This function lists all the conflicts between packages in the pseudomsir and other packages that you have loaded.
pseudomsir_conflicts()pseudomsir_conflicts
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.
pseudomsir_conflicts()
#> ── Conflicts ───────────────────────────────────────── pseudomsir_conflicts() ──
#> ✖ S4Vectors::%in%() masks BiocGenerics::%in%(), base::%in%()
#> ✖ stats4::AIC() masks stats::AIC()
#> ✖ stats4::BIC() masks stats::BIC()
#> ✖ S4Vectors::Filter() masks BiocGenerics::Filter(), base::Filter()
#> ✖ BiocGenerics::Find() masks base::Find()
#> ✖ BiocGenerics::IQR() masks stats::IQR()
#> ✖ BiocGenerics::Map() masks base::Map()
#> ✖ BiocGenerics::NCOL() masks base::NCOL()
#> ✖ BiocGenerics::NROW() masks base::NROW()
#> ✖ BiocGenerics::Position() masks base::Position()
#> ✖ S4Vectors::Reduce() masks BiocGenerics::Reduce(), base::Reduce()
#> ✖ S4Vectors::aggregate() masks stats::aggregate()
#> ✖ MSnbase::all.equal() masks base::all.equal()
#> ✖ S4Vectors::anyDuplicated() masks BiocGenerics::anyDuplicated(), base::anyDuplicated()
#> ✖ S4Vectors::append() masks BiocGenerics::append(), base::append()
#> ✖ S4Vectors::as.data.frame() masks BiocGenerics::as.data.frame(), base::as.data.frame()
#> ✖ ProtGenerics::as.list() masks S4Vectors::as.list(), BiocGenerics::as.list(), base::as.list()
#> ✖ BiocGenerics::basename() masks base::basename()
#> ✖ MSnbase::bin() masks ProtGenerics::bin()
#> ✖ BiocGenerics::boxplot() masks graphics::boxplot()
#> ✖ S4Vectors::cbind() masks BiocGenerics::cbind(), base::cbind()
#> ✖ mzR::close() masks base::close()
#> ✖ BiocGenerics::clusterApply() masks parallel::clusterApply()
#> ✖ BiocGenerics::clusterApplyLB() masks parallel::clusterApplyLB()
#> ✖ BiocGenerics::clusterCall() masks parallel::clusterCall()
#> ✖ BiocGenerics::clusterEvalQ() masks parallel::clusterEvalQ()
#> ✖ BiocGenerics::clusterExport() masks parallel::clusterExport()
#> ✖ BiocGenerics::clusterMap() masks parallel::clusterMap()
#> ✖ BiocGenerics::clusterSplit() masks parallel::clusterSplit()
#> ✖ stats4::coef() masks stats::coef()
#> ✖ BiocGenerics::colMeans() masks base::colMeans()
#> ✖ BiocGenerics::colSums() masks base::colSums()
#> ✖ S4Vectors::colnames() masks BiocGenerics::colnames(), base::colnames()
#> ✖ MSnbase::colnames<-() masks S4Vectors::colnames<-(), BiocGenerics::colnames<-(), base::colnames<-()
#> ✖ MSnbase::compareSpectra() masks ProtGenerics::compareSpectra()
#> ✖ 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()
#> ✖ BiocGenerics::dirname() masks base::dirname()
#> ✖ S4Vectors::do.call() masks BiocGenerics::do.call(), base::do.call()
#> ✖ S4Vectors::duplicated() masks BiocGenerics::duplicated(), base::duplicated()
#> ✖ S4Vectors::end() masks BiocGenerics::end(), stats::end()
#> ✖ S4Vectors::eval() masks BiocGenerics::eval(), base::eval()
#> ✖ BiocGenerics::evalq() masks base::evalq()
#> ✖ BiocGenerics::get() masks base::get()
#> ✖ S4Vectors::grep() masks BiocGenerics::grep(), base::grep()
#> ✖ S4Vectors::grepl() masks BiocGenerics::grepl(), base::grepl()
#> ✖ S4Vectors::head() masks utils::head()
#> ✖ MSnbase::image() masks BiocGenerics::image(), graphics::image()
#> ✖ S4Vectors::intersect() masks BiocGenerics::intersect(), base::intersect()
#> ✖ S4Vectors::is.unsorted() masks BiocGenerics::is.unsorted(), base::is.unsorted()
#> ✖ S4Vectors::lapply() masks BiocGenerics::lapply(), base::lapply()
#> ✖ stats4::logLik() masks stats::logLik()
#> ✖ BiocGenerics::mad() masks stats::mad()
