* using log directory ‘/srv/hornik/tmp/CRAN_pretest/pam.Rcheck’ * using R Under development (unstable) (2025-07-28 r88462) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.7 (3) Debian flang-new version 19.1.7 (3) * running under: Debian GNU/Linux 13 (trixie) * using session charset: UTF-8 * checking for file ‘pam/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘pam’ version ‘1.0.3’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [4s/6s] 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 serialization versions ... OK * checking whether package ‘pam’ can be installed ... [1s/1s] OK * 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 ... [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 ... [3s/3s] 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 examples ... [3s/3s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [9s/9s] ERROR Running ‘testthat.R’ [9s/9s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(pam) > > test_check("pam") [ FAIL 21 | WARN 4 | SKIP 0 | PASS 21 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-compare_regression_models_etr_I.R:11:5'): compare_regression_models etr I ── Error in `if (grepl("ubuntu", distro) || grepl("debian", distro)) { expect_no_error({ model_points_etr_I <- compare_regression_models_ETR_I(test_data_dir) }) expect_equal(model_points_etr_I[["eilers_peeters"]], 13) expect_equal(model_points_etr_I[["platt"]], 16) expect_equal(model_points_etr_I[["vollenweider"]], 30) expect_equal(model_points_etr_I[["walsby"]], 19) } else { skip(paste("Skipping test on unsupported Linux distribution:", distro)) }`: missing value where TRUE/FALSE needed ── Error ('test-compare_regression_models_etr_II.R:11:5'): compare_regression_models etr II ── Error in `if (grepl("ubuntu", distro) || grepl("debian", distro)) { expect_no_error({ model_points_etr_II <- compare_regression_models_ETR_II(test_data_dir) }) expect_equal(model_points_etr_II[["eilers_peeters"]], 41) expect_equal(model_points_etr_II[["platt"]], 24) expect_equal(model_points_etr_II[["vollenweider"]], 40) expect_equal(model_points_etr_II[["walsby"]], 9) } else { skip(paste("Skipping test on unsupported Linux distribution:", distro)) }`: missing value where TRUE/FALSE needed ── Error ('test-compare_regression_models_total.R:10:5'): compare_regression_models etr I + II ── Error in `if (grepl("ubuntu", distro) || grepl("debian", distro)) { expect_no_error({ model_points_etr_I <- compare_regression_models_ETR_I(test_data_dir) model_points_etr_II <- compare_regression_models_ETR_II(test_data_dir) eilers_peeters_total <- model_points_etr_I[["eilers_peeters"]] + model_points_etr_II[["eilers_peeters"]] platt_total <- model_points_etr_I[["platt"]] + model_points_etr_II[["platt"]] vollenweider_total <- model_points_etr_I[["vollenweider"]] + model_points_etr_II[["vollenweider"]] walsby_total <- model_points_etr_I[["walsby"]] + model_points_etr_II[["walsby"]] result <- c(eilers_peeters_total = eilers_peeters_total, platt_total = platt_total, vollenweider_total = vollenweider_total, walsby_total = walsby_total) }) expect_equal(result[["eilers_peeters_total"]], 54) expect_equal(result[["platt_total"]], 40) expect_equal(result[["vollenweider_total"]], 70) expect_equal(result[["walsby_total"]], 28) } else { skip(paste("Skipping test on unsupported Linux distribution:", distro)) }`: missing value where TRUE/FALSE needed ── Error ('test-eilers_peeters_etr_I.R:13:5'): test-eilers_peeters_etr_I generate regression 20240925.csv ── Error in `if (grepl("ubuntu", distro) || grepl("debian", distro)) { expect_equal(model_result[["sdiff"]], 53.4454062) expect_equal(model_result[["c"]], 2.8984079) expect_equal(model_result[["pm"]], 151.851986) expect_equal(model_result[["s"]], 0.345017) expect_equal(model_result[["ik"]], 440.1289906) expect_equal(model_result[["im"]], 