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Installation

Source: vignettes/articles/manual-00-installation.Rmd
manual-00-installation.Rmd

Manual

Requirements

  • Operating system: Windows, macOS, or Linux.
  • R: version 4.1 or newer, from CRAN.
  • R Editor (recommended): RStudio or Positron.
  • Quarto: bundled with recent RStudio and Positron releases; otherwise install it from quarto.org. Required only for rendering notebooks.

Installing and updating MRMhub

Important. Quit and reopen all RStudio/Positron sessions first. Many installation issues are caused by R packages that are loaded in another session while the installer tries to update them.

In a fresh R session, we recommend installing with pak:

if (!require("pak")) install.packages("pak")
pak::pak("SLINGhub/MRMhub")

To update MRMhub later, re-run the same command in a fresh session.

If pak fails, e.g. due to institutional network firewall or proxy settings, try remotes instead:

if (!require("remotes")) install.packages("remotes")
remotes::install_github("SLINGhub/MRMhub")

If installation fails, see the ZIP-file method below or Troubleshooting.

Installing from a downloaded repository ZIP file

If the methods above fail or R cannot reach GitHub, download a copy of the repository and install MRMhub from it:

  1. Open https://github.com/SLINGhub/MRMhub in a browser.
  2. Click the green Code button and choose Download ZIP (or download https://github.com/SLINGhub/MRMhub/archive/refs/heads/main.zip directly).
  3. Unzip the file. It expands to a folder named MRMhub-main.
  4. In a fresh R session, install from that folder with pak:
pak::local_install("path/to/MRMhub-main")

Replace path/to/MRMhub-main with the actual location of the unzipped folder, e.g. "~/Downloads/MRMhub-main".

Confirm mrmhub is successfully installed

If this loads without error, you are ready to go. If you plan to use any of the functions listed under Optional packages below, install those too. If it loads with errors, see Troubleshooting below.

Optional packages

To keep the base installation light, a number of specialised functions in mrmhub rely on additional packages that are not installed upfront. When such a function is called and its package is not yet installed, mrmhub offers to install it.

Function Optional package Enables
plot_runscatter() qpdf; mirai, carrier only for multi-threaded PDF output
plot_qc_summary_overall(with_venn = TRUE) ggvenn, patchwork Venn diagram of features excluded by QC criteria
plot_matrixeffects(), plot_interference_correction() ggbeeswarm beeswarm/quasirandom point layers
correct_isotopic_interferences(), calc_average_molweight() enviPat isotope-pattern and molecular-weight calculation
correct_batch_combat() sva ComBat batch correction
correct_batch_serrf() ranger SERRF batch correction
correct_drift_gam() mgcv GAM-based drift correction
build_workflow() shiny, bslib interactive workflow-builder app
save_dataset_summarizedexperiment() SummarizedExperiment, S4Vectors, lipidr (Bioconductor) export to a SummarizedExperiment
Lipid-name parsing (isotope correction, lipid plots) rgoslin (Bioconductor) parse and normalise lipid shorthand
get_response_curve_stats() lancer (GitHub) only for specific response-curve metrics

To install all of them upfront, run the following in a fresh R session (again, with all other RStudio/Positron sessions closed):

pak::pak(c(
  "sva", "ranger", "mgcv", "enviPat",
  "qpdf", "mirai", "carrier", "shiny", "bslib",
  "ggvenn", "patchwork", "ggbeeswarm",
  "rgoslin", "lipidr", "SummarizedExperiment", "S4Vectors",
  "SLINGhub/lancer"
))

Alternatively, install the CRAN packages with install.packages() and the Bioconductor ones (rgoslin, lipidr, SummarizedExperiment, S4Vectors) with BiocManager::install().

Troubleshooting

If the installation seemed successful but the package does not load, or loads with errors, run check_setup() to report the R version and flag any missing dependencies:

mrmhub::check_setup()

Frequent installation errors

See Troubleshooting & FAQ for a detailed list of errors and resolutions.

Error Cause Fix
namespace 'rlang' is already loaded An old dependency is still loaded in the session Restart R (Ctrl+Shift+F10) and retry the install
pak unavailable or failing pak not installed, or its cache is stale Install with remotes::install_github("SLINGhub/MRMhub")
cannot open URL Firewall or proxy blocking GitHub options(download.file.method = "libcurl"), or install from a downloaded repository ZIP file
Could not resolve host: api.github.com Firewall or proxy blocking the GitHub API Set http_proxy/https_proxy, or install from a downloaded repository ZIP file
SSL certificate problem: self signed certificate in certificate chain Corporate proxy inspecting TLS traffic Use remotes (it uses the system certificate store), or install your organisation’s root certificate
package 'X' was installed under R version … Package built for a different R install.packages("X") to rebuild it for your R
there is no package called 'mrmhub' Install did not finish Scroll up for the real error, then retry the install
ERROR: Rtools is required (Windows) A source-only dependency needs compilation Install Rtools matching your R version, restart R, retry
clang: error: ... (macOS) Compiler tools missing Run xcode-select --install in Terminal, retry
cannot find -lcurl (Linux) System libraries missing sudo apt install libcurl4-openssl-dev libxml2-dev libssl-dev libfontconfig1-dev

Next steps