Installation

In this short tutorial, we provide all the information for a successful installation of RMassBank and required programs.

Download required programs

• Download latest R version for your operation system
• Download latest R Studio Desktop
• Download Open Babel 3.1.1
• Download latest Proteowizard

Installation of required programas

Installation without administrative rights possible

• Install R (you don't need administration rights).

Installation only with administrative rights (see note)

• Install R Studio (you need administration rights).
• Install Open Babel 3.1.1
• Install ProteoWizard (e.g. in path c:\pwiz)

Notes:

• If you don't have an account with administration rights for your computer, ask your administrator for help.
• If you don't have experience with R, ask a person in your group to help you locally. Unfortunately, it is not possible to support absolute R beginners.

RMassBank and package dependecies

Start your R Studio Desktop and run the following commands to install package dependencies on your R Environment.

Install the BiocManager package:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

Install the RMassBank dependencies:

BiocManager::install(c("Rcpp", "XML","rjson","S4Vectors", "digest",
"rcdk", "yaml", "mzR", "methods", "Biobase", "MSnbase", "httr",
"enviPat", "assertthat", "logger", "readJDX", "webchem",
"ChemmineR", "ChemmineOB", "R.utils", "data.table", "glue", "xcms",
"CAMERA", "RMassBankData"), update = FALSE)

After successful installation of the dependecies, install RMassBank.

BiocManager::install("RMassBank", update = FALSE)

Note: During installation and loading of the package mzR, it will complain on a incompatability with the installed Rcppversion. Just ignore this warning, this does no affect RMassBank.

FAQ

Q1: My company runs a firewall. How can connect to the CRAN and the Bioconductor servers to install / update my R packages?

A1: There are two options:

1. Download all required packages (and dependencies) from Bioconductur or CRAN.org for your operation system and install it from a local folder.
2. Get the URLs of the preset repositories on your computer by running getOption("repos") in R to get the current CRAN repository. The URL to Bioconductor is always https://www.bioconductor.org. R connects with wget, curl or similar technologies and thus the protocol is TCP and the port 443. These are alle information required by your administrators to make a connection available.

To use a preferred repository, you can add the repository to the install commands: BiocManager::install("package", site_repository = "url_to_repository") or install.packages("packages", repos = "url_to_repository"). Here, you can find a list of CRAN mirrors to be used as repository.

Q2: My RMassBank and/or RMassBankData is obviously not the latest version.

A2: The version of RMassBank or RMassBankData is dependent on the Bioconductor version. The version is always dependent from the R version. You can check the version by running BiocManager::version() in R. The latest version is found on Bioconductur. To update run BiocManager::install(version = version_number). Experienced users could install RMassBank also based on the GitHub main or development versions by remotes::install_github(repo = "https://github.com/MassBank/RMassBank.git", credentials = git_credentials(), branch = "main") or remotes::install_github(repo = "https://github.com/MassBank/RMassBank.git", credentials = git_credentials(), branch = "dev").