I'm trying to perform a multiple amino acid alignment (101 sequences) and then output the alignment, however, msaPrettyPrint will not give me a pdf. I've relocated the output path to one that does not use spaces (which took a while to figure out from what looked like a blank warning message), but still get problems.
msaPrettyPrint(SEC4.alignment, output="pdf", showNames="none", showLogo="none", askForOverwrite=FALSE, verbose=FALSE, file=pdf_file) msaPrettyPrint(SEC4.alignment, output="tex", showNames="none", showLogo="none", askForOverwrite=FALSE, verbose=FALSE, file=tex_file) texi2pdf(tex_file, clean=TRUE)
I've also tried the two-step procedure involving creating a Tex file (see above), and then texi2pdf (as per A: Using msa msaPrettyPrint(): saving multiple alignement fasta file), and still end up with the warning message regardless of which way I try to create the pdf:
Warning message: running command '"C:\PROGRA~1\MIKTEX~1.9\miktex\bin\x64\texify.exe" --quiet --pdf "C:/Users/Cecil/OneDrive/Documents/Cornell/SEC4alignment.tex" --max-iterations=20 -I "C:/PROGRA~1/R/R-34~1.3/share/texmf/tex/latex" -I "C:/PROGRA~1/R/R-34~1.3/share/texmf/bibtex/bst"' had status 1
From what I've tried, I can't do anything with the .tex file either, so I'm a bit stuck here. Any advice would be appreciated!
sessionInfo() R version 3.4.3 (2017-11-30) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200) Matrix products: default locale:  LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252  LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C  LC_TIME=English_United Kingdom.1252 attached base packages:  tools stats4 parallel stats graphics grDevices utils datasets methods base other attached packages:  stringr_1.2.0 seqinr_3.4-5 BiocInstaller_1.28.0 msa_1.8.0 Biostrings_2.44.1  XVector_0.16.0 IRanges_2.10.2 S4Vectors_0.14.3 BiocGenerics_0.22.0 loaded via a namespace (and not attached): Error in x[["Version"]] : subscript out of bounds In addition: Warning message: In FUN(X[[i]], ...) : DESCRIPTION file of package 'zlibbioc' is missing or broken