msaprettyprint
0
0
Entering edit mode
SB775 • 0
@df68b2cf
Last seen 5 months ago
United Kingdom

Hi, Hope you can help. I'm trying as a test to run msaprettyprint in RStudio with the test data and example in the help menu. I can't seem to create a pdf even though tinytex is installed, error is unable to pdflatex. The tempfile step also seems to need the absolute path - placing the "." means it can't find the file. Any help would be great thanks.

Code should be placed in three backticks as shown below

> tmpFile <- tempfile(pattern="msa",tmpdir="C:\\Users\\b\\Documents\\IGHV",fileext=".pdf")
> tmpFile

> msaPrettyPrint(myFirstAlignment, file=tmpFile, output="pdf",showNames="left", 
+                showLogo="top",showConsensus = "bottom",logoColors = "rasmol",
+                verbose=FALSE,askForOverwrite=FALSE)

[1] "C:\Users\b\Documents\IGHV\msa1c3c59e851b0.pdf"

Error in texi2dvi(texfile, quiet = !verbose, pdf = identical(output, "pdf"), : unable to run pdflatex on 'C:\Users\b\Documents\IGHV\msa1c3c59e851b0.tex' LaTeX errors: !pdfTeX error: pdflatex.exe (file c:/Users/b/AppData/Roaming/TinyTeX/texmf-var/ fonts/map/pdftex/updmap/pdftex.map): fflush() failed (Bad file descriptor) ==> Fatal error occurred, no output PDF file produced!

please also include the results of running the following in an R session

sessionInfo( )

attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets methods base

other attached packages: [1] tinytex_0.31 msa_1.22.0 Biostrings_2.58.0 XVector_0.30.0
[5] IRanges_2.24.1 S4Vectors_0.28.1 BiocGenerics_0.36.1

loaded via a namespace (and not attached): [1] Rcpp_1.0.6 digest_0.6.27 crayon_1.4.1 evaluate_0.14
[5] rlang_0.4.11 zlibbioc_1.36.0 rmarkdown_2.8 tools_4.0.5
[9] xfun_0.23 yaml_2.2.1 compiler_4.0.5 BiocManager_1.30.15 [13] htmltools_0.5.1.1 knitr_1.33

```

msa prettyprint • 180 views
ADD COMMENT
0
Entering edit mode

Hmm, seems like a LaTeX issue, although I am not absolutely sure. The paths (about which LaTeX is quite picky on Windows systems) seem to be ok, too. Can you test the following:

  • Can you compile the LaTeX file (C:\Users\b\Documents\IGHV\msa1c3c59e851b0.tex) outside of R?
  • Can you compile other LaTeX files inside R using texi2dvi()?
ADD REPLY

Login before adding your answer.

Traffic: 319 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6