• using R version 4.5.0 beta (2025-03-29 r88069)
  • using platform: aarch64-apple-darwin20
  • R was compiled by     Apple clang version 14.0.0 (clang-1400.0.29.202)     GNU Fortran (GCC) 14.2.0
  • running under: macOS Ventura 13.4
  • using session charset: UTF-8
  • checking for file ‘lolR/DESCRIPTION’ ... OK
  • checking extension type ... Package
  • this is package ‘lolR’ version ‘2.1’
  • package encoding: UTF-8
  • 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 executable files ... OK
  • checking for hidden files and directories ... OK
  • checking for portable file names ... OK
  • checking for sufficient/correct file permissions ... OK
  • checking whether package ‘lolR’ can be installed ... [3s/6s] OK See the install log for details.
  • checking installed package size ... OK
  • checking package directory ... 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 ... [1s/1s] OK
  • checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
  • checking whether the package can be unloaded cleanly ... [1s/1s] OK
  • checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
  • checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
  • checking loading without being on the library search path ... [1s/1s] 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 ... [3s/4s] OK
  • checking Rd files ... [0s/0s] NOTE checkRd: (-1) lol.project.lrlda.Rd:18: Lost braces in \itemize; meant \describe ? checkRd: (-1) lol.project.lrlda.Rd:19: Lost braces in \itemize; meant \describe ? checkRd: (-1) lol.project.lrlda.Rd:20: Lost braces in \itemize; meant \describe ? checkRd: (-1) lol.project.lrlda.Rd:21: Lost braces in \itemize; meant \describe ? checkRd: (-1) lol.project.lrlda.Rd:22: Lost braces in \itemize; meant \describe ? checkRd: (-1) lol.project.pca.Rd:16: Lost braces in \itemize; meant \describe ? checkRd: (-1) lol.project.pca.Rd:17: Lost braces in \itemize; meant \describe ? checkRd: (-1) lol.project.pca.Rd:18: Lost braces in \itemize; meant \describe ? checkRd: (-1) lol.project.pca.Rd:19: Lost braces in \itemize; meant \describe ? checkRd: (-1) lol.project.pca.Rd:20: Lost braces in \itemize; meant \describe ? checkRd: (-1) lol.sims.fat_tails.Rd:25: Lost braces; missing escapes or markup?     25 | \item{f}{the fatness scaling of the tail. S2 = f*S1, where S1_{ij} = rho if i != j, and 1 if i == j. Defaults to \code{15}.}        | ^ checkRd: (-1) lol.sims.mean_diff.Rd:36: Lost braces; missing escapes or markup?     36 | \item{s}{the scaling parameter of the covariance matrix. S_{ij} = scaling*1 if i == j, or scaling*offdiag if i != j. Defaults to \code{1}.}        | ^ checkRd: (-1) lol.utils.decomp.Rd:21: Lost braces in \itemize; meant \describe ? checkRd: (-1) lol.utils.decomp.Rd:22: Lost braces in \itemize; meant \describe ? checkRd: (-1) lol.utils.decomp.Rd:23: Lost braces in \itemize; meant \describe ? checkRd: (-1) lol.utils.decomp.Rd:24: Lost braces in \itemize; meant \describe ? checkRd: (-1) lol.utils.decomp.Rd:25: Lost braces in \itemize; meant \describe ? checkRd: (-1) lol.xval.eval.Rd:31: Lost braces; missing escapes or markup?     31 | \item{alg}{the algorithm to use for embedding. Should be a function that accepts inputs \code{X}, \code{Y}, and has a parameter for \code{alg.dimname} if \code{alg} is supervised, or just \code{X} and \code{alg.dimname} if \code{alg} is unsupervised.This algorithm should return a list containing a matrix that embeds from {d} to {r <= d} dimensions.}        | ^ checkRd: (-1) lol.xval.eval.Rd:31: Lost braces; missing escapes or markup?     