1399.76963) expect_equal(model_result[["w"]], 1.180362267) } else { skip(paste("Skipping test on unsupported Linux distribution:", distro)) }`: missing value where TRUE/FALSE needed ── Error ('test-eilers_peeters_etr_I.R:74:5'): test-eilers_peeters_etr_I generate regression modified 20240925.csv ── Error in `if (grepl("ubuntu", distro) || grepl("debian", distro)) { expect_equal(model_result[["sdiff"]], 53.4454062) expect_equal(model_result[["c"]], 2.8984079) expect_equal(model_result[["d"]], NA_real_) expect_equal(model_result[["alpha"]], 0.345017) expect_equal(model_result[["beta"]], NA_real_) expect_equal(model_result[["etrmax_with_photoinhibition"]], 151.851986) expect_equal(model_result[["etrmax_without_photoinhibition"]], NA_real_) expect_equal(model_result[["ik_with_photoinhibition"]], 440.1289906) expect_equal(model_result[["ik_without_photoinhibition"]], NA_real_) expect_equal(model_result[["im_with_photoinhibition"]], 1399.76963) expect_equal(model_result[["w"]], 1.180362267) expect_equal(model_result[["ib"]], NA_real_) expect_equal(model_result[["etrmax_with_without_ratio"]], NA_real_) } else { skip(paste("Skipping test on unsupported Linux distribution:", distro)) }`: missing value where TRUE/FALSE needed ── Error ('test-eilers_peeters_etr_II.R:13:5'): test-eilers_peeters_etr_II generate regression 20240925.csv ── Error in `if (grepl("ubuntu", distro) || grepl("debian", distro)) { expect_equal(model_result[["sdiff"]], 5.7818334) expect_equal(model_result[["c"]], 6.1088971) expect_equal(model_result[["pm"]], 44.5224748) expect_equal(model_result[["s"]], 0.16369567) expect_equal(model_result[["ik"]], 271.98322) expect_equal(model_result[["im"]], 731.801329) expect_equal(model_result[["w"]], 0.690612084) } else { skip(paste("Skipping test on unsupported Linux distribution:", distro)) }`: missing value where TRUE/FALSE needed ── Error ('test-eilers_peeters_etr_II.R:57:5'): test-eilers_peeters_etr_II modified 20240925.csv ── Error in `if (grepl("ubuntu", distro) || grepl("debian", distro)) { expect_equal(model_result[["sdiff"]], 5.7818334) expect_equal(model_result[["c"]], 6.1088971) expect_equal(model_result[["d"]], NA_real_) expect_equal(model_result[["alpha"]], 0.16369567) expect_equal(model_result[["beta"]], NA_real_) expect_equal(model_result[["etrmax_with_photoinhibition"]], 44.5224748) expect_equal(model_result[["etrmax_without_photoinhibition"]], NA_real_) expect_equal(model_result[["ik_with_photoinhibition"]], 271.98322) expect_equal(model_result[["ik_without_photoinhibition"]], NA_real_) expect_equal(model_result[["im_with_photoinhibition"]], 731.801329) expect_equal(model_result[["w"]], 0.690612084) expect_equal(model_result[["ib"]], NA_real_) expect_equal(model_result[["etrmax_with_without_ratio"]], NA_real_) } else { skip(paste("Skipping test on unsupported Linux distribution:", distro)) }`: missing value where TRUE/FALSE needed ── Error ('test-eilers_peeters_etr_II_junior_pam.R:13:5'): test-eilers_peeters_etr_II generate regression junior_pam_20250613.csv.csv ── Error in `if (grepl("ubuntu", distro) || grepl("debian", distro)) { expect_equal(model_result[["sdiff"]], 18.5975058) expect_equal(model_result[["b"]], 0.01213671) expect_equal(model_result[["c"]], 2.77837046) expect_equal(model_result[["pm"]], 61.1793644) expect_equal(model_result[["s"]], 0.3599232) expect_equal(model_result[["ik"]], 169.978939) expect_equal(model_result[["im"]], 1320.3078) expect_equal(model_result[["w"]], 5.7674788) } else { skip(paste("Skipping test on unsupported Linux distribution:", distro)) }`: missing value where TRUE/FALSE needed ── Error ('test-eilers_peeters_etr_II_junior_pam.R:57:5'): test-eilers_peeters_etr_II junior_pam_20250613.csv.csv ── Error in `if (grepl("ubuntu", distro) || grepl("debian", distro)) { expect_equal(model_result[["sdiff"]], 