Hi,

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:
[1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252   
[3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C                           
[5] LC_TIME=English_United Kingdom.1252    

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

other attached packages:
[1] stringr_1.2.0        seqinr_3.4-5         BiocInstaller_1.28.0 msa_1.8.0            Biostrings_2.44.1   
[6] 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

Seems like a LaTeX error. I see two possible sources: (1) There is a problem with your TeX system. (2) The LaTeX code created by msaPrettyPrint() cannot be processed successfully. This can happen if the alignment is too large. 101 sequences seems problematic to me, since 101 is more than the number of rows/lines that fit on one page. 

In any case, I suggest you write your LaTeX code to a .tex file (like in your second example) and try to process the file by running the 'pdflatex' command on the command line. What errors are produced exactly? 

Moreover, you can try to run msaPrettyPrint() on a subset of sequences and see whether this works. I suggest you start with no more than 30 sequences and then gradually increase the number of sequences.