This function lists all the conflicts between packages in the metpath and other packages that you have loaded.

metpath_conflicts()

Value

metpath_conflicts

Details

There are four conflicts that are deliberately ignored: intersect, union, setequal, and setdiff from dplyr. These functions make the base equivalents generic, so shouldn't negatively affect any existing code.

Examples

metpath_conflicts()
#> ── Conflicts ──────────────────────────────────────────── metpath_conflicts() ──
#>  stats4::AIC()               masks stats::AIC()
#>  stats4::BIC()               masks stats::BIC()
#>  BiocGenerics::IQR()         masks stats::IQR()
#>  BiocGenerics::Position()    masks ggplot2::Position(), base::Position()
#>  S4Vectors::aggregate()      masks stats::aggregate()
#>  massdataset::apply()        masks base::apply()
#>  methods::body<-()           masks base::body<-()
#>  stats4::coef()              masks stats::coef()
#>  BiocGenerics::colMeans()    masks massdataset::colMeans(), base::colMeans()
#>  BiocGenerics::colSums()     masks massdataset::colSums(), base::colSums()
#>  MSnbase::combine()          masks Biobase::combine(), BiocGenerics::combine(), dplyr::combine()
#>  S4Vectors::complete.cases() masks stats::complete.cases()
#>  stats4::confint()           masks stats::confint()
#>  S4Vectors::cor()            masks stats::cor()
#>  S4Vectors::cov()            masks stats::cov()
#>  BiocGenerics::density()     masks stats::density()
#>  S4Vectors::end()            masks BiocGenerics::end(), stats::end()
#>  massdataset::filter()       masks dplyr::filter(), metid::filter(), metpath::filter(), stats::filter()
#>  S4Vectors::first()          masks dplyr::first()
#>  S4Vectors::head()           masks utils::head()
#>  S4Vectors::intersect()      masks BiocGenerics::intersect(), massdataset::intersect(), base::intersect()
#>  methods::kronecker()        masks base::kronecker()
#>  dplyr::lag()                masks stats::lag()
#>  stats4::logLik()            masks stats::logLik()
#>  BiocGenerics::mad()         masks stats::mad()
#>  S4Vectors::na.exclude()     masks stats::na.exclude()
#>  S4Vectors::na.omit()        masks stats::na.omit()
#>  stats4::nobs()              masks stats::nobs()
#>  stats4::profile()           masks stats::profile()
#>  Rcpp::prompt()              masks utils::prompt()
#>  BiocGenerics::relist()      masks utils::relist()
#>  S4Vectors::rename()         masks massdataset::rename(), dplyr::rename()
#>  BiocGenerics::residuals()   masks stats::residuals()
#>  BiocGenerics::rowMeans()    masks massdataset::rowMeans(), base::rowMeans()
#>  BiocGenerics::rowSums()     masks massdataset::rowSums(), base::rowSums()
#>  S4Vectors::sd()             masks BiocGenerics::sd(), stats::sd()
#>  MSnbase::smooth()           masks ProtGenerics::smooth(), stats::smooth()
#>  S4Vectors::stack()          masks utils::stack()
#>  S4Vectors::start()          masks BiocGenerics::start(), stats::start()
#>  S4Vectors::tail()           masks utils::tail()
#>  stats4::update()            masks stats::update()
#>  S4Vectors::var()            masks BiocGenerics::var(), stats::var()
#>  stats4::vcov()              masks stats::vcov()
#>  BiocGenerics::weights()     masks stats::weights()
#>  S4Vectors::window()         masks stats::window()
#>  S4Vectors::xtabs()          masks BiocGenerics::xtabs(), stats::xtabs()