• using R version 4.5.0 alpha (2025-03-24 r88048)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-14 (Debian 14.2.0-19) 14.2.0     GNU Fortran (Debian 14.2.0-19) 14.2.0
• running under: Debian GNU/Linux trixie/sid
• using session charset: UTF-8
• checking for file ‘PCPS/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘PCPS’ version ‘1.0.7’
• 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 ‘PCPS’ can be installed ... WARNING Found the following significant warnings:   Rd warning: define.clade.Rd:31: missing link ‘makeNodeLabel’   Rd warning: define.clade.Rd:43: missing link ‘makeNodeLabel’   Rd warning: matrix.p.null.Rd:29: missing link ‘vegdist’   Rd warning: matrix.p.null.Rd:56: missing link ‘matrix.p’   Rd warning: organize.pcps.Rd:37: missing link ‘organize.syncsa’   Rd warning: organize.pcps.Rd:43: missing link ‘organize.syncsa’   Rd warning: organize.pcps.Rd:53: missing link ‘organize.syncsa’   Rd warning: organize.pcps.Rd:60: missing link ‘organize.syncsa’   Rd warning: pcoa.sig.Rd:32: missing link ‘vegdist’   Rd warning: pcoa.sig.Rd:103: missing link ‘pcoa’   Rd warning: pcoa.sig.Rd:103: missing link ‘procrustes’   Rd warning: pcps.Rd:53: missing link ‘vegdist’   Rd warning: pcps.Rd:86: missing link ‘matrix.p’   Rd warning: pcps.Rd:103: missing link ‘ordispider’   Rd warning: pcps.Rd:124: missing link ‘matrix.p’   Rd warning: pcps.Rd:124: missing link ‘wcmdscale’   Rd warning: pcps.Rd:124: missing link ‘ordispider’   Rd warning: pcps.Rd:124: missing link ‘ordilabel’   Rd warning: pcps.curve.Rd:60: missing link ‘vegdist’   Rd warning: pcps.curve.Rd:159: missing link ‘matrix.p’   Rd warning: pcps.sig.Rd:103: missing link ‘vegdist’   Rd warning: pcps.sig.Rd:112: missing link ‘vegdist’   Rd warning: pcps.sig.Rd:123: missing link ‘vegdist’   Rd warning: pcps.sig.Rd:145: missing link ‘matrix.p’   Rd warning: pcps.sig.Rd:147: missing link ‘mantel’   Rd warning: pcps.sig.Rd:147: missing link ‘adonis’   Rd warning: pcps.sig.Rd:147: missing link ‘adonis2’   Rd warning: pcps.sig.Rd:153: missing link ‘rda’   Rd warning: pcps.sig.Rd:175: missing link ‘procrustes’   Rd warning: pcps.sig.Rd:196: missing link ‘mantel’   Rd warning: pcps.sig.Rd:204: missing link ‘adonis’   Rd warning: pcps.sig.Rd:212: missing link ‘adonis2’   Rd warning: pcps.sig.Rd:215: missing link ‘adonis2’   Rd warning: pcps.sig.Rd:217: missing link ‘adonis2’   Rd warning: pcps.sig.Rd:277: missing link ‘rda’   Rd warning: pcps.sig.Rd:402: missing link ‘matrix.p’   Rd warning: pcps.sig.Rd:402: missing link ‘procrustes’   Rd warning: pcps.sig.Rd:403: missing link ‘rda’   Rd warning: pcps.sig.Rd:403: missing link ‘adonis’   Rd warning: pcps.sig.Rd:403: missing link ‘adonis2’   Rd warning: pcps.sig.Rd:404: missing link ‘mantel’   Rd warning: self.belonging.Rd:47: missing link ‘belonging’   Rd warning: wcmdscale.org.Rd:31: missing link ‘wcmdscale’   Rd warning: wcmdscale.org.Rd:32: missing link ‘vegdist’   Rd warning: wcmdscale.org.Rd:34: missing link ‘wcmdscale’   Rd warning: wcmdscale.org.Rd:13: missing link ‘vegdist’   Rd warning: wcmdscale.org.Rd:38: missing link ‘vegdist’   Rd warning: wcmdscale.org.Rd:38: missing link ‘wcmdscale’ See the install log for details.
• checking package directory ... OK
• checking for future file timestamps ... 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 ... [4s/5s] OK
• checking whether the package can be loaded with stated dependencies ... [3s/4s] OK
• checking whether the package can be unloaded cleanly ... [3s/5s] OK
• checking whether the namespace can be loaded with stated dependencies ... [3s/4s] OK
• checking whether the namespace can be unloaded cleanly ... [4s/5s] OK
• checking loading without being on the library search path ... [4s/6s] 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 ... [20s/24s] OK
• checking Rd files ... [0s/1s] OK
• checking Rd metadata ... OK
• checking Rd line widths ... OK
• checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors:   define.clade.Rd: makeNodeLabel   matrix.p.null.Rd: vegdist, matrix.p   organize.pcps.Rd: organize.syncsa   pcoa.sig.Rd: vegdist, pcoa, procrustes   pcps.Rd: vegdist, matrix.p, ordispider, wcmdscale, ordilabel   pcps.curve.Rd: vegdist, matrix.p   pcps.sig.Rd: vegdist, matrix.p, mantel, adonis, adonis2, gls, lme,     rda, procrustes, anova.gls, anova.lme   self.belonging.Rd: belonging   wcmdscale.org.Rd: wcmdscale, vegdist Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages.
• 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 examples ... [4s/5s] OK
• checking PDF version of manual ... [5s/6s] OK
• checking HTML version of manual ... [1s/1s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 WARNING, 1 NOTE