18.5975058) expect_equal(model_result[["b"]], 0.01213671) expect_equal(model_result[["c"]], 2.77837046) expect_equal(model_result[["d"]], NA_real_) expect_equal(model_result[["alpha"]], 0.3599232) expect_equal(model_result[["beta"]], NA_real_) expect_equal(model_result[["etrmax_with_photoinhibition"]], 61.1793644) expect_equal(model_result[["etrmax_without_photoinhibition"]], NA_real_) expect_equal(model_result[["ik_with_photoinhibition"]], 169.978939) expect_equal(model_result[["ik_without_photoinhibition"]], NA_real_) expect_equal(model_result[["im_with_photoinhibition"]], 1320.3078) expect_equal(model_result[["w"]], 5.7674788) expect_equal(model_result[["ib"]], NA_real_) expect_equal(model_result[["etrmax_with_without_ratio"]], NA_real_) } else { skip(paste("Skipping test on unsupported Linux distribution:", distro)) }`: missing value where TRUE/FALSE needed ── Error ('test-platt_etr_I.R:13:5'): test-platt_etr_I generate regression 20240925.csv ── Error in `if (grepl("ubuntu", distro) || grepl("debian", distro)) { expect_equal(model_result[["sdiff"]], 55.4812913) expect_equal(model_result[["alpha"]], 0.35079243) expect_equal(model_result[["beta"]], 0.05625881) expect_equal(model_result[["ps"]], 242.02871) expect_equal(model_result[["pm"]], 151.85573) expect_equal(model_result[["ik"]], 432.8934096) expect_equal(model_result[["is"]], 689.94849) expect_equal(model_result[["ib"]], 4302.05878) expect_equal(model_result[["im"]], 1365.3918) } else { skip(paste("Skipping test on unsupported Linux distribution:", distro)) }`: missing value where TRUE/FALSE needed ── Error ('test-platt_etr_I.R:54:5'): test-platt_etr_I generate regression modified 20240925.csv ── Error in `if (grepl("ubuntu", distro) || grepl("debian", distro)) { expect_equal(model_result[["sdiff"]], 55.4812913) expect_equal(model_result[["a"]], 242.02871) expect_equal(model_result[["b"]], 0.35079243) expect_equal(model_result[["c"]], 0.05625881) expect_equal(model_result[["d"]], NA_real_) expect_equal(model_result[["alpha"]], 0.35079243) expect_equal(model_result[["beta"]], 0.05625881) expect_equal(model_result[["etrmax_with_photoinhibition"]], 151.85573) expect_equal(model_result[["etrmax_without_photoinhibition"]], 242.02871) expect_equal(model_result[["ik_with_photoinhibition"]], 432.8934096) expect_equal(model_result[["ik_without_photoinhibition"]], 689.94849) expect_equal(model_result[["im_with_photoinhibition"]], 1365.3918) expect_equal(model_result[["w"]], NA_real_) expect_equal(model_result[["ib"]], 4302.05878) expect_equal(model_result[["etrmax_with_without_ratio"]], 1.593806867) } else { skip(paste("Skipping test on unsupported Linux distribution:", distro)) }`: missing value where TRUE/FALSE needed ── Error ('test-platt_etr_II.R:13:5'): test-platt_etr_II generate regression 20240925.csv ── Error in `if (grepl("ubuntu", distro) || grepl("debian", distro)) { expect_equal(model_result[["sdiff"]], 12.0348133) expect_equal(model_result[["alpha"]], 0.178182825) expect_equal(model_result[["beta"]], 0.035606479) expect_equal(model_result[["ps"]], 76.53219) expect_equal(model_result[["pm"]], 44.5824637) expect_equal(model_result[["ik"]], 250.2062903) expect_equal(model_result[["is"]], 429.514971) expect_equal(model_result[["ib"]], 2149.38944) expect_equal(model_result[["im"]], 769.88984) } else { skip(paste("Skipping test on unsupported Linux distribution:", distro)) }`: missing value where TRUE/FALSE needed ── Error ('test-platt_etr_II.R:71:5'): test-platt_etr_II generate regression modified 20240925.csv ── Error in `if (grepl("ubuntu", distro) || grepl("debian", distro)) { expect_equal(model_result[["sdiff"]], 12.0348133) expect_equal(model_result[["a"]], 76.53219) expect_equal(model_result[["b"]], 0.178182825) expect_equal(model_result[["c"]], 