* using log directory ‘/data/gannet/ripley/R/packages/tests-devel/clustrd.Rcheck’
* using R Under development (unstable) (2025-02-14 r87716)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
    GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
* running under: Fedora Linux 40 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘clustrd/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘clustrd’ version ‘1.4.0’
* 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 ‘clustrd’ can be installed ... [34s/78s] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-gcc/clustrd-00install.html' for details.
* checking package 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 ... [8s/16s] OK
* checking whether the package can be loaded with stated dependencies ... [6s/14s] OK
* checking whether the package can be unloaded cleanly ... [7s/13s] OK
* checking whether the namespace can be loaded with stated dependencies ... [6s/13s] OK
* checking whether the namespace can be unloaded cleanly ... [7s/15s] OK
* checking loading without being on the library search path ... [7s/15s] 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 ... [55s/99s] OK
* checking Rd files ... NOTE
checkRd: (-1) global_bootclus.Rd:38: Lost braces; missing escapes or markup?
    38 | \emph{Step 1. Resampling:} Draw bootstrap samples S_i and T_i of size \emph{n} from the data and use the original data, X, as evaluation set E_i = X. Apply the clustering method of choice to S_i and T_i and obtain C^{S_i} and C^{T_i}.
       |                                                                                                                                                                                                                         ^
checkRd: (-1) global_bootclus.Rd:38: Lost braces; missing escapes or markup?
    38 | \emph{Step 1. Resampling:} Draw bootstrap samples S_i and T_i of size \emph{n} from the data and use the original data, X, as evaluation set E_i = X. Apply the clustering method of choice to S_i and T_i and obtain C^{S_i} and C^{T_i}.
       |                                                                                                                                                                                                                                     ^
checkRd: (-1) global_bootclus.Rd:40: Lost braces; missing escapes or markup?
    40 | \emph{Step 2. Mapping:} Assign each observation x_i to the closest centers of C^{S_i} and C^{T_i} using Euclidean distance, resulting in partitions C^{XS_i} and C^{XT_i}, where C^{XS_i} is the partition of the original data, X, predicted from clustering bootstrap sample S_i (same for T_i and C^{XT_i}).
       |                                                                                 ^
checkRd: (-1) global_bootclus.Rd:40: Lost braces; missing escapes or markup?
    40 | \emph{Step 2. Mapping:} Assign each observation x_i to the closest centers of C^{S_i} and C^{T_i} using Euclidean distance, resulting in partitions C^{XS_i} and C^{XT_i}, where C^{XS_i} is the partition of the original data, X, predicted from clustering bootstrap sample S_i (same for T_i and C^{XT_i}).
       |                                                                                             ^
checkRd: (-1) global_bootclus.Rd:40: Lost braces; missing escapes or markup?
    40 | \emph{Step 2. Mapping:} Assign each observation x_i to the closest centers of C^{S_i} and C^{T_i} using Euclidean distance, resulting in partitions C^{XS_i} and C^{XT_i}, where C^{XS_i} is the partition of the original data, X, predicted from clustering bootstrap sample S_i (same for T_i and C^{XT_i}).
       |                                                                                                                                                       ^
checkRd: (-1) global_bootclus.Rd:40: Lost braces; missing escapes or markup?
    40 | \emph{Step 2. Mapping:} Assign each observation x_i to the closest centers of C^{S_i} and C^{T_i} using Euclidean distance, resulting in partitions C^{XS_i} and C^{XT_i}, where C^{XS_i} is the partition of the original data, X, predicted from clustering bootstrap sample S_i (same for T_i and C^{XT_i}).
       |                                                                                                                                                                    ^
checkRd: (-1) global_bootclus.Rd:40: Lost braces; missing escapes or markup?
    40 | \emph{Step 2. Mapping:} Assign each observation x_i to the closest centers of C^{S_i} and C^{T_i} using Euclidean distance, resulting in partitions C^{XS_i} and C^{XT_i}, where C^{XS_i} is the partition of the original data, X, predicted from clustering bootstrap sample S_i (same for T_i and C^{XT_i}).
       |                                                                                                                                                                                    ^
checkRd: (-1) global_bootclus.Rd:40: Lost braces; missing escapes or markup?
