Hello, I am trying to load a fast file with the package 'openPrimeR'. The manual (https://www.bioconductor.org/packages/release/bioc/vignettes/openPrimeR/inst/doc/openPrimeR_vignette.html) says to use:

fasta.file <- system.file("extdata", "IMGT_data", "templates",
                "Homo_sapiens_IGH_functional_exon.fasta", package =
"openPrimeR")
# Load the template sequences from 'fasta.file'
seq.df.simple <- read_templates(fasta.file)

but if I give these commands to a local file:

fasta.file <- system.file("extdata", "IMGT_data", "templates",
                "stx.fa", package = "openPrimeR")
fasta.file <- system.file("stx.fa", package = "openPrimeR")

where stx.fa il the file I wanted to open and that is present in the working directly. I get only an empty object. What am I getting wrong? Thank you

sessionInfo( )

R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library("openPrimeR")
There are missing/non-functioning external tools.
To use the full potential of openPrimeR, please make sure
that the required versions of the speciied tools are

                installed and that they are functional:
o MELTING (http://www.ebi.ac.uk/biomodels/tools/melting/)
o ViennaRNA (http://www.tbi.univie.ac.at/RNA/)
o OligoArrayAux (http://unafold.rna.albany.edu/OligoArrayAux.php)
o MAFFT (http://mafft.cbrc.jp/alignment/software/)
o Pandoc (http://pandoc.org)
Warning messages:
1: In fun(libname, pkgname) :
  'Pandoc' is non-functional, since 'pdflatex' is not installed on your system.
2: In parallel_setup(default.nbr.cores) :
  Please install 'doParallel' to use multiple cores.
> fasta.file <- system.file("/home/gigiux/Documents/PCR_Book/stx.fa", package = "openPrimeR")
> fasta.file
[1] ""
> sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.2 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
LC_TIME=en_GB.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_US.UTF-8
LC_PAPER=en_GB.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] openPrimeR_1.12.1

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.6              plyr_1.8.6              pillar_1.4.7
      compiler_4.0.3
 [5] RColorBrewer_1.1-2      GenomeInfoDb_1.26.2     XVector_0.30.0
      bitops_1.0-6
 [9] iterators_1.0.13        tools_4.0.3             zlibbioc_1.36.0
      lifecycle_1.0.0
[13] tibble_3.0.6            gtable_0.3.0            pkgconfig_2.0.3
      rlang_0.4.10
[17] foreach_1.5.1           rstudioapi_0.13         parallel_4.0.3
      GenomeInfoDbData_1.2.4
[21] stringr_1.4.0           dplyr_1.0.4             Biostrings_2.58.0
      generics_0.1.0
[25] S4Vectors_0.28.1        vctrs_0.3.6             IRanges_2.24.1
      stats4_4.0.3
[29] grid_4.0.3              tidyselect_1.1.0        glue_1.4.2
      R6_2.5.0
[33] reshape2_1.4.4          ggplot2_3.3.3           purrr_0.3.4
      magrittr_2.0.1
[37] scales_1.1.1            codetools_0.2-18        ellipsis_0.3.1
      BiocGenerics_0.36.0
[41] GenomicRanges_1.42.0    colorspace_2.0-0        stringi_1.5.3
      lpSolveAPI_5.5.2.0-17.7
[45] RCurl_1.98-1.2          munsell_0.5.0           crayon_1.4.1

When a package author wants to show how to do something that uses data provided in the package, the author has to be able to figure out where the data in the package exists on an arbitrary install (like yours) that the author can't have any a priori knowledge about. The system.file function is a way to do that, and is essentially asking R to provide the path to the library installation directory on your system.

But you as an end user should never need to use system.file to load up your own data! You already know where the data are, and in general they should be in your working directory (e.g., where you started R). So you can skip that first step and go right to the second, doing something like

seq.df.simple <- read_templates("styx.fa")