scanning input file Rd2.idx....done (32 entries accepted, 0 rejected).
Sorting entries....done (164 comparisons).
Generating output file Rd2.ind....done (57 lines written, 1 warning).
Output written in Rd2.ind.
Transcript written in Rd2.ilg.
This is pdfTeX, Version 3.14159265-2.6-1.40.21 (TeX Live 2020) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
LaTeX2e <2020-02-02> patch level 5
L3 programming layer <2020-03-06> (./Rd2.tex
(/usr/local/texlive/2020/texmf-dist/tex/latex/base/book.cls
Document Class: book 2019/12/20 v1.4l Standard LaTeX document class
(/usr/local/texlive/2020/texmf-dist/tex/latex/base/bk10.clo))
(/Library/Frameworks/R.framework/Resources/share/texmf/tex/latex/Rd.sty
(/usr/local/texlive/2020/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/tools/bm.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/base/alltt.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/url/url.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/base/textcomp.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/base/fontenc.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/inconsolata/zi4.sty
`inconsolata-zi4' v1.12, 2019/05/17 Text macros for Inconsolata (msharpe)
(/usr/local/texlive/2020/texmf-dist/tex/latex/xkeyval/xkeyval.sty
(/usr/local/texlive/2020/texmf-dist/tex/generic/xkeyval/xkeyval.tex
(/usr/local/texlive/2020/texmf-dist/tex/generic/xkeyval/xkvutils.tex
(/usr/local/texlive/2020/texmf-dist/tex/generic/xkeyval/keyval.tex)))))
(/usr/local/texlive/2020/texmf-dist/tex/latex/graphics/color.sty
(/usr/local/texlive/2020/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/local/texlive/2020/texmf-dist/tex/latex/graphics-def/pdftex.def))
(/usr/local/texlive/2020/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/local/texlive/2020/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty)
(/usr/local/texlive/2020/texmf-dist/tex/generic/iftex/iftex.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/pdftexcmds/pdftexcmds.sty
(/usr/local/texlive/2020/texmf-dist/tex/generic/infwarerr/infwarerr.sty))
(/usr/local/texlive/2020/texmf-dist/tex/generic/kvsetkeys/kvsetkeys.sty)
(/usr/local/texlive/2020/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty)
(/usr/local/texlive/2020/texmf-dist/tex/generic/pdfescape/pdfescape.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/hycolor/hycolor.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/auxhook/auxhook.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/kvoptions/kvoptions.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/local/texlive/2020/texmf-dist/tex/generic/intcalc/intcalc.sty)
(/usr/local/texlive/2020/texmf-dist/tex/generic/etexcmds/etexcmds.sty)
(/usr/local/texlive/2020/texmf-dist/tex/generic/bitset/bitset.sty
(/usr/local/texlive/2020/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty))
(/usr/local/texlive/2020/texmf-dist/tex/generic/atbegshi/atbegshi.sty))
(/usr/local/texlive/2020/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/local/texlive/2020/texmf-dist/tex/latex/atveryend/atveryend.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty

(/usr/local/texlive/2020/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty
)))

Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref)                setting the option has no effect on input line 377.


Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref)                setting the option has no effect on input line 377.

) (/usr/local/texlive/2020/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/base/inputenc.sty)
Writing index file Rd2.idx
(/usr/local/texlive/2020/texmf-dist/tex/latex/l3backend/l3backend-pdfmode.def)
(./Rd2.aux) (/usr/local/texlive/2020/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/local/texlive/2020/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/local/texlive/2020/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/local/texlive/2020/texmf-dist/tex/latex/refcount/refcount.sty)
(/usr/local/texlive/2020/texmf-dist/tex/generic/gettitlestring/gettitlestring.s
ty)) (./Rd2.out) (./Rd2.out)
(/usr/local/texlive/2020/texmf-dist/tex/latex/inconsolata/t1zi4.fd) [1{/usr/loc
al/texlive/2020/texmf-var/fonts/map/pdftex/updmap/pdftex.map}]
(/usr/local/texlive/2020/texmf-dist/tex/latex/psnfss/t1phv.fd

LaTeX Warning: Font shape declaration has incorrect series value `mc'.
               It should not contain an `m'! Please correct it.
               Found on input line 20.


LaTeX Warning: Font shape declaration has incorrect series value `mc'.
               It should not contain an `m'! Please correct it.
               Found on input line 23.


LaTeX Warning: Font shape declaration has incorrect series value `mc'.
               It should not contain an `m'! Please correct it.
               Found on input line 26.


LaTeX Warning: Font shape declaration has incorrect series value `mc'.
               It should not contain an `m'! Please correct it.
               Found on input line 46.

) (./Rd2.toc) [2]
(/usr/local/texlive/2020/texmf-dist/tex/latex/psnfss/ts1ptm.fd)
Overfull \hbox (5.4502pt too wide) in paragraph at lines 155--166
[]\T1/ptm/m/n/10 Other an-no-tate: [][]\T1/zi4/m/n/10 ANNOTATE.plot_missense[][
][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SNPs_by_mutation_type[][][]()\T1/ptm/m
/n/10 , [][]\T1/zi4/m/n/10 biomart_geneInfo[][][]()\T1/ptm/m/n/10 ,

Overfull \hbox (65.84094pt too wide) in paragraph at lines 155--166
[][]\T1/zi4/m/n/10 biomart_snp_info[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 
biomart_snps_to_geneInfo[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 epigenetics
_enrichment[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 epigenetics_summary[][][
]()\T1/ptm/m/n/10 ,
[3]
Overfull \hbox (25.4502pt too wide) in paragraph at lines 199--210
[]\T1/ptm/m/n/10 Other an-no-tate: [][]\T1/zi4/m/n/10 ANNOTATE.annotate_missens
e[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SNPs_by_mutation_type[][][]()\T1/p
tm/m/n/10 , [][]\T1/zi4/m/n/10 biomart_geneInfo[][][]()\T1/ptm/m/n/10 ,

Overfull \hbox (65.84094pt too wide) in paragraph at lines 199--210
[][]\T1/zi4/m/n/10 biomart_snp_info[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 
biomart_snps_to_geneInfo[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 epigenetics
_enrichment[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 epigenetics_summary[][][
]()\T1/ptm/m/n/10 ,

Overfull \hbox (0.77168pt too wide) in paragraph at lines 217--217
 []\T1/zi4/m/n/9 gg_missense <- ANNOTATE.plot_missense(merged_DT=merged_DT, snp
_filter="Consensus_SNP==T")[] 
[4] [5]
! You can't use `macro parameter character #' in horizontal mode.
l.331 #
       # Not run:
? 
! Emergency stop.
l.331 #
       # Not run:
!  ==> Fatal error occurred, no output PDF file produced!
Transcript written on Rd2.log.
Error in running tools::texi2pdf()
Error: Failed to build manual

from echolocator.

bschilder avatar bschilder commented on June 2, 2024

Two years later....finally was able to figure out a fix for this!

brew install texlive

Documented the journey here:
https://gist.github.com/bschilder/af3960b7d7b911274198e3febae535a9

from echolocator.

Related Issues (20)

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. 📊📈🎉

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google ❤️ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.