0.035606479) expect_equal(model_result[["d"]], NA_real_) expect_equal(model_result[["alpha"]], 0.178182825) expect_equal(model_result[["beta"]], 0.035606479) expect_equal(model_result[["etrmax_with_photoinhibition"]], 44.5824637) expect_equal(model_result[["etrmax_without_photoinhibition"]], 76.53219) expect_equal(model_result[["ik_with_photoinhibition"]], 250.2062903) expect_equal(model_result[["ik_without_photoinhibition"]], 429.514971) expect_equal(model_result[["im_with_photoinhibition"]], 769.88984) expect_equal(model_result[["w"]], NA_real_) expect_equal(model_result[["ib"]], 2149.38944) expect_equal(model_result[["etrmax_with_without_ratio"]], 1.71664337) } else { skip(paste("Skipping test on unsupported Linux distribution:", distro)) }`: missing value where TRUE/FALSE needed ── Error ('test-vollenweider_etr_I.R:13:5'): test-vollenweider_etr_I generate regression 20240925.csv ── Error in `if (grepl("ubuntu", distro) || grepl("debian", distro)) { expect_equal(model_result[["sdiff"]], 57.4445851) expect_equal(model_result[["pmax"]], 165.46686) expect_equal(model_result[["n"]], 34.8365884) expect_equal(model_result[["ik"]], 536.24749) expect_equal(model_result[["popt"]], 153.09957) expect_equal(model_result[["iik"]], 496.16738) expect_equal(model_result[["pmax_popt_and_ik_iik_ratio"]], 1.08077941) } else { skip(paste("Skipping test on unsupported Linux distribution:", distro)) }`: missing value where TRUE/FALSE needed ── Error ('test-vollenweider_etr_I.R:71:5'): test-vollenweider_etr_I generate regression modified 20240925.csv ── Error in `if (grepl("ubuntu", distro) || grepl("debian", distro)) { expect_equal(model_result[["sdiff"]], 57.4445851) expect_equal(model_result[["a"]], 165.46686) expect_equal(model_result[["d"]], 34.8365884) expect_equal(model_result[["alpha"]], 0.30856436) expect_equal(model_result[["beta"]], NA_real_) expect_equal(model_result[["etrmax_with_photoinhibition"]], 153.09957) expect_equal(model_result[["etrmax_without_photoinhibition"]], 165.46686) expect_equal(model_result[["ik_with_photoinhibition"]], 496.16738) expect_equal(model_result[["ik_without_photoinhibition"]], 536.24749) expect_equal(model_result[["im_with_photoinhibition"]], 1420) expect_equal(model_result[["w"]], NA_real_) expect_equal(model_result[["ib"]], NA_real_) expect_equal(model_result[["etrmax_with_without_ratio"]], 1.08077941) } else { skip(paste("Skipping test on unsupported Linux distribution:", distro)) }`: missing value where TRUE/FALSE needed ── Error ('test-vollenweider_etr_II.R:13:5'): test-vollenweider_etr_II generate regression 20240925.csv ── Error in `if (grepl("ubuntu", distro) || grepl("debian", distro)) { expect_equal(model_result[["sdiff"]], 2.5104818) expect_equal(model_result[["pmax"]], 53.404027) expect_equal(model_result[["n"]], 2.34641) expect_equal(model_result[["ik"]], 351.3752) expect_equal(model_result[["popt"]], 44.16714) expect_equal(model_result[["iik"]], 290.60051) expect_equal(model_result[["pmax_popt_and_ik_iik_ratio"]], 1.209134835) } else { skip(paste("Skipping test on unsupported Linux distribution:", distro)) }`: missing value where TRUE/FALSE needed ── Error ('test-vollenweider_etr_II.R:71:5'): test-vollenweider_etr_II generate regression modified 20240925.csv ── Error in `if (grepl("ubuntu", distro) || grepl("debian", distro)) { expect_equal(model_result[["sdiff"]], 2.5104818) expect_equal(model_result[["a"]], 53.404027) expect_equal(model_result[["d"]], 2.34641) expect_equal(model_result[["alpha"]], 0.15198576) expect_equal(model_result[["beta"]], NA_real_) expect_equal(model_result[["etrmax_with_photoinhibition"]], 44.16714) expect_equal(model_result[["etrmax_without_photoinhibition"]], 53.404027) expect_equal(model_result[["ik_with_photoinhibition"]], 290.60051) expect_equal(model_result[["ik_without_photoinhibition"]], 