* using log directory ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/scpoisson.Rcheck’
* using R Under development (unstable) (2024-04-27 r86487)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 18.1.4 (1)
    Debian flang-new version 18.1.4 (1)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘scpoisson/DESCRIPTION’ ... OK
* this is package ‘scpoisson’ version ‘0.0.1’
* 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 serialization versions ... OK
* checking whether package ‘scpoisson’ can be installed ... OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-clang/scpoisson-00install.html' for details.
* 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 ... [3s/4s] OK
* checking whether the package can be loaded with stated dependencies ... [3s/3s] OK
* checking whether the package can be unloaded cleanly ... [3s/4s] OK
* checking whether the namespace can be loaded with stated dependencies ... [3s/3s] OK
* checking whether the namespace can be unloaded cleanly ... [3s/4s] OK
* checking loading without being on the library search path ... [3s/4s] 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 ... [21s/24s] OK
* checking Rd files ... [4s/4s] NOTE
checkRd: (-1) HclustDepart.Rd:23: Lost braces; missing escapes or markup?
    23 | \item{\code{res2}}: {a data frame contains two columns: names (cell names) and clusters (cluster label)}
       |                     ^
checkRd: (-1) HclustDepart.Rd:24-26: Lost braces
    24 | \item{\code{sigclust_p}}: {a matrix with cells to cluster as rows, split index as columns,
       |                           ^
checkRd: (-1) HclustDepart.Rd:27-29: Lost braces
    27 | \item{\code{sigclust_z}}: {a matrix with cells to cluster as rows, split index as columns,
       |                           ^
checkRd: (-1) LouvainDepart.Rd:38: Lost braces; missing escapes or markup?
    38 | \item{\code{sdata}}: {a Seurat object}
       |                      ^
checkRd: (-1) LouvainDepart.Rd:39-40: Lost braces
    39 | \item{\code{tsne_data}}: {a matrix containing t-SNE dimension reduction results,
       |                          ^
checkRd: (-1) LouvainDepart.Rd:41-42: Lost braces
    41 | \item{\code{umap_data}}: {a matrix containing UMAP dimension reduction results,
       |                          ^
checkRd: (-1) LouvainDepart.Rd:43: Lost braces; missing escapes or markup?
    43 | \item{\code{res_clust}}: {a data frame contains two columns: names (cell names) and clusters (cluster label)}
       |                          ^
checkRd: (-1) sigp.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{\code{p}}: {p-value for the first split}
       |                  ^
checkRd: (-1) sigp.Rd:20: Lost braces; missing escapes or markup?
    20 | \item{\code{z}}: {z-score for the first split}
       |                  ^
checkRd: (-1) sigp.Rd:21: Lost braces
    21 | \item{\code{shc_result}}: {a \code{shc} S3-object as defined in sigclust2 package}
       |                           ^
checkRd: (-1) sigp.Rd:22: Lost braces; missing escapes or markup?
    22 | \item{\code{clust2}}: {a vector with group index for each cell}
       |                       ^
checkRd: (-1) sigp.Rd:23: Lost braces; missing escapes or markup?
    23 | \item{\code{clust_dat}}: {a matrix of data representation used as input for hierarchical clustering}
       |                          ^
* 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 R/sysdata.rda ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [11s/13s] OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
LouvainDepart 7.168   0.36   8.817
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [14s/18s] OK
  Running ‘testthat.R’ [14s/18s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [401s/483s] OK
* checking PDF version of manual ... [6s/9s] OK
* checking HTML version of manual ... [1s/3s] OK
* checking for non-standard things in the check directory ... OK
* DONE
Status: 1 NOTE