• using R Under development (unstable) (2026-08-01 r90334)
• 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: 2026-08-02 16:50:23 UTC
• checking for file ‘photosynthesis/DESCRIPTION’ ... OK
• this is package ‘photosynthesis’ version ‘2.1.5’
• 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 ‘photosynthesis’ 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 ... NOTE   Missing dependency on R >= 4.1.0 because package code uses the pipe   |> or function shorthand \(...) syntax added in R 4.1.0.   File(s) using such syntax:     ‘bake-par.R’ ‘bake.R’ ‘calculated-parameters.R’ ‘conductance.R’     ‘constants.R’ ‘enviro-par.R’ ‘fit_aq_response.R’     ‘fit_aq_response2.Rd’ ‘fit_photosynthesis.R’ ‘fit_r_light.R’     ‘fit_r_light2.Rd’ ‘leaf-par.R’ ‘make_parameters.R’ ‘models.R’     ‘parameter_names.R’ ‘photosynthesis.R’ ‘read_licor.R’     ‘simulate_error.R’ ‘simulate_error.Rd’ ‘utils.R’
• 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 ... [2s/2s] OK
• checking whether the package can be loaded with stated dependencies ... [1s/2s] OK
• checking whether the package can be unloaded cleanly ... [2s/2s] OK
• checking whether the namespace can be loaded with stated dependencies ... [1s/2s] OK
• checking whether the namespace can be unloaded cleanly ... [2s/2s] OK
• checking loading without being on the library search path ... [2s/3s] 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 ... [14s/19s] OK
• checking Rd files ... [0s/1s] 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 contents of ‘data’ directory ... OK
• checking data for non-ASCII characters ... [0s/0s] 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 ... [6s/8s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [23s/28s] OK   Running ‘testthat.R’ [23s/28s]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [65s/97s] OK
• checking PDF version of manual ... [6s/9s] OK
• checking HTML version of manual ... [3s/4s] 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/Rtmp0Hqw7r’ ‘~/tmp/scratch/Rtmp0mFSmk’   ‘~/tmp/scratch/Rtmp0pTyv1’ ‘~/tmp/scratch/Rtmp1IizD9’   ‘~/tmp/scratch/Rtmp1KpYFE’ ‘~/tmp/scratch/Rtmp28cg2B’   ‘~/tmp/scratch/Rtmp2EGtOR’ ‘~/tmp/scratch/Rtmp2bVrSk’   ‘~/tmp/scratch/Rtmp37caOW’ ‘~/tmp/scratch/Rtmp3GsmEp’   ‘~/tmp/scratch/Rtmp3QLNmc’ ‘~/tmp/scratch/Rtmp3hj7zh’   ‘~/tmp/scratch/Rtmp4ERo36’ ‘~/tmp/scratch/Rtmp4igMdv’   ‘~/tmp/scratch/Rtmp57bvq7’ ‘~/tmp/scratch/Rtmp5QogMh’   ‘~/tmp/scratch/Rtmp5e64QV’ ‘~/tmp/scratch/Rtmp5yQhUc’   ‘~/tmp/scratch/Rtmp6JKInd’ ‘~/tmp/scratch/Rtmp6TQRLd’   ‘~/tmp/scratch/Rtmp6rA7iC’ ‘~/tmp/scratch/Rtmp6rBhaE’   ‘~/tmp/scratch/Rtmp79N37h’ ‘~/tmp/scratch/Rtmp9dO0xf’   ‘~/tmp/scratch/Rtmp9o2agT’ ‘~/tmp/scratch/RtmpA8ZSKf’   ‘~/tmp/scratch/RtmpABX3mZ’ ‘~/tmp/scratch/RtmpAydMlX’   ‘~/tmp/scratch/RtmpB1MQkw’ ‘~/tmp/scratch/RtmpBjIrvS’   ‘~/tmp/scratch/RtmpCILtr8’ ‘~/tmp/scratch/RtmpCrVYfb’   ‘~/tmp/scratch/RtmpD0Ef27’ ‘~/tmp/scratch/RtmpD1DX89’   ‘~/tmp/scratch/RtmpDnFjjs’ ‘~/tmp/scratch/RtmpEEkKbc’   ‘~/tmp/scratch/RtmpEfNen1’ ‘~/tmp/scratch/RtmpEmfUJx’   ‘~/tmp/scratch/RtmpEoqTGw’ ‘~/tmp/scratch/RtmpFLmWtp’   ‘~/tmp/scratch/RtmpG1eW5Z’ ‘~/tmp/scratch/RtmpGUvtjV’   ‘~/tmp/scratch/RtmpGdO1S2’ ‘~/tmp/scratch/RtmpGgiTtt’   ‘~/tmp/scratch/RtmpHIzvnd’ ‘~/tmp/scratch/RtmpHWRelJ’   ‘~/tmp/scratch/RtmpIFZiC4’ ‘~/tmp/scratch/RtmpIGXNsE’   ‘~/tmp/scratch/RtmpJajydY’ ‘~/tmp/scratch/RtmpK5zpS4’   ‘~/tmp/scratch/RtmpKAKEAD’ ‘~/tmp/scratch/RtmpKHoimA’   ‘~/tmp/scratch/RtmpKzkUcg’ ‘~/tmp/scratch/RtmpLqOEyg’   ‘~/tmp/scratch/RtmpM5mSNa’ ‘~/tmp/scratch/RtmpMguFFY’   ‘~/tmp/scratch/RtmpNUinfq’ ‘~/tmp/scratch/RtmpNVeH73’   ‘~/tmp/scratch/RtmpNdSP4C’ ‘~/tmp/scratch/RtmpNilLLb’   ‘~/tmp/scratch/RtmpOI53DN’ ‘~/tmp/scratch/RtmpOV4Cr1’   ‘~/tmp/scratch/RtmpP41RBv’ ‘~/tmp/scratch/RtmpP4yyoQ’   ‘~/tmp/scratch/RtmpPvpwMK’ ‘~/tmp/scratch/RtmpQEEg30’   ‘~/tmp/scratch/RtmpQSiYDi’ ‘~/tmp/scratch/RtmpQcxssM’   ‘~/tmp/scratch/RtmpQnMKuG’ ‘~/tmp/scratch/RtmpQyXw7w’   ‘~/tmp/scratch/RtmpR7EE0S’ ‘~/tmp/scratch/RtmpR8HSHS’   ‘~/tmp/scratch/RtmpRQ5LiM’ ‘~/tmp/scratch/RtmpRc81aG’   ‘~/tmp/scratch/RtmpS72Az7’ ‘~/tmp/scratch/RtmpS7v1SR’   ‘~/tmp/scratch/RtmpSbiZgv’ ‘~/tmp/scratch/RtmpSwEpXe’   ‘~/tmp/scratch/RtmpT9F17t’ ‘~/tmp/scratch/RtmpTC3G4B’   ‘~/tmp/scratch/RtmpTmNK6Q’ ‘~/tmp/scratch/RtmpTyVrNw’   ‘~/tmp/scratch/RtmpUND9vB’ ‘~/tmp/scratch/RtmpUiY1gE’   ‘~/tmp/scratch/RtmpVi4LQc’ ‘~/tmp/scratch/RtmpWvKRb2’   ‘~/tmp/scratch/RtmpXD54B6’ ‘~/tmp/scratch/RtmpXKstSR’   ‘~/tmp/scratch/RtmpXPDNy6’ ‘~/tmp/scratch/RtmpXRB04n’   ‘~/tmp/scratch/RtmpXiI6xm’ ‘~/tmp/scratch/RtmpXwLHND’   ‘~/tmp/scratch/RtmpYXETPA’ ‘~/tmp/scratch/RtmpYbUvyF’   ‘~/tmp/scratch/RtmpYmp9Sg’ ‘~/tmp/scratch/RtmpZpBoG1’   ‘~/tmp/scratch/RtmpaH3C8Y’ ‘~/tmp/scratch/RtmpaYaOYa’   ‘~/tmp/scratch/RtmpaaChYp’ ‘~/tmp/scratch/Rtmpau1dOa’   ‘~/tmp/scratch/RtmpbxHXB8’ ‘~/tmp/scratch/Rtmpcaunrf’   ‘~/tmp/scratch/RtmpdFv1PB’ ‘~/tmp/scratch/RtmpdTXTAv’   ‘~/tmp/scratch/RtmpdV5lpM’ ‘~/tmp/scratch/RtmpdZo2u0’   ‘~/tmp/scratch/RtmpdkcVhY’ ‘~/tmp/scratch/Rtmpe00GVN’   ‘~/tmp/scratch/RtmpeCLimL’ ‘~/tmp/scratch/RtmpeiZVld’   ‘~/tmp/scratch/RtmperXG2A’ ‘~/tmp/scratch/RtmpesdMzw’   ‘~/tmp/scratch/Rtmpfe4s4c’ ‘~/tmp/scratch/RtmpfuoGGa’   ‘~/tmp/scratch/RtmpggHVDF’ ‘~/tmp/scratch/RtmpgrJ8eG’   ‘~/tmp/scratch/RtmphC9Okz’ ‘~/tmp/scratch/Rtmphcd5F9’   ‘~/tmp/scratch/Rtmphlng56’ ‘~/tmp/scratch/RtmphqJJmq’   ‘~/tmp/scratch/RtmphqoJg5’ ‘~/tmp/scratch/RtmpiTRodP’   ‘~/tmp/scratch/RtmpiTWkMh’ ‘~/tmp/scratch/RtmpirCy4C’   ‘~/tmp/scratch/Rtmpj8ICxe’ ‘~/tmp/scratch/RtmpjCX2c5’   ‘~/tmp/scratch/RtmpjIsfvg’ ‘~/tmp/scratch/RtmpjLUntG’   ‘~/tmp/scratch/RtmpjY0Ngx’ ‘~/tmp/scratch/RtmpjiGLxq’   ‘~/tmp/scratch/RtmpjwCpEC’ ‘~/tmp/scratch/RtmpkW4dby’   ‘~/tmp/scratch/Rtmpkmz1S3’ ‘~/tmp/scratch/RtmpmfjC45’   ‘~/tmp/scratch/RtmpnjAW5P’ ‘~/tmp/scratch/Rtmpo7Gh9r’   ‘~/tmp/scratch/RtmpohADYr’ ‘~/tmp/scratch/RtmppdfUCn’   ‘~/tmp/scratch/RtmppvaLo8’ ‘~/tmp/scratch/RtmpqSmHwH’   ‘~/tmp/scratch/RtmpqVdRQj’ ‘~/tmp/scratch/Rtmpr8qicl’   ‘~/tmp/scratch/RtmprRRZK9’ ‘~/tmp/scratch/Rtmps8E24d’   ‘~/tmp/scratch/RtmpsDsnb3’ ‘~/tmp/scratch/RtmpsFEfUI’   ‘~/tmp/scratch/RtmpsIcU0w’ ‘~/tmp/scratch/RtmpsVVhit’   ‘~/tmp/scratch/RtmpsxBAW4’ ‘~/tmp/scratch/RtmptVTm2Y’   ‘~/tmp/scratch/RtmpttRk3L’ ‘~/tmp/scratch/RtmptufuDx’   ‘~/tmp/scratch/RtmpuQWDAt’ ‘~/tmp/scratch/RtmpucTepv’   ‘~/tmp/scratch/RtmpunCZVz’ ‘~/tmp/scratch/RtmpupraKW’   ‘~/tmp/scratch/RtmpuzVj2m’ ‘~/tmp/scratch/RtmpvJEMUJ’   ‘~/tmp/scratch/RtmpvPYpz3’ ‘~/tmp/scratch/RtmpvinjaT’   ‘~/tmp/scratch/RtmpvkZNX7’ ‘~/tmp/scratch/RtmpwGW9Vy’   ‘~/tmp/scratch/Rtmpwappgx’ ‘~/tmp/scratch/RtmpwgY1ea’   ‘~/tmp/scratch/Rtmpwsouuk’ ‘~/tmp/scratch/RtmpxFs3ka’   ‘~/tmp/scratch/RtmpyAztlj’ ‘~/tmp/scratch/RtmpyrBIZU’   ‘~/tmp/scratch/Rtmpzac0NJ’   ‘~/tmp/scratch/quarto-sessionc4784eaca63a1151’   ‘~/tmp/scratch/xvfb-run.0KcRrz’ ‘~/tmp/scratch/xvfb-run.1lM0dT’   ‘~/tmp/scratch/xvfb-run.1ocL5f’ ‘~/tmp/scratch/xvfb-run.1op7oZ’   ‘~/tmp/scratch/xvfb-run.3V73gs’ ‘~/tmp/scratch/xvfb-run.5DlRuZ’   ‘~/tmp/scratch/xvfb-run.60mVs0’ ‘~/tmp/scratch/xvfb-run.6OiK46’   ‘~/tmp/scratch/xvfb-run.80ICRs’ ‘~/tmp/scratch/xvfb-run.8LTwhx’   ‘~/tmp/scratch/xvfb-run.8Z625U’ ‘~/tmp/scratch/xvfb-run.8fFjWP’   ‘~/tmp/scratch/xvfb-run.9wDqqP’ ‘~/tmp/scratch/xvfb-run.Awxuge’   ‘~/tmp/scratch/xvfb-run.B0Tci5’ ‘~/tmp/scratch/xvfb-run.B6MVV3’   ‘~/tmp/scratch/xvfb-run.BRofsV’ ‘~/tmp/scratch/xvfb-run.C112eL’   ‘~/tmp/scratch/xvfb-run.DSBH66’ ‘~/tmp/scratch/xvfb-run.EkDvwn’   ‘~/tmp/scratch/xvfb-run.GnWMyj’ ‘~/tmp/scratch/xvfb-run.HuciY2’   ‘~/tmp/scratch/xvfb-run.IBtB52’ ‘~/tmp/scratch/xvfb-run.JD0e09’   ‘~/tmp/scratch/xvfb-run.KQw60r’ ‘~/tmp/scratch/xvfb-run.Kb9zH2’   ‘~/tmp/scratch/xvfb-run.LxPOMp’ ‘~/tmp/scratch/xvfb-run.Owm7J8’   ‘~/tmp/scratch/xvfb-run.PKyx2f’ ‘~/tmp/scratch/xvfb-run.Pvnd4N’   ‘~/tmp/scratch/xvfb-run.QlGW9p’ ‘~/tmp/scratch/xvfb-run.Rgz444’   ‘~/tmp/scratch/xvfb-run.Rk28Qi’ ‘~/tmp/scratch/xvfb-run.RlpGlG’   ‘~/tmp/scratch/xvfb-run.SV0xxS’ ‘~/tmp/scratch/xvfb-run.TgOwTO’   ‘~/tmp/scratch/xvfb-run.TwNXw5’ ‘~/tmp/scratch/xvfb-run.UowUjH’   ‘~/tmp/scratch/xvfb-run.WfxWPe’ ‘~/tmp/scratch/xvfb-run.Y9qIEX’   ‘~/tmp/scratch/xvfb-run.ZFZeJk’ ‘~/tmp/scratch/xvfb-run.Zn13MA’   ‘~/tmp/scratch/xvfb-run.ZsaiPA’ ‘~/tmp/scratch/xvfb-run.aKuZ3l’   ‘~/tmp/scratch/xvfb-run.agZH2p’ ‘~/tmp/scratch/xvfb-run.arZwoc’   ‘~/tmp/scratch/xvfb-run.cWLEyh’ ‘~/tmp/scratch/xvfb-run.ciDuzY’   ‘~/tmp/scratch/xvfb-run.dKGE3d’ ‘~/tmp/scratch/xvfb-run.dMJbZ9’   ‘~/tmp/scratch/xvfb-run.dPvzg8’ ‘~/tmp/scratch/xvfb-run.e2YDwD’   ‘~/tmp/scratch/xvfb-run.f4WtZy’ ‘~/tmp/scratch/xvfb-run.gOEzkb’   ‘~/tmp/scratch/xvfb-run.hSrZ3G’ ‘~/tmp/scratch/xvfb-run.hfEjRS’   ‘~/tmp/scratch/xvfb-run.hn6i1o’ ‘~/tmp/scratch/xvfb-run.i1kpTP’   ‘~/tmp/scratch/xvfb-run.jAc35f’ ‘~/tmp/scratch/xvfb-run.jCnkoM’   ‘~/tmp/scratch/xvfb-run.nc5Xs4’ ‘~/tmp/scratch/xvfb-run.nera2W’   ‘~/tmp/scratch/xvfb-run.nsv0Te’ ‘~/tmp/scratch/xvfb-run.p8TipH’   ‘~/tmp/scratch/xvfb-run.pbN6u8’ ‘~/tmp/scratch/xvfb-run.pgJpD4’   ‘~/tmp/scratch/xvfb-run.r2YXYY’ ‘~/tmp/scratch/xvfb-run.rAgb9V’   ‘~/tmp/scratch/xvfb-run.rWRhvL’ ‘~/tmp/scratch/xvfb-run.reyYjr’   ‘~/tmp/scratch/xvfb-run.rv7zwC’ ‘~/tmp/scratch/xvfb-run.siXLj7’   ‘~/tmp/scratch/xvfb-run.uH5mUl’ ‘~/tmp/scratch/xvfb-run.vNfS82’   ‘~/tmp/scratch/xvfb-run.xKKlPD’ ‘~/tmp/scratch/xvfb-run.xRJjk2’   ‘~/tmp/scratch/xvfb-run.zFW7tv’
• DONE

Status: 2 NOTEs