* using log directory ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/CommKern.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 ‘CommKern/DESCRIPTION’ ... OK
* this is package ‘CommKern’ version ‘1.0.1’
* 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 whether package ‘CommKern’ can be installed ... OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-clang/CommKern-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 ... [0s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [0s/0s] 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 ... [9s/11s] OK
* checking Rd files ... [1s/1s] NOTE
checkRd: (-1) count_pairs.Rd:19-20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) count_pairs.Rd:21-22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) count_pairs.Rd:23-24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) count_pairs.Rd:25-26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) count_pairs.Rd:27-28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) entropy.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) entropy.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) entropy.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) entropy.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) score_log_nonparam.Rd:36: Lost braces; missing escapes or markup?
    36 | {0, 1}.
       | ^
checkRd: (-1) score_log_semiparam.Rd:40: Lost braces; missing escapes or markup?
    40 | values in {0, 1}.
       |           ^
checkRd: (-1) sort_pairs.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sort_pairs.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sort_pairs.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sort_pairs.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sort_pairs.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sort_pairs.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
* 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 ... [0s/1s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [15s/18s] OK
Examples with CPU (user + system) or elapsed time > 5s
     user system elapsed
hms 4.358  0.052   5.386
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [14s/19s] OK
  Running ‘test-NMI.R’ [0s/1s]
  Running ‘test-adj_RI.R’ [0s/0s]
  Running ‘test-community_allegiance.R’ [0s/0s]
  Running ‘test-compute_mod_matrix.R’ [1s/1s]
  Running ‘test-compute_multimodal_mod.R’ [0s/1s]
  Running ‘test-consensus_similarity.R’ [2s/3s]
  Running ‘test-count_pairs.R’ [0s/1s]
  Running ‘test-degree.R’ [0s/1s]
  Running ‘test-entropy.R’ [0s/0s]
  Running ‘test-ext_distance.R’ [1s/2s]
  Running ‘test-ham_distance.R’ [1s/2s]
  Running ‘test-hms.R’ [0s/1s]
  Running ‘test-kernel.R’ [0s/1s]
  Running ‘test-matrix_to_df.R’ [1s/1s]
  Running ‘test-purity.R’ [0s/1s]
  Running ‘test-score_cont_nonparam.R’ [0s/1s]
  Running ‘test-score_cont_semiparam.R’ [0s/1s]
  Running ‘test-score_log_nonparam.R’ [0s/1s]
  Running ‘test-score_log_semiparam.R’ [0s/1s]
  Running ‘test-sort_pairs.R’ [0s/1s]
  Running ‘test-subset_matrix_to_df.R’ [0s/1s]
  Running ‘test-trace.R’ [0s/0s]
  Running ‘test-up_low.R’ [0s/0s]
  Running ‘test-zrand.R’ [0s/0s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [55s/67s] OK
* checking PDF version of manual ... [7s/10s] OK
* checking HTML version of manual ... [2s/3s] OK
* checking for non-standard things in the check directory ... OK
* DONE
Status: 1 NOTE