351.3752) expect_equal(model_result[["im_with_photoinhibition"]], 757) expect_equal(model_result[["w"]], NA_real_) expect_equal(model_result[["ib"]], NA_real_) expect_equal(model_result[["etrmax_with_without_ratio"]], 1.209134835) } else { skip(paste("Skipping test on unsupported Linux distribution:", distro)) }`: missing value where TRUE/FALSE needed ── Error ('test-walsby_etr_I.R:13:5'): test-walsby_etr_I generate regression 20240925.csv ── Error in `if (grepl("ubuntu", distro) || grepl("debian", distro)) { expect_equal(model_result[["sdiff"]], 55.5823146) expect_equal(model_result[["etr_max"]], 221.23782) expect_equal(model_result[["alpha"]], 0.387249932) expect_equal(model_result[["beta"]], -0.035964253) } else { skip(paste("Skipping test on unsupported Linux distribution:", distro)) }`: missing value where TRUE/FALSE needed ── Error ('test-walsby_etr_I.R:61:5'): test-walsby_etr_I generate regression modified 20240925.csv ── Error in `if (grepl("ubuntu", distro) || grepl("debian", distro)) { expect_equal(model_result[["sdiff"]], 55.5823146) expect_equal(model_result[["a"]], 221.23782) expect_equal(model_result[["b"]], 0.387249932) expect_equal(model_result[["c"]], -0.035964253) expect_equal(model_result[["d"]], NA_real_) expect_equal(model_result[["alpha"]], 0.387249932) expect_equal(model_result[["beta"]], -0.035964253) expect_equal(model_result[["etrmax_with_photoinhibition"]], 151.8614464) expect_equal(model_result[["etrmax_without_photoinhibition"]], 221.23782) expect_equal(model_result[["ik_with_photoinhibition"]], 392.15358) expect_equal(model_result[["ik_without_photoinhibition"]], 571.305) expect_equal(model_result[["im_with_photoinhibition"]], 1358) expect_equal(model_result[["w"]], NA_real_) expect_equal(model_result[["ib"]], NA_real_) expect_equal(model_result[["etrmax_with_without_ratio"]], 1.456839939) } else { skip(paste("Skipping test on unsupported Linux distribution:", distro)) }`: missing value where TRUE/FALSE needed ── Error ('test-walsby_etr_II.R:13:5'): test-walsby_etr_II generate regression 20240925.csv ── Error in `if (grepl("ubuntu", distro) || grepl("debian", distro)) { expect_equal(model_result[["sdiff"]], 13.3218134) expect_equal(model_result[["etr_max"]], 64.6205229) expect_equal(model_result[["alpha"]], 0.19796623) expect_equal(model_result[["beta"]], -0.018109036) } else { skip(paste("Skipping test on unsupported Linux distribution:", distro)) }`: missing value where TRUE/FALSE needed ── Error ('test-walsby_etr_II.R:61:5'): test-walsby_etr_II generate regression modified 20240925.csv ── Error in `if (grepl("ubuntu", distro) || grepl("debian", distro)) { expect_equal(model_result[["sdiff"]], 13.3218134) expect_equal(model_result[["a"]], 64.6205229) expect_equal(model_result[["b"]], 0.19796623) expect_equal(model_result[["c"]], -0.018109036) expect_equal(model_result[["d"]], NA_real_) expect_equal(model_result[["alpha"]], 0.19796623) expect_equal(model_result[["beta"]], -0.018109036) expect_equal(model_result[["etrmax_with_photoinhibition"]], 44.5716344) expect_equal(model_result[["etrmax_without_photoinhibition"]], 64.6205229) expect_equal(model_result[["ik_with_photoinhibition"]], 225.14766) expect_equal(model_result[["ik_without_photoinhibition"]], 326.421945) expect_equal(model_result[["im_with_photoinhibition"]], 781) expect_equal(model_result[["w"]], NA_real_) expect_equal(model_result[["ib"]], NA_real_) expect_equal(model_result[["etrmax_with_without_ratio"]], 1.449812727) } else { skip(paste("Skipping test on unsupported Linux distribution:", distro)) }`: missing value where TRUE/FALSE needed [ FAIL 21 | WARN 4 | SKIP 0 | PASS 21 ] Error: Test failures Execution halted * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [1s/1s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR