• using R Under development (unstable) (2026-07-31 r90332)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-16 (Debian 16.1.0-3) 16.1.0     GNU Fortran (Debian 16.1.0-3) 16.1.0
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8 * current time: 2026-08-01 16:52:31 UTC
• checking for file ‘phylospatial/DESCRIPTION’ ... OK
• this is package ‘phylospatial’ version ‘1.4.0’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [2s/2s] OK
• 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 ‘phylospatial’ can be installed ... OK See the install log 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/0s] 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 ... [5s/7s] OK
• checking Rd files ... [0s/0s] OK
• 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 installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [14s/20s] OK Examples with CPU (user + system) or elapsed time > 5s                    user system elapsed plot.phylospatial 5.635 0.045 7.954
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [51s/104s] OK   Running ‘testthat.R’ [51s/104s]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [43s/55s] OK
• checking PDF version of manual ... [5s/7s] OK
• checking HTML version of manual ... [1s/2s] OK
• checking for non-standard things in the check directory ... OK
• checking for new files in some other directories ... NOTE Found the following files/directories:   ‘~/tmp/scratch/Rtmp0EPkj6’ ‘~/tmp/scratch/Rtmp0ff3zN’   ‘~/tmp/scratch/Rtmp0ydVk1’ ‘~/tmp/scratch/Rtmp15gRip’   ‘~/tmp/scratch/Rtmp1KLwwj’ ‘~/tmp/scratch/Rtmp2AXcGm’   ‘~/tmp/scratch/Rtmp2Dnbtb’ ‘~/tmp/scratch/Rtmp2ry5JN’   ‘~/tmp/scratch/Rtmp30uyLW’ ‘~/tmp/scratch/Rtmp3KTwWT’   ‘~/tmp/scratch/Rtmp3lesFX’ ‘~/tmp/scratch/Rtmp3mWEBu’   ‘~/tmp/scratch/Rtmp5u113s’ ‘~/tmp/scratch/Rtmp6U7gdN’   ‘~/tmp/scratch/Rtmp7DNaay’ ‘~/tmp/scratch/Rtmp7PUabc’   ‘~/tmp/scratch/Rtmp7QIYWB’ ‘~/tmp/scratch/Rtmp7l5BpW’   ‘~/tmp/scratch/Rtmp7mXiH1’ ‘~/tmp/scratch/Rtmp8riuHE’   ‘~/tmp/scratch/Rtmp978aDm’ ‘~/tmp/scratch/Rtmp9IEcxI’   ‘~/tmp/scratch/Rtmp9WZ8Ej’ ‘~/tmp/scratch/Rtmp9e4uht’   ‘~/tmp/scratch/RtmpAi3fjk’ ‘~/tmp/scratch/RtmpAolY4x’   ‘~/tmp/scratch/RtmpAtWqxo’ ‘~/tmp/scratch/RtmpCEWpVI’   ‘~/tmp/scratch/RtmpCQ90gN’ ‘~/tmp/scratch/RtmpCT6NeW’   ‘~/tmp/scratch/RtmpCgSQqk’ ‘~/tmp/scratch/RtmpD8geqe’   ‘~/tmp/scratch/RtmpDs3jI3’ ‘~/tmp/scratch/RtmpDzzJUe’   ‘~/tmp/scratch/RtmpEaOQ4F’ ‘~/tmp/scratch/RtmpEhIgUf’   ‘~/tmp/scratch/RtmpEjqsMA’ ‘~/tmp/scratch/RtmpFnPFMm’   ‘~/tmp/scratch/RtmpGDewyo’ ‘~/tmp/scratch/RtmpGH5LCZ’   ‘~/tmp/scratch/RtmpGRoR5s’ ‘~/tmp/scratch/RtmpHwjvSK’   ‘~/tmp/scratch/RtmpHwvcHk’ ‘~/tmp/scratch/RtmpI3tPKF’   ‘~/tmp/scratch/RtmpIIDPW8’ ‘~/tmp/scratch/RtmpIgtFv8’   ‘~/tmp/scratch/RtmpJSBChB’ ‘~/tmp/scratch/RtmpKDYi06’   ‘~/tmp/scratch/RtmpKaAHmz’ ‘~/tmp/scratch/RtmpKxO5Dr’   ‘~/tmp/scratch/RtmpLDJYLX’ ‘~/tmp/scratch/RtmpLDPpyY’   ‘~/tmp/scratch/RtmpM2XxJm’ ‘~/tmp/scratch/RtmpMS79s5’   ‘~/tmp/scratch/RtmpNLHcJs’ ‘~/tmp/scratch/RtmpNR4shT’   ‘~/tmp/scratch/RtmpNo3PYw’ ‘~/tmp/scratch/RtmpO1NfYZ’   ‘~/tmp/scratch/RtmpOLlV3O’ ‘~/tmp/scratch/RtmpOrIMvl’   ‘~/tmp/scratch/RtmpOvWa62’ ‘~/tmp/scratch/RtmpP3LcBj’   ‘~/tmp/scratch/RtmpPiPq0Y’ ‘~/tmp/scratch/RtmpQ91cng’   ‘~/tmp/scratch/RtmpQPY7yI’ ‘~/tmp/scratch/RtmpQX1h0A’   ‘~/tmp/scratch/RtmpRC8fjn’ ‘~/tmp/scratch/RtmpRkWpgn’   ‘~/tmp/scratch/RtmpRnaju5’ ‘~/tmp/scratch/RtmpSFujyh’   ‘~/tmp/scratch/RtmpSKU5cs’ ‘~/tmp/scratch/RtmpSW2AE9’   ‘~/tmp/scratch/RtmpSdBjHV’ ‘~/tmp/scratch/RtmpSqrZU5’   ‘~/tmp/scratch/RtmpTBOrG9’ ‘~/tmp/scratch/RtmpTMj73o’   ‘~/tmp/scratch/RtmpU6hr1G’ ‘~/tmp/scratch/RtmpUGFRFI’   ‘~/tmp/scratch/RtmpUS62eW’ ‘~/tmp/scratch/RtmpUe7qG6’   ‘~/tmp/scratch/RtmpUp5o5w’ ‘~/tmp/scratch/RtmpV9QThI’   ‘~/tmp/scratch/RtmpVvkQZF’ ‘~/tmp/scratch/RtmpWtS97Z’   ‘~/tmp/scratch/RtmpX7QFFG’ ‘~/tmp/scratch/RtmpXAN1qw’   ‘~/tmp/scratch/RtmpXOjMl6’ ‘~/tmp/scratch/RtmpXc0oMT’   ‘~/tmp/scratch/RtmpYGMXLB’ ‘~/tmp/scratch/RtmpYmlrwU’   ‘~/tmp/scratch/RtmpZT32Xs’ ‘~/tmp/scratch/RtmpaCIc77’   ‘~/tmp/scratch/RtmpaIpgaP’ ‘~/tmp/scratch/Rtmpam0h1j’   ‘~/tmp/scratch/RtmpanxCs9’ ‘~/tmp/scratch/RtmpawCr3C’   ‘~/tmp/scratch/Rtmpb7SEoz’ ‘~/tmp/scratch/RtmpbVXeKX’   ‘~/tmp/scratch/Rtmpbfm6Aa’ ‘~/tmp/scratch/RtmpdOvmYZ’   ‘~/tmp/scratch/RtmpdZfy0M’ ‘~/tmp/scratch/RtmpdiIgRZ’   ‘~/tmp/scratch/RtmpduwdXh’ ‘~/tmp/scratch/Rtmpe37KGS’   ‘~/tmp/scratch/RtmpeKaGLC’ ‘~/tmp/scratch/RtmpeVlYWQ’   ‘~/tmp/scratch/RtmpeaXhCm’ ‘~/tmp/scratch/Rtmpevozzr’   ‘~/tmp/scratch/RtmpfK1CXq’ ‘~/tmp/scratch/RtmpfRzeAj’   ‘~/tmp/scratch/RtmpfTsE9h’ ‘~/tmp/scratch/RtmpfdRGMB’   ‘~/tmp/scratch/RtmpfkyV5T’ ‘~/tmp/scratch/RtmpgIE47m’   ‘~/tmp/scratch/RtmpgKsTCs’ ‘~/tmp/scratch/RtmpgVgrNp’   ‘~/tmp/scratch/RtmpgqhgZA’ ‘~/tmp/scratch/RtmphB523N’   ‘~/tmp/scratch/RtmphbAUyJ’ ‘~/tmp/scratch/Rtmpi1sXcM’   ‘~/tmp/scratch/RtmpicGZnY’ ‘~/tmp/scratch/RtmpjPtJH0’   ‘~/tmp/scratch/RtmplFwnGw’ ‘~/tmp/scratch/RtmplR5MdJ’   ‘~/tmp/scratch/RtmplROmK6’ ‘~/tmp/scratch/RtmplhNOWk’   ‘~/tmp/scratch/Rtmplxpf4b’ ‘~/tmp/scratch/RtmpmEzSYx’   ‘~/tmp/scratch/RtmpmGhONd’ ‘~/tmp/scratch/RtmpmRd81f’   ‘~/tmp/scratch/RtmpmpkroH’ ‘~/tmp/scratch/RtmpmsjzUV’   ‘~/tmp/scratch/RtmpnDTKrV’ ‘~/tmp/scratch/RtmpnSjivO’   ‘~/tmp/scratch/Rtmpo9Ds7O’ ‘~/tmp/scratch/RtmpoylMaV’   ‘~/tmp/scratch/RtmppQlZK8’ ‘~/tmp/scratch/RtmppWtCjL’   ‘~/tmp/scratch/RtmpptoizN’ ‘~/tmp/scratch/Rtmppv5wWa’   ‘~/tmp/scratch/RtmpqEh2Yu’ ‘~/tmp/scratch/RtmpqoIdJs’   ‘~/tmp/scratch/Rtmpr2mN9I’ ‘~/tmp/scratch/Rtmpr9Epc2’   ‘~/tmp/scratch/RtmprZwurg’ ‘~/tmp/scratch/RtmprgjC1f’   ‘~/tmp/scratch/RtmpruoMWm’ ‘~/tmp/scratch/RtmpsMoja8’   ‘~/tmp/scratch/RtmpscRISK’ ‘~/tmp/scratch/RtmpsulkT1’   ‘~/tmp/scratch/RtmpsyoWSG’ ‘~/tmp/scratch/RtmptAaCWm’   ‘~/tmp/scratch/RtmptIE0qY’ ‘~/tmp/scratch/RtmptWUFfw’   ‘~/tmp/scratch/Rtmptz8TSf’ ‘~/tmp/scratch/Rtmpu5cRwi’   ‘~/tmp/scratch/RtmpuSbwdT’ ‘~/tmp/scratch/RtmpvJDcoJ’   ‘~/tmp/scratch/RtmpwqiF3I’ ‘~/tmp/scratch/Rtmpwvkkdl’   ‘~/tmp/scratch/Rtmpwx67W3’ ‘~/tmp/scratch/RtmpxCJgVn’   ‘~/tmp/scratch/RtmpxFxMZg’ ‘~/tmp/scratch/RtmpxNEJ0D’   ‘~/tmp/scratch/RtmpyCdFvr’ ‘~/tmp/scratch/RtmpyciFEt’   ‘~/tmp/scratch/Rtmpyup9s0’ ‘~/tmp/scratch/Rtmpz7WcfQ’   ‘~/tmp/scratch/RtmpzacY84’   ‘~/tmp/scratch/quarto-sessionf78e2f81be2b21f3’   ‘~/tmp/scratch/xvfb-run.1OqJIu’ ‘~/tmp/scratch/xvfb-run.1aN191’   ‘~/tmp/scratch/xvfb-run.2FdqiF’ ‘~/tmp/scratch/xvfb-run.2PRdXe’   ‘~/tmp/scratch/xvfb-run.3B2EZo’ ‘~/tmp/scratch/xvfb-run.3MncYd’   ‘~/tmp/scratch/xvfb-run.54ftyJ’ ‘~/tmp/scratch/xvfb-run.66fetY’   ‘~/tmp/scratch/xvfb-run.74y1m8’ ‘~/tmp/scratch/xvfb-run.7vCUma’   ‘~/tmp/scratch/xvfb-run.83L7W8’ ‘~/tmp/scratch/xvfb-run.8b1KeU’   ‘~/tmp/scratch/xvfb-run.8gBejF’ ‘~/tmp/scratch/xvfb-run.9jJDdb’   ‘~/tmp/scratch/xvfb-run.A8HWb7’ ‘~/tmp/scratch/xvfb-run.BAECH7’   ‘~/tmp/scratch/xvfb-run.BRL04H’ ‘~/tmp/scratch/xvfb-run.BbSi2b’   ‘~/tmp/scratch/xvfb-run.BtoyQu’ ‘~/tmp/scratch/xvfb-run.BuXXmw’   ‘~/tmp/scratch/xvfb-run.CYCdiK’ ‘~/tmp/scratch/xvfb-run.Cjyz5w’   ‘~/tmp/scratch/xvfb-run.DYGutV’ ‘~/tmp/scratch/xvfb-run.Dx91ZX’   ‘~/tmp/scratch/xvfb-run.E6w6ur’ ‘~/tmp/scratch/xvfb-run.KUqAZW’   ‘~/tmp/scratch/xvfb-run.KYwNpA’ ‘~/tmp/scratch/xvfb-run.KoyHlR’   ‘~/tmp/scratch/xvfb-run.LRvmDj’ ‘~/tmp/scratch/xvfb-run.Lv03uC’   ‘~/tmp/scratch/xvfb-run.M8i7on’ ‘~/tmp/scratch/xvfb-run.NMTg87’   ‘~/tmp/scratch/xvfb-run.OWfnUe’ ‘~/tmp/scratch/xvfb-run.On9NTA’   ‘~/tmp/scratch/xvfb-run.OnnCeV’ ‘~/tmp/scratch/xvfb-run.QRx3Sh’   ‘~/tmp/scratch/xvfb-run.QcpmAA’ ‘~/tmp/scratch/xvfb-run.Rwutlg’   ‘~/tmp/scratch/xvfb-run.SGh2rF’ ‘~/tmp/scratch/xvfb-run.TPwuC4’   ‘~/tmp/scratch/xvfb-run.UFto6Y’ ‘~/tmp/scratch/xvfb-run.Ulan66’   ‘~/tmp/scratch/xvfb-run.VitMLk’ ‘~/tmp/scratch/xvfb-run.WFwiQV’   ‘~/tmp/scratch/xvfb-run.WXPh2P’ ‘~/tmp/scratch/xvfb-run.XOU2id’   ‘~/tmp/scratch/xvfb-run.XTfsoD’ ‘~/tmp/scratch/xvfb-run.YgT1pa’   ‘~/tmp/scratch/xvfb-run.bYBNWL’ ‘~/tmp/scratch/xvfb-run.bevqps’   ‘~/tmp/scratch/xvfb-run.cSk8Lt’ ‘~/tmp/scratch/xvfb-run.gUyd8w’   ‘~/tmp/scratch/xvfb-run.kHZr8b’ ‘~/tmp/scratch/xvfb-run.lcQYfw’   ‘~/tmp/scratch/xvfb-run.lj6L9t’ ‘~/tmp/scratch/xvfb-run.nTvv0T’   ‘~/tmp/scratch/xvfb-run.ni6YLY’ ‘~/tmp/scratch/xvfb-run.nuNmjI’   ‘~/tmp/scratch/xvfb-run.pQbBN2’ ‘~/tmp/scratch/xvfb-run.pRCnAr’   ‘~/tmp/scratch/xvfb-run.pYlMXF’ ‘~/tmp/scratch/xvfb-run.pxvu5M’   ‘~/tmp/scratch/xvfb-run.q72X7m’ ‘~/tmp/scratch/xvfb-run.qmsIes’   ‘~/tmp/scratch/xvfb-run.qquEvr’ ‘~/tmp/scratch/xvfb-run.r9fXNz’   ‘~/tmp/scratch/xvfb-run.s2Jwmr’ ‘~/tmp/scratch/xvfb-run.sNxh4B’   ‘~/tmp/scratch/xvfb-run.uIN6W7’ ‘~/tmp/scratch/xvfb-run.ujnfn5’   ‘~/tmp/scratch/xvfb-run.w2qwFE’ ‘~/tmp/scratch/xvfb-run.wShgim’   ‘~/tmp/scratch/xvfb-run.y1PoHj’ ‘~/tmp/scratch/xvfb-run.zOHaKt’   ‘~/tmp/scratch/xvfb-run.zp8fto’ ‘~/.cache/quarto/sass/sass.kv-shm’   ‘~/.cache/quarto/sass/sass.kv-wal’
• DONE

Status: 1 NOTE