diff --git a/R/create.R b/R/create.R index 3aab2eed..1509ed17 100644 --- a/R/create.R +++ b/R/create.R @@ -152,30 +152,30 @@ createGiottoObject <- function(expression, ## data.table vars cell_ID <- feat_ID <- NULL - ## check if all optional packages are installed - # TODO: update at the end - # TODO: extract from suggest field of DESCRIPTION - extra_packages <- c( - "scran", "MAST", "png", "tiff", "biomaRt", - "trendsceek", "multinet", "RTriangle", "FactoMineR" - ) - - pack_index <- extra_packages %in% rownames(utils::installed.packages()) - extra_installed_packages <- extra_packages[pack_index] - extra_not_installed_packages <- extra_packages[!pack_index] - - if (any(pack_index == FALSE) == TRUE) { - wrap_msg( - "Consider to install these (optional) packages to run all possible", - "Giotto commands for spatial analyses: ", - extra_not_installed_packages - ) - wrap_msg( - "Giotto does not automatically install all these packages as they", - "are not absolutely required and this reduces the number of - dependencies" - ) - } + # ## check if all optional packages are installed + # # TODO: update at the end + # # TODO: extract from suggest field of DESCRIPTION + # extra_packages <- c( + # "scran", "MAST", "png", "tiff", "biomaRt", + # "trendsceek", "multinet", "RTriangle", "FactoMineR" + # ) + # + # pack_index <- extra_packages %in% rownames(utils::installed.packages()) + # extra_installed_packages <- extra_packages[pack_index] + # extra_not_installed_packages <- extra_packages[!pack_index] + # + # if (any(pack_index == FALSE) == TRUE) { + # wrap_msg( + # "Consider to install these (optional) packages to run all possible", + # "Giotto commands for spatial analyses: ", + # extra_not_installed_packages + # ) + # wrap_msg( + # "Giotto does not automatically install all these packages as they", + # "are not absolutely required and this reduces the number of + # dependencies" + # ) + # } ## if cores is not set, then set number of cores automatically, but with