- using R Under development (unstable) (2024-11-22 r87365)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
clang version 19.1.3
flang-new version 19.1.3
- running under: Fedora Linux 36 (Workstation Edition)
- using session charset: UTF-8
- using option ‘--no-stop-on-test-error’
- 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 ... [16s/35s] 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 ... 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 ... NOTE
Namespace in Imports field not imported from: ‘ggplot2’
All declared Imports should be used.
- checking S3 generic/method consistency ... OK
- checking replacement functions ... OK
- checking foreign function calls ... OK
- checking R code for possible problems ... [23s/62s] OK
- checking Rd files ... 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 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 LazyData ... INFO
'LazyData' is specified without a 'data' directory
- checking installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... [15s/43s] OK
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [23s/62s] OK
Running ‘testthat.R’ [23s/60s]
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [206s/571s] OK
- checking PDF version of manual ... [12s/45s] OK
- checking HTML version of manual ... [3s/15s] OK
- checking for non-standard things in the check directory ... OK
- checking for detritus in the temp directory ... OK
- DONE
Status: 2 NOTEs