    40 | \emph{Step 2. Mapping:} Assign each observation x_i to the closest centers of C^{S_i} and C^{T_i} using Euclidean distance, resulting in partitions C^{XS_i} and C^{XT_i}, where C^{XS_i} is the partition of the original data, X, predicted from clustering bootstrap sample S_i (same for T_i and C^{XT_i}).
       |                                                                                                                                                                                                                                                                                                        ^
checkRd: (-1) global_bootclus.Rd:53: Lost braces; missing escapes or markup?
    53 | \item{clust1}{Partitions, C^{XS_i} of the original data, X, predicted from clustering bootstrap sample S_i (see Details)}
       |                             ^
checkRd: (-1) global_bootclus.Rd:54: Lost braces; missing escapes or markup?
    54 | \item{clust2}{Partitions, C^{XT_i} of the original data, X, predicted from clustering bootstrap sample T_i (see Details)}
       |                             ^
checkRd: (-1) local_bootclus.Rd:37: Lost braces; missing escapes or markup?
    37 | \emph{Step 1. Resampling:} Draw bootstrap samples S_i and T_i of size n from the data and use the original data as evaluation set E_i = X. Apply a joint dimension reduction and clustering method to S_i and T_i and obtain C^{S_i} and C^{T_i}.
       |                                                                                                                                                                                                                                ^
checkRd: (-1) local_bootclus.Rd:37: Lost braces; missing escapes or markup?
    37 | \emph{Step 1. Resampling:} Draw bootstrap samples S_i and T_i of size n from the data and use the original data as evaluation set E_i = X. Apply a joint dimension reduction and clustering method to S_i and T_i and obtain C^{S_i} and C^{T_i}.
       |                                                                                                                                                                                                                                            ^
checkRd: (-1) local_bootclus.Rd:39: Lost braces; missing escapes or markup?
    39 | \emph{Step 2. Mapping}: Assign each observation x_i to the closest centers of C^{S_i} and C^{T_i} using Euclidean distance, resulting in partitions C^{XS_i} and C^{XT_i}.
       |                                                                                 ^
checkRd: (-1) local_bootclus.Rd:39: Lost braces; missing escapes or markup?
    39 | \emph{Step 2. Mapping}: Assign each observation x_i to the closest centers of C^{S_i} and C^{T_i} using Euclidean distance, resulting in partitions C^{XS_i} and C^{XT_i}.
       |                                                                                             ^
checkRd: (-1) local_bootclus.Rd:39: Lost braces; missing escapes or markup?
    39 | \emph{Step 2. Mapping}: Assign each observation x_i to the closest centers of C^{S_i} and C^{T_i} using Euclidean distance, resulting in partitions C^{XS_i} and C^{XT_i}.
       |                                                                                                                                                       ^
checkRd: (-1) local_bootclus.Rd:39: Lost braces; missing escapes or markup?
    39 | \emph{Step 2. Mapping}: Assign each observation x_i to the closest centers of C^{S_i} and C^{T_i} using Euclidean distance, resulting in partitions C^{XS_i} and C^{XT_i}.
       |                                                                                                                                                                    ^
checkRd: (-1) local_bootclus.Rd:41: Lost braces; missing escapes or markup?
    41 | \emph{Step 3. Evaluation}: Obtain the maximum Jaccard agreement between each original cluster C_k and each one of the two bootstrap clusters, C_^k'{XS_i} and C_^k'{XT_i} as measure of agreement and stability, and take the average of each pair.
       |                                                                                                                                                    ^
checkRd: (-1) local_bootclus.Rd:41: Lost braces; missing escapes or markup?
    41 | \emph{Step 3. Evaluation}: Obtain the maximum Jaccard agreement between each original cluster C_k and each one of the two bootstrap clusters, C_^k'{XS_i} and C_^k'{XT_i} as measure of agreement and stability, and take the average of each pair.
       |                                                                                                                                                                    ^
checkRd: (-1) local_bootclus.Rd:54: Lost braces; missing escapes or markup?
    54 | \item{clust1}{Partitions, C^{XS_i} of the original data, X, predicted from clustering bootstrap sample S_i (see Details)}
       |                             ^
checkRd: (-1) local_bootclus.Rd:55: Lost braces; missing escapes or markup?
    55 | \item{clust2}{Partitions, C^{XT_i} of the original data, X, predicted from clustering bootstrap sample T_i (see Details)}
       |                             ^
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... [48s/74s] OK
* checking PDF version of manual ... [7s/11s] OK
* checking HTML version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 NOTE