Conflicts between the massprocesser and other packages

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

massprocesser_conflicts()

Value

massprocesser_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

massprocesser_conflicts()
#> ── Conflicts ────────────────────────────────────── massprocesser_conflicts() ──
#> ✖ stats4::AIC()               masks stats::AIC()
#> ✖ stats4::BIC()               masks stats::BIC()
#> ✖ BiocGenerics::IQR()         masks stats::IQR()
#> ✖ ggplot2::Position()         masks BiocGenerics::Position(), base::Position()
#> ✖ S4Vectors::aggregate()      masks stats::aggregate()
#> ✖ MSnbase::all.equal()        masks base::all.equal()
#> ✖ massdataset::apply()        masks base::apply()
#> ✖ methods::body<-()           masks base::body<-()
#> ✖ mzR::close()                masks base::close()
#> ✖ stats4::coef()              masks stats::coef()
#> ✖ massdataset::colMeans()     masks BiocGenerics::colMeans(), base::colMeans()
#> ✖ massdataset::colSums()      masks BiocGenerics::colSums(), base::colSums()
#> ✖ dplyr::collect()            masks xcms::collect()
#> ✖ MSnbase::colnames<-()       masks S4Vectors::colnames<-(), BiocGenerics::colnames<-(), base::colnames<-()
#> ✖ dplyr::combine()            masks MSnbase::combine(), Biobase::combine(), BiocGenerics::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()
#> ✖ xcms::dirname()             masks BiocGenerics::dirname(), base::dirname()
#> ✖ S4Vectors::end()            masks BiocGenerics::end(), stats::end()
#> ✖ xcms::family()              masks stats::family()
#> ✖ massdataset::filter()       masks dplyr::filter(), stats::filter()
#> ✖ dplyr::first()              masks S4Vectors::first()
#> ✖ dplyr::groups()             masks xcms::groups()
#> ✖ S4Vectors::head()           masks utils::head()
#> ✖ xcms::image()               masks MSnbase::image(), BiocGenerics::image(), graphics::image()
#> ✖ xcms::integrate()           masks stats::integrate()
#> ✖ massdataset::intersect()    masks S4Vectors::intersect(), BiocGenerics::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()
#> ✖ xcms::plot()                masks MSnbase::plot(), stats4::plot(), graphics::plot(), base::plot()
#> ✖ stats4::profile()           masks stats::profile()
#> ✖ Rcpp::prompt()              masks utils::prompt()
#> ✖ BiocGenerics::relist()      masks utils::relist()
#> ✖ massdataset::rename()       masks dplyr::rename(), S4Vectors::rename()
#> ✖ BiocGenerics::residuals()   masks stats::residuals()
#> ✖ massdataset::rowMeans()     masks BiocGenerics::rowMeans(), base::rowMeans()
#> ✖ massdataset::rowSums()      masks BiocGenerics::rowSums(), base::rowSums()
#> ✖ MSnbase::scale()            masks base::scale()
#> ✖ S4Vectors::sd()             masks BiocGenerics::sd(), stats::sd()
#> ✖ xcms::sigma()               masks stats::sigma()
#> ✖ xcms::smooth()              masks MSnbase::smooth(), ProtGenerics::smooth(), stats::smooth()
#> ✖ xcms::split()               masks MSnbase::split(), S4Vectors::split(), base::split()
#> ✖ S4Vectors::stack()          masks utils::stack()
#> ✖ S4Vectors::start()          masks BiocGenerics::start(), stats::start()
#> ✖ xcms::subset()              masks S4Vectors::subset(), BiocGenerics::subset(), base::subset()
#> ✖ MSnbase::t()                masks S4Vectors::t(), BiocGenerics::t(), base::t()
#> ✖ S4Vectors::tail()           masks utils::tail()
#> ✖ MSnbase::trimws()           masks base::trimws()
#> ✖ 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()