#> ✖ BiocGenerics::mapply() masks base::mapply()
#> ✖ S4Vectors::match() masks BiocGenerics::match(), base::match()
#> ✖ BiocGenerics::mean() masks base::mean()
#> ✖ BiocGenerics::mget() masks base::mget()
#> ✖ S4Vectors::na.exclude() masks stats::na.exclude()
#> ✖ S4Vectors::na.omit() masks stats::na.omit()
#> ✖ S4Vectors::ncol() masks BiocGenerics::ncol(), base::ncol()
#> ✖ stats4::nobs() masks stats::nobs()
#> ✖ S4Vectors::nrow() masks BiocGenerics::nrow(), base::nrow()
#> ✖ S4Vectors::order() masks BiocGenerics::order(), base::order()
#> ✖ BiocGenerics::parApply() masks parallel::parApply()
#> ✖ BiocGenerics::parCapply() masks parallel::parCapply()
#> ✖ BiocGenerics::parLapply() masks parallel::parLapply()
#> ✖ BiocGenerics::parLapplyLB() masks parallel::parLapplyLB()
#> ✖ BiocGenerics::parRapply() masks parallel::parRapply()
#> ✖ BiocGenerics::parSapply() masks parallel::parSapply()
#> ✖ BiocGenerics::parSapplyLB() masks parallel::parSapplyLB()
#> ✖ BiocGenerics::paste() masks base::paste()
#> ✖ MSnbase::plot() masks stats4::plot(), graphics::plot(), base::plot()
#> ✖ BiocGenerics::pmax() masks base::pmax()
#> ✖ BiocGenerics::pmax.int() masks base::pmax.int()
#> ✖ BiocGenerics::pmin() masks base::pmin()
#> ✖ BiocGenerics::pmin.int() masks base::pmin.int()
#> ✖ stats4::profile() masks stats::profile()
#> ✖ Rcpp::prompt() masks utils::prompt()
#> ✖ S4Vectors::rank() masks BiocGenerics::rank(), base::rank()
#> ✖ S4Vectors::rbind() masks BiocGenerics::rbind(), base::rbind()
#> ✖ BiocGenerics::relist() masks utils::relist()
#> ✖ S4Vectors::rep.int() masks BiocGenerics::rep.int(), base::rep.int()
#> ✖ BiocGenerics::residuals() masks stats::residuals()
#> ✖ BiocGenerics::rowMeans() masks base::rowMeans()
#> ✖ BiocGenerics::rowSums() masks base::rowSums()
#> ✖ S4Vectors::rownames() masks BiocGenerics::rownames(), base::rownames()
#> ✖ S4Vectors::rownames<-() masks BiocGenerics::rownames<-(), base::rownames<-()
#> ✖ S4Vectors::sapply() masks BiocGenerics::sapply(), base::sapply()
#> ✖ MSnbase::scale() masks base::scale()
#> ✖ S4Vectors::sd() masks BiocGenerics::sd(), stats::sd()
#> ✖ S4Vectors::setdiff() masks BiocGenerics::setdiff(), base::setdiff()
#> ✖ MSnbase::smooth() masks ProtGenerics::smooth(), stats::smooth()
#> ✖ S4Vectors::sort() masks BiocGenerics::sort(), base::sort()
#> ✖ MSnbase::split() masks S4Vectors::split(), base::split()
#> ✖ S4Vectors::stack() masks utils::stack()
#> ✖ S4Vectors::start() masks BiocGenerics::start(), stats::start()
#> ✖ S4Vectors::subset() masks BiocGenerics::subset(), base::subset()
#> ✖ MSnbase::t() masks S4Vectors::t(), BiocGenerics::t(), base::t()
#> ✖ BiocGenerics::table() masks base::table()
#> ✖ S4Vectors::tail() masks utils::tail()
#> ✖ BiocGenerics::tapply() masks base::tapply()
#> ✖ MSnbase::trimws() masks base::trimws()
#> ✖ S4Vectors::union() masks BiocGenerics::union(), base::union()
#> ✖ S4Vectors::unique() masks BiocGenerics::unique(), base::unique()
#> ✖ BiocGenerics::unsplit() masks base::unsplit()
#> ✖ stats4::update() masks stats::update()
#> ✖ S4Vectors::var() masks BiocGenerics::var(), stats::var()
#> ✖ stats4::vcov() masks stats::vcov()
#> ✖ BiocGenerics::weights() masks stats::weights()
#> ✖ BiocGenerics::which() masks base::which()
#> ✖ BiocGenerics::which.max() masks base::which.max()
#> ✖ BiocGenerics::which.min() masks base::which.min()
#> ✖ S4Vectors::window() masks stats::window()
#> ✖ S4Vectors::xtabs() masks BiocGenerics::xtabs(), stats::xtabs()