31 | \item{alg}{the algorithm to use for embedding. Should be a function that accepts inputs \code{X}, \code{Y}, and has a parameter for \code{alg.dimname} if \code{alg} is supervised, or just \code{X} and \code{alg.dimname} if \code{alg} is unsupervised.This algorithm should return a list containing a matrix that embeds from {d} to {r <= d} dimensions.}        | ^ checkRd: (-1) lol.xval.eval.Rd:68: Lost braces     68 | \item{if ]code{rank.low == TRUE}, users cross-validation method with \code{ntrain = min((k-1)/k*n, d)} sample training sets, where \code{d} is the number of dimensions in \code{X}. This ensures that the training data is always low-rank, \code{ntrain < d + 1}. Note that the resulting training sets may have \code{ntrain < (k-1)/k*n}, but the resulting testing sets will always be properly rotated \code{ntest = n/k} to ensure no dependencies in fold-wise testing.}        | ^ checkRd: (-1) lol.xval.optimal_dimselect.Rd:32: Lost braces; missing escapes or markup?     32 | \item{alg}{the algorithm to use for embedding. Should be a function that accepts inputs \code{X} and \code{Y} and embedding dimension \code{r} if \code{alg} is supervised, or just \code{X} and embedding dimension \code{r} if \code{alg} is unsupervised.This algorithm should return a list containing a matrix that embeds from {d} to {r < d} dimensions.}        | ^ checkRd: (-1) lol.xval.optimal_dimselect.Rd:32: Lost braces; missing escapes or markup?     32 | \item{alg}{the algorithm to use for embedding. Should be a function that accepts inputs \code{X} and \code{Y} and embedding dimension \code{r} if \code{alg} is supervised, or just \code{X} and embedding dimension \code{r} if \code{alg} is unsupervised.This algorithm should return a list containing a matrix that embeds from {d} to {r < d} dimensions.}        | ^ checkRd: (-1) lol.xval.optimal_dimselect.Rd:75: Lost braces     75 | \item{if ]code{rank.low == TRUE}, users cross-validation method with \code{ntrain = min((k-1)/k*n, d)} sample training sets, where \code{d} is the number of dimensions in \code{X}. This ensures that the training data is always low-rank, \code{ntrain < d + 1}. Note that the resulting training sets may have \code{ntrain < (k-1)/k*n}, but the resulting testing sets will always be properly rotated \code{ntest = n/k} to ensure no dependencies in fold-wise testing.}        | ^ checkRd: (-1) predict.nearestCentroid.Rd:12: Lost braces in \itemize; meant \describe ? checkRd: (-1) predict.nearestCentroid.Rd:13: Lost braces in \itemize; meant \describe ? checkRd: (-1) predict.nearestCentroid.Rd:14: Lost braces in \itemize; meant \describe ? checkRd: (-1) predict.randomChance.Rd:12: Lost braces in \itemize; meant \describe ? checkRd: (-1) predict.randomChance.Rd:13: Lost braces in \itemize; meant \describe ? checkRd: (-1) predict.randomGuess.Rd:12: Lost braces in \itemize; meant \describe ? checkRd: (-1) predict.randomGuess.Rd:13: Lost braces in \itemize; meant \describe ?
  • checking Rd metadata ... 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 LazyData ... INFO   'LazyData' is specified without a 'data' directory
  • checking installed files from ‘inst/doc’ ... OK
  • checking files in ‘vignettes’ ... OK
  • checking examples ... [3s/4s] OK
  • checking for unstated dependencies in ‘tests’ ... OK
  • checking tests ... [5s/7s] OK   Running ‘testthat.R’ [5s/7s]
  • checking for unstated dependencies in vignettes ... OK
  • checking package vignettes ... OK
  • checking re-building of vignette outputs ... [51s/80s] OK
  • checking PDF version of manual ... [6s/7s] OK
  • DONE Status: 1 NOTE
  • using check arguments '--no-clean-on-error '