* using log directory 'd:/RCompile/CRANincoming/R-devel/sgs.Rcheck' * using R Under development (unstable) (2024-07-10 r86888 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'sgs/DESCRIPTION' ... OK * this is package 'sgs' version '0.2.0' * package encoding: UTF-8 * checking CRAN incoming feasibility ... [13s] NOTE Maintainer: 'Fabio Feser ' Possibly misspelled words in DESCRIPTION: Brzyski (8:383) Evangelou (8:68, 8:548) SGS (8:52, 8:491) gSLOPE (8:374, 8:480) Found the following (possibly) invalid URLs: URL: %7Bhttps://arxiv.org/abs/2405.15357 From: inst/doc/reproducible_example.html Message: Invalid URI scheme Found the following (possibly) invalid file URIs: URI: arxiv.org/abs/2305.09467 From: inst/CITATION URI: arxiv.org/abs/2405.15357 From: inst/CITATION URI: CRAN.R-project.org/package=sgs From: inst/CITATION Found the following (possibly) invalid DOIs: DOI: 2305.09467 From: inst/CITATION Message: Invalid DOI DOI: 2405.15357 From: inst/CITATION Message: Invalid DOI The Description field contains ) models are also implemented. Please write DOIs as . The Description field contains ) models. Linear and logistic regression models are and Evangelou (2024) ) for computational speed-up. Please refer to arXiv e-prints via their arXiv DOI . The Date field is over a month old. Found the following \keyword or \concept entries which likely give several index terms: File 'as_sgs.Rd': \concept{model-selection, SGS-methods} File 'coef.sgs.Rd': \concept{SGS-methods, gSLOPE-methods} File 'fit_gslope_cv.Rd': \concept{gSLOPE-methods, model-selection} File 'fit_sgs_cv.Rd': \concept{model-selection, SGS-methods} File 'plot.sgs.Rd': \concept{SGS-methods, gSLOPE-methods} File 'predict.sgs.Rd': \concept{SGS-methods, gSLOPE-methods} File 'print.sgs.Rd': \concept{SGS-methods, gSLOPE-methods} File 'scaled_sgs.Rd': \concept{model-selection, SGS-methods} Found the following URLs which should use \doi (with the DOI name only): File 'fit_gslope.Rd': https://doi.org/10.1080/01621459.2017.1411269 File 'fit_gslope_cv.Rd': https://doi.org/10.1080/01621459.2017.1411269 File 'gen_pens.Rd': https://doi.org/10.1080/01621459.2017.1411269 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking serialization versions ... OK * checking whether package 'sgs' can be installed ... OK * used C++ compiler: 'g++.exe (GCC) 13.2.0' * checking installed package size ... OK * checking package directory ... OK * checking for future file timestamps ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [24s] OK * checking Rd files ... NOTE checkRd: (-1) fit_gslope.Rd:81: Lost braces 81 | \item{beta}{The fitted values from the regression. Taken to be the more stable fit between \code{x} and \code{z}, which is usually the former. A filter is applied to remove very small values, where ATOS has not been able to shrink exactly to zero. Check this against code{x} and \code{z}.} | ^ checkRd: (-1) fit_sgs.Rd:91: Lost braces 91 | \item{beta}{The fitted values from the regression. Taken to be the more stable fit between \code{x} and \code{z}, which is usually the former. A filter is applied to remove very small values, where ATOS has not been able to shrink exactly to zero. Check this against code{x} and \code{z}.} | ^ checkRd: (-1) gen_toy_data.Rd:35: Lost braces 35 | \item{groups}{If item{grouped=TRUE}, the grouping structure is required. Each input variable should have a group id.} | ^ checkRd: (-1) gen_toy_data.Rd:58: Lost braces 58 | \item{true_grp_id}{Indices of which groups are non-zero in item{true_beta}.} | ^ checkRd: (-1) predict.sgs.Rd:18: Lost braces 18 | item{response}{The predicted response. In the logistic case, this represents the predicted class probabilities.} | ^ checkRd: (-1) predict.sgs.Rd:18: Lost braces 18 | item{response}{The predicted response. In the logistic case, this represents the predicted class probabilities.} | ^ checkRd: (-1) predict.sgs.Rd:19: Lost braces 19 | item{class}{The predicted class assignments. Only returned if type = "logistic" in the \code{"sgs"} object.} | ^ checkRd: (-1) predict.sgs.Rd:19: Lost braces 19 | item{class}{The predicted class assignments. Only returned if type = "logistic" in the \code{"sgs"} object.} | ^ * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK * checking pragmas in C/C++ headers and code ... OK * checking compilation flags used ... OK * checking compiled code ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... [23s] OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... [52s] OK Running 'testthat.R' [52s] * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [105s] OK * checking PDF version of manual ... [21s] OK * checking HTML version of manual ... OK * DONE Status: 2 NOTEs