In tidymass/masscleaner: Data cleaning for LC-MS based metabolomics data

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  warning = FALSE,
  message = TRUE,
  out.width = "100%"
)

Uninstall tinyTools

tinyTools has been renamed as tinytools. So please uninstall it before you install masscleaner. And don't use it any more.

1. detach it by:

detach("package:tinyTools")

1. Remove it by:

remove.packages(pkgs = "tinyTools")

1. Restart your R session.

If there are errors, ignore them.

Install masscleaner from GitLab

remotes::install_gitlab("jaspershen/masscleaner", dependencies = TRUE)

In the installation, it will ask if you want to update some packages for few times, just press enter key to skip it.

Install masscleaner from GitHub

remotes::install_github("tidymass/masscleaner", dependencies = TRUE)

In the installation, it will ask if you want to update some packages for few times, just press enter key to skip it.

If there is a error like below:

Error: Failed to install 'masscleaner' from GitHub: HTTP error 403. API rate limit exceeded for 171.66.10.237. (But here's the good news: Authenticated requests get a higher rate limit. Check out the documentation for more details.)

Try to resolve it by:

1. In you R console, type this code:

usethis::create_github_token()

It will open a page in browser, and create a "New personal access token" and copy it.


1. Then type this code:

usethis::edit_r_environ()

and then add one line like below:

GITHUB_PAT=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

The GITHUB_PAT should be yours that is created in step 1.

And then restart R session and try again.

Frequently Asked Questions

1. Can not install dependent packages raster and Cario

raster is a package in CRAN, try to install it first and then install masscleaner.

install.packages("raster")

Cario is a package in CRAN, try to install it first and then install masscleaner.

install.packages("Cairo")

Session information

sessionInfo()

tidymass/masscleaner documentation built on Sept. 4, 2023, 3:21 a.m.