diff --git a/DESCRIPTION b/DESCRIPTION index 153fb4f3..88ebf42d 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: familiar Title: End-to-End Automated Machine Learning and Model Evaluation -Version: 1.4.5 +Version: 1.4.6 Authors@R: c( person("Alex", "Zwanenburg", email = "alexander.zwanenburg@nct-dresden.de", diff --git a/NEWS.md b/NEWS.md index 89768cba..7dd0fc25 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,9 @@ +# Version 1.4.6 (Talented Toad) + +## Bug fixes + +- Fixes unused arguments appearing in documentation. + # Version 1.4.5 (Reminiscing Rat) ## Bug fixes diff --git a/R/FamiliarDataComputationVimp.R b/R/FamiliarDataComputationVimp.R index 677c4427..b2ade171 100644 --- a/R/FamiliarDataComputationVimp.R +++ b/R/FamiliarDataComputationVimp.R @@ -20,10 +20,6 @@ setClass("familiarDataElementVimpData", #'@description Aggregate variable importance from models in a #' `familiarEnsemble`. #' -#'@param feature_similarity_table Table containing pairwise distance between -#' features. This is used to determine cluster information, and indicate -#' co-clustered important features. The table is created by the -#' `extract_feature_similarity` method. #'@inheritParams extract_data #' #'@return A list containing variable importance information. diff --git a/R/Iterations.R b/R/Iterations.R index 7e7c6af7..4aaf6e75 100644 --- a/R/Iterations.R +++ b/R/Iterations.R @@ -1,6 +1,6 @@ #' Internal function for creating or retrieving iteration data #' -#' @param file_dir Path to directory where iteration files are stored. +#' @param file_paths Set of paths to relevant files and directories. #' @param data Data set as loaded using the `.load_data` function. #' @param experiment_setup data.table with subsampler information at different #' levels of the experimental design. diff --git a/R/LearnerMain.R b/R/LearnerMain.R index 18db880d..4320b18d 100644 --- a/R/LearnerMain.R +++ b/R/LearnerMain.R @@ -226,10 +226,6 @@ setMethod("promote_learner", signature(object="familiarModel"), #' #' @param data_obj dataObject class object which contains the data on which the #' preset parameters are determined. -#' @param outcome_type Type of oucome. Default settings are determined, among -#' others by the the outcome type. For example, one default signature size -#' depends on the number of events for `survival` outcomes, based on rules of -#' thumb. #' @param restrict_samples Logical indicating whether the signature size should #' be limited by the number of samples in addition to the number of available #' features. This may help convergence of OLS-based methods. diff --git a/cran-comments.md b/cran-comments.md index b384e2c5..b2d41bb2 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,4 +1,4 @@ -Update familiar to version 1.4.1 +Update familiar to version 1.4.6 Vignettes are pre-compiled to avoid long compilation times on build (several minutes). @@ -12,22 +12,28 @@ R CMD check was run on R-hub using rhub::check_for_cran(), producing the followi ---------------------------------- Windows Server 2022, R-devel, 64 bit: -0 errors | 0 warnings | 3 notes +0 errors | 0 warnings | 4 notes * checking installed package size ... NOTE installed size is 5.8Mb sub-directories of 1Mb or more: R 3.5Mb doc 1.0Mb - help 1.1Mb + help 1.2Mb -**Maintainer**: The size of the R-directory is due to source code. Addressing the size of the R directory would require creating a set of mutually dependent packages. This would likely result in a larger footprint across the packages. +**Maintainer**: The size of the R-directory is due to source code. Addressing the size of the R directory would require creating a set of mutually dependent packages. This would likely result in a larger footprint across the packages. -* checking HTML version of manual ... [37s] NOTE +* checking HTML version of manual ... [39s] NOTE Skipping checking math rendering: package 'V8' unavailable **Maintainer**: I am not sure what the cause is, but it might be because the V8 package was not available on rhub. - + +* checking for non-standard things in the check directory ... NOTE +Found the following files/directories: + ''NULL'' + +**Maintainer**: I am not sure what the cause is. However, NULL is not present as a directory or file. + * checking for detritus in the temp directory ... NOTE Found the following files/directories: 'lastMiKTeXException' @@ -35,28 +41,17 @@ Found the following files/directories: **Maintainer**: This note only appeared on the Windows server test. It didn't appear locally (Windows 10) or the other builds. + ---------------------------------- Fedora Linux, R-devel, clang, gfortran: -0 errors | 0 warnings | 3 notes - -* checking package dependencies ... NOTE -Packages suggested but not available for checking: 'fastglm' - -**Maintainer**: The package uses stats::glm as a fallback if fastglm is not available. +0 errors | 0 warnings | 1 notes * checking installed package size ... NOTE installed size is 5.8Mb sub-directories of 1Mb or more: R 3.5Mb doc 1.0Mb - help 1.1Mb - -* checking HTML version of manual ... NOTE -Skipping checking HTML validation: no command 'tidy' found -Skipping checking math rendering: package 'V8' unavailable - - -**Maintainer**: I am unsure what causes this note. It doesn't appear locally. + help 1.2Mb @@ -67,10 +62,9 @@ Ubuntu Linux 20.04.1 LTS, R-release, GCC: * checking installed package size ... NOTE installed size is 5.9Mb sub-directories of 1Mb or more: - R 3.5Mb doc 1.0Mb - help 1.2Mb - + help 1.1Mb + R 3.6Mb diff --git a/inst/CITATION b/inst/CITATION index b5b9b597..3ec94c5d 100644 --- a/inst/CITATION +++ b/inst/CITATION @@ -1,22 +1,19 @@ -citHeader("To cite the \"familiar\" package in publications, please use:") - -citEntry(entry = "Misc", - title = paste0(meta$Package, ": ", meta$Title), - author = c(person("Alex", "Zwanenburg"), - person("Steffen", "Löck")), - year = 2021, - url = "https://github.com/alexzwanenburg/familiar", - textVersion = paste0("Alex Zwanenburg and Steffen Löck. ", - paste0(meta$Package, ": ", meta$Title), " (2021). ", - "https://github.com/alexzwanenburg/familiar") +bibentry( + bibtype = "Misc", + title = paste0(meta$Package, ": ", meta$Title), + author = c( + person("Alex", "Zwanenburg"), + person("Steffen", "Löck") + ), + year = 2021, + url = "https://github.com/alexzwanenburg/familiar" ) -citEntry(entry = "Manual", - header = "If you cite the manual, vignettes or other part of the documentation, please use:", - title = "familiar: Vignettes and Documentation", - author = c(person("Alex", "Zwanenburg")), - year = 2021, - url = "https://github.com/alexzwanenburg/familiar", - textVersion = paste0("Alex Zwanenburg. ", - "familiar: Vignettes and Documentation (2021). ", - "https://github.com/alexzwanenburg/familiar")) +bibentry( + bibtype = "Manual", + header = "If you cite the manual, vignettes or other part of the documentation, please use:", + title = "familiar: Vignettes and Documentation", + author = c(person("Alex", "Zwanenburg")), + year = 2021, + url = "https://github.com/alexzwanenburg/familiar", +)