Comments (2)
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.
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)
- Problem with "N" using echodata::construct_colmaps HOT 2
- Problem with "N" using munged data HOT 8
- ABF fails when running for a qt trait -- proportion_cases is missing
- MAF cannot be inferred HOT 3
- finemap_loci fails using echodata::construct_colmaps if some parameters are set to NULL HOT 1
- Column names in topSNPs do not agree with co HOT 2
- Installation Errors HOT 3
- Conda Install Link Not Found HOT 1
- Conditional SNP error HOT 7
- Problems with echolocatoR::finemap_loci HOT 9
- Update documentation website
- GHA Docker: ` API rate limit exceeded` HOT 6
- vignettes causing errors in GHA (but not locally) HOT 4
- Incorporating POLYFUN HOT 2
- ModuleNotFoundError: No module named 'scipy'
- Singularity image fail to start HOT 5
- Can echolocatoR support co-localization analysis between GWAS-GWAS? HOT 1
- A valid target path could not be found HOT 5
- Error at step 1: compression in fwrite uses zlib library
- Functionnal fine-mapping
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from echolocator.