• 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 16:51:59 UTC
• checking for file ‘photosynthesis/DESCRIPTION’ ... OK
• this is package ‘photosynthesis’ version ‘2.1.5’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [2s/3s] 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/1s] OK
• checking whether the package can be unloaded cleanly ... [1s/2s] OK
• checking whether the namespace can be loaded with stated dependencies ... [1s/2s] OK
• checking whether the namespace can be unloaded cleanly ... [1s/2s] OK
• checking loading without being on the library search path ... [2s/2s] 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/17s] 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 ... [8s/10s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [22s/24s] OK   Running ‘testthat.R’ [22s/24s]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [62s/71s] OK
• checking PDF version of manual ... [5s/7s] OK
• checking HTML version of manual ... [2s/3s] 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/Rtmp0TEIA1’ ‘~/tmp/scratch/Rtmp0bYze5’   ‘~/tmp/scratch/Rtmp0e6CTK’ ‘~/tmp/scratch/Rtmp0ff3zN’   ‘~/tmp/scratch/Rtmp0ydVk1’ ‘~/tmp/scratch/Rtmp15gRip’   ‘~/tmp/scratch/Rtmp1lz276’ ‘~/tmp/scratch/Rtmp3CFoqJ’   ‘~/tmp/scratch/Rtmp4fCxv4’ ‘~/tmp/scratch/Rtmp5YL4xl’   ‘~/tmp/scratch/Rtmp5wxlQ5’ ‘~/tmp/scratch/Rtmp60ysSM’   ‘~/tmp/scratch/Rtmp7AGWHs’ ‘~/tmp/scratch/Rtmp7XNBUY’   ‘~/tmp/scratch/Rtmp7mXiH1’ ‘~/tmp/scratch/Rtmp8cxfts’   ‘~/tmp/scratch/Rtmp8yqxE7’ ‘~/tmp/scratch/Rtmp9Mo4E0’   ‘~/tmp/scratch/Rtmp9WZ8Ej’ ‘~/tmp/scratch/RtmpAiLD9e’   ‘~/tmp/scratch/RtmpAtWqxo’ ‘~/tmp/scratch/RtmpBAEFBT’   ‘~/tmp/scratch/RtmpBQX6wt’ ‘~/tmp/scratch/RtmpBr86DB’   ‘~/tmp/scratch/RtmpC1W95V’ ‘~/tmp/scratch/RtmpCEWpVI’   ‘~/tmp/scratch/RtmpCMqGzO’ ‘~/tmp/scratch/RtmpCQ90gN’   ‘~/tmp/scratch/RtmpCuuvRg’ ‘~/tmp/scratch/RtmpCvvfgL’   ‘~/tmp/scratch/RtmpDRZebI’ ‘~/tmp/scratch/RtmpDT8RcV’   ‘~/tmp/scratch/RtmpDs3jI3’ ‘~/tmp/scratch/RtmpDzJw2T’   ‘~/tmp/scratch/RtmpDzhYKU’ ‘~/tmp/scratch/RtmpE7suEm’   ‘~/tmp/scratch/RtmpEc5dTi’ ‘~/tmp/scratch/RtmpF447zv’   ‘~/tmp/scratch/RtmpFJKlm9’ ‘~/tmp/scratch/RtmpFUQ8XD’   ‘~/tmp/scratch/RtmpFc0xI4’ ‘~/tmp/scratch/RtmpGDewyo’   ‘~/tmp/scratch/RtmpH2DCQi’ ‘~/tmp/scratch/RtmpH8Egpj’   ‘~/tmp/scratch/RtmpHK5t1Y’ ‘~/tmp/scratch/RtmpHxf8IG’   ‘~/tmp/scratch/RtmpIUQQRb’ ‘~/tmp/scratch/RtmpIgtFv8’   ‘~/tmp/scratch/RtmpIyeHRu’ ‘~/tmp/scratch/RtmpJ26Cni’   ‘~/tmp/scratch/RtmpJ8kDw9’ ‘~/tmp/scratch/RtmpJS1b9u’   ‘~/tmp/scratch/RtmpJpwHIx’ ‘~/tmp/scratch/RtmpJrwT6E’   ‘~/tmp/scratch/RtmpKomrTq’ ‘~/tmp/scratch/RtmpKxO5Dr’   ‘~/tmp/scratch/RtmpLDJYLX’ ‘~/tmp/scratch/RtmpLDPpyY’   ‘~/tmp/scratch/RtmpM2zA2e’ ‘~/tmp/scratch/RtmpMBuOOo’   ‘~/tmp/scratch/RtmpMjGuRD’ ‘~/tmp/scratch/RtmpNLHcJs’   ‘~/tmp/scratch/RtmpNfhXcX’ ‘~/tmp/scratch/RtmpNo3PYw’   ‘~/tmp/scratch/RtmpOHdWoH’ ‘~/tmp/scratch/RtmpOLlV3O’   ‘~/tmp/scratch/RtmpP1E65a’ ‘~/tmp/scratch/RtmpPOmNW7’   ‘~/tmp/scratch/RtmpPiPq0Y’ ‘~/tmp/scratch/RtmpQ8sMZ8’   ‘~/tmp/scratch/RtmpQguKuw’ ‘~/tmp/scratch/RtmpQhZvDo’   ‘~/tmp/scratch/RtmpSETWiU’ ‘~/tmp/scratch/RtmpSTkRAv’   ‘~/tmp/scratch/RtmpSj6JDI’ ‘~/tmp/scratch/RtmpSpBWhl’   ‘~/tmp/scratch/RtmpTHuYXs’ ‘~/tmp/scratch/RtmpTQTigV’   ‘~/tmp/scratch/RtmpUE90D4’ ‘~/tmp/scratch/RtmpUS62eW’   ‘~/tmp/scratch/RtmpX0EpIm’ ‘~/tmp/scratch/RtmpX3fH9C’   ‘~/tmp/scratch/RtmpX7QFFG’ ‘~/tmp/scratch/RtmpX7S0JA’   ‘~/tmp/scratch/RtmpXc0oMT’ ‘~/tmp/scratch/RtmpXeEXOG’   ‘~/tmp/scratch/RtmpY4tAL2’ ‘~/tmp/scratch/RtmpYDTSdU’   ‘~/tmp/scratch/RtmpYHNxN2’ ‘~/tmp/scratch/RtmpYMszAR’   ‘~/tmp/scratch/RtmpYT7VvJ’ ‘~/tmp/scratch/RtmpYa38i1’   ‘~/tmp/scratch/RtmpYnwamK’ ‘~/tmp/scratch/RtmpZ3GU4c’   ‘~/tmp/scratch/RtmpZYiPeh’ ‘~/tmp/scratch/Rtmpa6idfg’   ‘~/tmp/scratch/RtmpaCIc77’ ‘~/tmp/scratch/RtmpaXW3if’   ‘~/tmp/scratch/RtmpaqZpkH’ ‘~/tmp/scratch/RtmpbDzvMu’   ‘~/tmp/scratch/RtmpbVXeKX’ ‘~/tmp/scratch/Rtmpba70Of’   ‘~/tmp/scratch/RtmpbvEDtn’ ‘~/tmp/scratch/Rtmpcxr8Au’   ‘~/tmp/scratch/Rtmpd1Dy0A’ ‘~/tmp/scratch/Rtmpd2zT9I’   ‘~/tmp/scratch/RtmpdcWbR7’ ‘~/tmp/scratch/RtmpdeaINM’   ‘~/tmp/scratch/Rtmpdfpd1o’ ‘~/tmp/scratch/RtmpdgXtFy’   ‘~/tmp/scratch/RtmpdiIgRZ’ ‘~/tmp/scratch/Rtmpe37KGS’   ‘~/tmp/scratch/Rtmpehtvo0’ ‘~/tmp/scratch/Rtmpezgy2c’   ‘~/tmp/scratch/RtmpfK1CXq’ ‘~/tmp/scratch/RtmpfTsE9h’   ‘~/tmp/scratch/RtmpgMrUOr’ ‘~/tmp/scratch/RtmpgVgrNp’   ‘~/tmp/scratch/Rtmph4BaEq’ ‘~/tmp/scratch/RtmphMJf1J’   ‘~/tmp/scratch/RtmpiHwnEQ’ ‘~/tmp/scratch/RtmpifChmq’   ‘~/tmp/scratch/RtmpjPtJH0’ ‘~/tmp/scratch/RtmpjXJZGw’   ‘~/tmp/scratch/Rtmpk4oyFU’ ‘~/tmp/scratch/RtmpkUPaqF’   ‘~/tmp/scratch/RtmpkwKjcT’ ‘~/tmp/scratch/RtmploRze1’   ‘~/tmp/scratch/Rtmplxpf4b’ ‘~/tmp/scratch/RtmpmEzSYx’   ‘~/tmp/scratch/RtmpmGhONd’ ‘~/tmp/scratch/RtmpmJ8RlW’   ‘~/tmp/scratch/RtmpmdDtWM’ ‘~/tmp/scratch/RtmpmrWD4v’   ‘~/tmp/scratch/RtmpnDTKrV’ ‘~/tmp/scratch/RtmpnoCIXI’   ‘~/tmp/scratch/Rtmpnp1bDi’ ‘~/tmp/scratch/Rtmpnz9UFd’   ‘~/tmp/scratch/Rtmpo9Ds7O’ ‘~/tmp/scratch/RtmpoZEHzA’   ‘~/tmp/scratch/RtmpoylMaV’ ‘~/tmp/scratch/Rtmpp5LSum’   ‘~/tmp/scratch/RtmppQlZK8’ ‘~/tmp/scratch/Rtmpq2kVvD’   ‘~/tmp/scratch/Rtmpq4p8Wf’ ‘~/tmp/scratch/RtmpqoIdJs’   ‘~/tmp/scratch/Rtmpr2mN9I’ ‘~/tmp/scratch/RtmprQzyHu’   ‘~/tmp/scratch/RtmpsLvCMZ’ ‘~/tmp/scratch/RtmpsulkT1’   ‘~/tmp/scratch/RtmpsyoWSG’ ‘~/tmp/scratch/RtmptUh38x’   ‘~/tmp/scratch/RtmpuLyGhf’ ‘~/tmp/scratch/RtmpufZ6TD’   ‘~/tmp/scratch/RtmpuyEvQm’ ‘~/tmp/scratch/RtmpvD0wJA’   ‘~/tmp/scratch/RtmpveGgaB’ ‘~/tmp/scratch/RtmpvpemvQ’   ‘~/tmp/scratch/Rtmpvpzgtm’ ‘~/tmp/scratch/RtmpwZFlf4’   ‘~/tmp/scratch/Rtmpwajlnd’ ‘~/tmp/scratch/RtmpwoIQ1z’   ‘~/tmp/scratch/Rtmpwzw9Tn’ ‘~/tmp/scratch/RtmpxXrKnb’   ‘~/tmp/scratch/RtmpxYYbem’ ‘~/tmp/scratch/RtmpxbPk0e’   ‘~/tmp/scratch/RtmpyBnhAH’ ‘~/tmp/scratch/RtmpyWeTFm’   ‘~/tmp/scratch/RtmpyciFEt’ ‘~/tmp/scratch/RtmpyjXda0’   ‘~/tmp/scratch/Rtmpyup9s0’ ‘~/tmp/scratch/Rtmpz9guEx’   ‘~/tmp/scratch/RtmpzjkPsG’ ‘~/tmp/scratch/RtmpzpFg5t’   ‘~/tmp/scratch/xvfb-run.0pRCGF’ ‘~/tmp/scratch/xvfb-run.18SlnE’   ‘~/tmp/scratch/xvfb-run.1c8rsf’ ‘~/tmp/scratch/xvfb-run.1dz4b4’   ‘~/tmp/scratch/xvfb-run.26Lkyz’ ‘~/tmp/scratch/xvfb-run.2FdqiF’   ‘~/tmp/scratch/xvfb-run.3KmeRP’ ‘~/tmp/scratch/xvfb-run.54ftyJ’   ‘~/tmp/scratch/xvfb-run.66fetY’ ‘~/tmp/scratch/xvfb-run.7hga3r’   ‘~/tmp/scratch/xvfb-run.7vCUma’ ‘~/tmp/scratch/xvfb-run.9HMAWi’   ‘~/tmp/scratch/xvfb-run.9jJDdb’ ‘~/tmp/scratch/xvfb-run.9rj7yC’   ‘~/tmp/scratch/xvfb-run.Aszdyv’ ‘~/tmp/scratch/xvfb-run.BWzEbf’   ‘~/tmp/scratch/xvfb-run.BbSi2b’ ‘~/tmp/scratch/xvfb-run.BtoyQu’   ‘~/tmp/scratch/xvfb-run.CKw4me’ ‘~/tmp/scratch/xvfb-run.CYCdiK’   ‘~/tmp/scratch/xvfb-run.Cjyz5w’ ‘~/tmp/scratch/xvfb-run.DPXcpU’   ‘~/tmp/scratch/xvfb-run.EjhzMN’ ‘~/tmp/scratch/xvfb-run.Ekng0L’   ‘~/tmp/scratch/xvfb-run.FuGTnt’ ‘~/tmp/scratch/xvfb-run.GlApcD’   ‘~/tmp/scratch/xvfb-run.JIqdy9’ ‘~/tmp/scratch/xvfb-run.K4u5Ft’   ‘~/tmp/scratch/xvfb-run.KUqAZW’ ‘~/tmp/scratch/xvfb-run.KYwNpA’   ‘~/tmp/scratch/xvfb-run.M5kBzF’ ‘~/tmp/scratch/xvfb-run.MDeK64’   ‘~/tmp/scratch/xvfb-run.MKkTMR’ ‘~/tmp/scratch/xvfb-run.NQRN20’   ‘~/tmp/scratch/xvfb-run.OWfnUe’ ‘~/tmp/scratch/xvfb-run.On9NTA’   ‘~/tmp/scratch/xvfb-run.OnnCeV’ ‘~/tmp/scratch/xvfb-run.PSPPVQ’   ‘~/tmp/scratch/xvfb-run.Pxwr0p’ ‘~/tmp/scratch/xvfb-run.QI3m76’   ‘~/tmp/scratch/xvfb-run.R3739I’ ‘~/tmp/scratch/xvfb-run.Rwutlg’   ‘~/tmp/scratch/xvfb-run.TPwuC4’ ‘~/tmp/scratch/xvfb-run.TgBVCG’   ‘~/tmp/scratch/xvfb-run.UIXaSH’ ‘~/tmp/scratch/xvfb-run.Ulan66’   ‘~/tmp/scratch/xvfb-run.UqOjgs’ ‘~/tmp/scratch/xvfb-run.VNJk6K’   ‘~/tmp/scratch/xvfb-run.WFwiQV’ ‘~/tmp/scratch/xvfb-run.WHhknx’   ‘~/tmp/scratch/xvfb-run.Wnnqk2’ ‘~/tmp/scratch/xvfb-run.XTfsoD’   ‘~/tmp/scratch/xvfb-run.axGhhV’ ‘~/tmp/scratch/xvfb-run.bFEQq8’   ‘~/tmp/scratch/xvfb-run.bevqps’ ‘~/tmp/scratch/xvfb-run.byjDhd’   ‘~/tmp/scratch/xvfb-run.epaK2Y’ ‘~/tmp/scratch/xvfb-run.jGOOSz’   ‘~/tmp/scratch/xvfb-run.jJ1LT5’ ‘~/tmp/scratch/xvfb-run.k4kcWS’   ‘~/tmp/scratch/xvfb-run.lcQYfw’ ‘~/tmp/scratch/xvfb-run.lj6L9t’   ‘~/tmp/scratch/xvfb-run.neHVOt’ ‘~/tmp/scratch/xvfb-run.ni6YLY’   ‘~/tmp/scratch/xvfb-run.pMlmF6’ ‘~/tmp/scratch/xvfb-run.pQyGVl’   ‘~/tmp/scratch/xvfb-run.pmbB68’ ‘~/tmp/scratch/xvfb-run.qmsIes’   ‘~/tmp/scratch/xvfb-run.sUQ5CY’ ‘~/tmp/scratch/xvfb-run.sb2ND5’   ‘~/tmp/scratch/xvfb-run.tNHHi0’ ‘~/tmp/scratch/xvfb-run.tiDbGV’   ‘~/tmp/scratch/xvfb-run.uMOsDr’ ‘~/tmp/scratch/xvfb-run.w2qwFE’   ‘~/tmp/scratch/xvfb-run.wGPXJe’ ‘~/tmp/scratch/xvfb-run.zOHaKt’
• DONE

Status: 2 NOTEs