Question

msaprettyprint error in R

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Entering edit mode

liripo • 0

@liripo-24038

Last seen 3.7 years ago

msaPrettyPrint

I use msa package by Rstudio in widowns，but the msaPrettyPrint keep reporting errors. This is my code.

mySequenceFile <- system.file("examples", "exampleAA.fasta", package="msa")
mySequences <- readAAStringSet(mySequenceFile)
mySequences
myFirstAlignment <- msa(mySequences)
msaPrettyPrint(myFirstAlignment, output="pdf", showNames="none",
showLogo="none", askForOverwrite=FALSE, verbose=FALSE)

And it Error in file(con, "r") : Unable to open link so I use output = "tex",It can work well.but when I open the tex ,found the

\begin{texshade}{C:/Users/ADMINI~1/AppData/Local/Temp/Rtmpo7310M/seq114c7f3453.fasta}

I can't open this fasta file.so I have to change it look this

\begin{texshade}{C:/Users/Administrator/AppData/Local/Temp/Rtmpo7310M/seq114c7f3453.fasta}

I guess it maybe by chinese. But when I change it,I use Rstduio compile pdf.It have an error. enter image description here Is there any good solution？ This is my sessionInfo

> sessionInfo()
R version 4.0.0 (2020-04-24)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)

Matrix products: default

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.936 
[2] LC_CTYPE=Chinese (Simplified)_China.936   
[3] LC_MONETARY=Chinese (Simplified)_China.936
[4] LC_NUMERIC=C                              
[5] LC_TIME=Chinese (Simplified)_China.936    

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

other attached packages:
[1] dplyr_1.0.1         msa_1.20.0          Biostrings_2.56.0  
[4] XVector_0.28.0      IRanges_2.22.2      S4Vectors_0.26.1   
[7] BiocGenerics_0.34.0

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.4.6          rstudioapi_0.11       magrittr_1.5         
 [4] knitr_1.29            zlibbioc_1.34.0       tidyselect_1.1.0     
 [7] RcppTOML_0.1.6        R6_2.4.1              rlang_0.4.7          
[10] tools_4.0.0           xfun_0.16             ellipsis_0.3.1       
[13] htmltools_0.5.0       yaml_2.2.1            digest_0.6.25        
[16] tibble_3.0.3          lifecycle_0.2.0       crayon_1.3.4         
[19] bookdown_0.20         purrr_0.3.4           BiocManager_1.30.10.5
[22] vctrs_0.3.2           rsconnect_0.8.16      glue_1.4.1           
[25] evaluate_0.14         rmarkdown_2.3         blogdown_0.20        
[28] pillar_1.4.6          compiler_4.0.0        generics_0.0.2       
[31] pkgconfig_2.0.3

msa • 2.5k views

ADD COMMENT • link updated 3.4 years ago by UBod ▴ 290 • written 3.7 years ago by liripo • 0

score 1 · Answer 1 · 2020-08-24

1

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UBod ▴ 290

@ubodenhofer-5425

Last seen 1 day ago

University of Applied Sciences Upper Au…

If I run your code in plain R on Windows without RStudio, everything works fine. Running the same on RStudio on Windows, I can reproduce the error. If I add verbose=TRUE to the msaPrettyPrint() command, then texi2dvi() shows the entire LaTeX output and everything works fine. I have no idea what the source of the error is. It seems that texi2dvi() does not work properly on RStudio with the setting index=FALSE and quiet=TRUE. The simplest workaround is to include the option verbose=TRUE.

ADD COMMENT • link 3.7 years ago UBod ▴ 290

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I have the same problem, that is not suppresed with verbose=TRUE
It seems to be when you have a long username in Windows then tempfile() makes a short version containing ~
TeXShade then has a issue that it converts the ~ to \nobreakspace {} before trying to load the FASTA file which fails.

I worked around this by getting msaPrettyPrint() to output a tex file, then substituting ~ in that file with \string~ which stops TeXShade converting ~ in the path e.g. with

x <- readLines(fileName)
y <- gsub( "~", "\\\\string~", x )
cat(y, file=fileName, sep="\n")

then converting the corrected tex file to pdf

ADD REPLY • link 3.4 years ago Freddie ▴ 40

score 0 · Answer 2 · 2020-12-09

Unfortunately, LaTeX is a bit picky about file names and paths. It often has problems to accept file names and paths with spaces and also with some special characters or, as in your case, abbreviated Windows file names. As a quick workaround, I suggest you use the file and/or alFile arguments of msaPrettyPrint() to direct the output to directories with paths that LaTeX can handle.