Entering edit mode
SB775 • 0
Last seen 2.3 years 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/ 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 • 846 views
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()?

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