Luigi Marongiu
2020-May-28 07:06 UTC
[R] How to use msaPrettyPrint in memory efficient mode?
Hello,
I have an alignment made with the package MSA. I installed latex on my
ubuntu machine with
`sudo apt-get install texlive-full` but I could not find the package
texshade that is mentioned in the MSA's manual.
When I run msaPrettyPrint I get:
```
Multiple alignment written to temporary file
/tmp/RtmpmW9Nnm/seq12f4d6e21e744.fasta
File aln.tex created
This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian)
(preloaded format=pdflatex)
restricted \write18 enabled.
entering extended mode
(./aln.tex
LaTeX2e <2020-02-02> patch level 2
L3 programming layer <2020-02-14>
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2019/12/20 v1.4l Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))
(/home/gigiux/R/x86_64-pc-linux-gnu-library/4.0/msa/tex/texshade.sty
Package `texshade', Version 1.24 of 2011/12/01.
(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/dvips.def)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/dvipsnam.def))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty)))
(/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdfmode.def)
No file aln.aux.
(/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))
(/tmp/RtmpmW9Nnm/seq12f4d6e21e744.fasta:
! TeX capacity exceeded, sorry [save size=80000].
\inf@@get ...@ {#5} \else \def \fourth@ {99999999}
\fi \fi \def \fifth@ {#5}...
l.25 ...e}{/tmp/RtmpmW9Nnm/seq12f4d6e21e744.fasta}
! ==> Fatal error occurred, no output PDF file produced!
Transcript written on aln.log.
Error in texi2dvi(texfile, quiet = !verbose, pdf = identical(output,
"pdf"), :
unable to run pdflatex on 'aln.tex'
LaTeX errors:
! TeX capacity exceeded, sorry [save size=80000].
\inf@@get ...@ {#5} \else \def \fourth@ {99999999}
\fi \fi \def \fifth@ {#5}...
l.25 ...e}{/tmp/RtmpmW9Nnm/seq12f4d6e21e744.fasta}
! ==> Fatal error occurred, no output PDF file produced!
>
```
Looks like texshade has been installed but there is a problem with
memory. How can I set the memory limit for msaPrettyPrint?
--
Best regards,
Luigi