• using R Under development (unstable) (2025-01-14 r87571)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-14 (GCC) 14.2.0     GNU Fortran (GCC) 14.2.0
• running under: Fedora Linux 36 (Workstation Edition)
• using session charset: UTF-8
• using option ‘--no-stop-on-test-error’
• checking for file ‘pam/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘pam’ version ‘1.0.0’
• 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 whether package ‘pam’ can be installed ... OK See the install log for details.
• checking package 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 ... OK
• checking whether the package can be loaded with stated dependencies ... OK
• checking whether the package can be unloaded cleanly ... OK
• checking whether the namespace can be loaded with stated dependencies ... OK
• checking whether the namespace can be unloaded cleanly ... OK
• checking loading without being on the library search path ... 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 ... OK
• checking Rd files ... 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 ... OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [36s/36s] ERROR   Running ‘testthat.R’ [35s/36s] 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")   file: 20231123_03.csv processed with warning: simpleWarning in value[[3L]](cond): warning while calculating eilers peeters model: simpleWarning in value[[3L]](cond): failed to calculate etr_max: warning: simpleWarning in sqrt(a * c): NaNs produced            file: 20231123_04.csv processed with warning: simpleWarning in value[[3L]](cond): warning while calculating eilers peeters model: simpleWarning in value[[3L]](cond): failed to calculate etr_max: warning: simpleWarning in sqrt(a * c): NaNs produced            file: 20231123_06.csv processed with warning: simpleWarning in value[[3L]](cond): warning while calculating platt model: simpleWarning in value[[3L]](cond): failed to calculate im: warning: simpleWarning in log((alpha + beta)/beta): NaNs produced            file: 20231214.csv processed with warning: simpleWarning in value[[3L]](cond): warning while calculating platt model: simpleWarning in value[[3L]](cond): failed to calculate im: warning: simpleWarning in log((alpha + beta)/beta): NaNs produced            file: 20231214_11.csv processed with warning: simpleWarning in value[[3L]](cond): warning while calculating eilers peeters model: simpleWarning in value[[3L]](cond): failed to calculate etr_max: warning: simpleWarning in sqrt(a * c): NaNs produced            file: 20231214_14.csv processed with warning: simpleWarning in value[[3L]](cond): warning while calculating eilers peeters model: simpleWarning in value[[3L]](cond): failed to calculate etr_max: warning: simpleWarning in sqrt(a * c): NaNs produced            file: 20231214_15.csv processed with warning: simpleWarning in value[[3L]](cond): warning while calculating eilers peeters model: simpleWarning in value[[3L]](cond): failed to calculate etr_max: warning: simpleWarning in sqrt(a * c): NaNs produced            file: 20231214_10.csv processed with warning: simpleWarning in value[[3L]](cond): warning while calculating platt model: simpleWarning in value[[3L]](cond): failed to calculate im: warning: simpleWarning in log((alpha + beta)/beta): NaNs produced            file: 20231123_03.csv processed with warning: simpleWarning in value[[3L]](cond): warning while calculating eilers peeters model: simpleWarning in value[[3L]](cond): failed to calculate etr_max: warning: simpleWarning in sqrt(a * c): NaNs produced            file: 20231123_04.csv processed with warning: simpleWarning in value[[3L]](cond): warning while calculating eilers peeters model: simpleWarning in value[[3L]](cond): failed to calculate etr_max: warning: simpleWarning in sqrt(a * c): NaNs produced            file: 20231123_06.csv processed with warning: simpleWarning in value[[3L]](cond): warning while calculating platt model: simpleWarning in value[[3L]](cond): failed to calculate im: warning: simpleWarning in log((alpha + beta)/beta): NaNs produced            file: 20231214.csv processed with warning: simpleWarning in value[[3L]](cond): warning while calculating platt model: simpleWarning in value[[3L]](cond): failed to calculate im: warning: simpleWarning in log((alpha + beta)/beta): NaNs produced            file: 20231214_11.csv processed with warning: simpleWarning in value[[3L]](cond): warning while calculating eilers peeters model: simpleWarning in value[[3L]](cond): failed to calculate etr_max: warning: simpleWarning in sqrt(a * c): NaNs produced            file: 20231214_14.csv processed with warning: simpleWarning in value[[3L]](cond): warning while calculating eilers peeters model: simpleWarning in value[[3L]](cond): failed to calculate etr_max: warning: simpleWarning in sqrt(a * c): NaNs produced            file: 20231214_15.csv processed with warning: simpleWarning in value[[3L]](cond): warning while calculating eilers peeters model: simpleWarning in value[[3L]](cond): failed to calculate etr_max: warning: simpleWarning in sqrt(a * c): NaNs produced            file: 20231214_10.csv processed with warning: simpleWarning in value[[3L]](cond): warning while calculating platt model: simpleWarning in value[[3L]](cond): failed to calculate im: warning: simpleWarning in log((alpha + beta)/beta): NaNs produced            [ FAIL 51 | WARN 16 | SKIP 0 | PASS 149 ]      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Failure ('test-platt_etr_I.R:10:5'): test-platt_etr_I generate regression 20240925.csv ──   model_result[["alpha"]] (`actual`) not equal to 0.35079243 (`expected`).        `actual`: 0.350792437   `expected`: 0.350792430   ── Failure ('test-platt_etr_I.R:11:5'): test-platt_etr_I generate regression 20240925.csv ──   model_result[["beta"]] (`actual`) not equal to 0.05625881 (`expected`).        `actual`: 0.056258772   `expected`: 0.056258810   ── Failure ('test-platt_etr_I.R:12:5'): test-platt_etr_I generate regression 20240925.csv ──   model_result[["ps"]] (`actual`) not equal to 242.02871 (`expected`).        `actual`: 242.028655   `expected`: 242.028710   ── Failure ('test-platt_etr_I.R:14:5'): test-platt_etr_I generate regression 20240925.csv ──   model_result[["ik"]] (`actual`) not equal to 432.8934096 (`expected`).        `actual`: 432.8934027   `expected`: 432.8934096   ── Failure ('test-platt_etr_I.R:15:5'): test-platt_etr_I generate regression 20240925.csv ──   model_result[["is"]] (`actual`) not equal to 689.94849 (`expected`).        `actual`: 689.94833   `expected`: 689.94849   ── Failure ('test-platt_etr_I.R:16:5'): test-platt_etr_I generate regression 20240925.csv ──   model_result[["ib"]] (`actual`) not equal to 4302.05878 (`expected`).        `actual`: 4302.0607   `expected`: 4302.0588   ── Failure ('test-platt_etr_I.R:17:5'): test-platt_etr_I generate regression 20240925.csv ──   model_result[["im"]] (`actual`) not equal to 1365.3918 (`expected`).        `actual`: 1365.391883   `expected`: 1365.391800   ── Failure ('test-platt_etr_I.R:44:5'): test-platt_etr_I generate regression modified 20240925.csv ──   model_result[["a"]] (`actual`) not equal to 242.02871 (`expected`).        `actual`: 242.028655   `expected`: 242.028710   ── Failure ('test-platt_etr_I.R:45:5'): test-platt_etr_I generate regression modified 20240925.csv ──   model_result[["b"]] (`actual`) not equal to 0.35079243 (`expected`).        `actual`: 0.350792437   `expected`: 0.350792430   ── Failure ('test-platt_etr_I.R:46:5'): test-platt_etr_I generate regression modified 20240925.csv ──   model_result[["c"]] (`actual`) not equal to 0.05625881 (`expected`).        `actual`: 0.056258772   `expected`: 0.056258810   ── Failure ('test-platt_etr_I.R:48:5'): test-platt_etr_I generate regression modified 20240925.csv ──   model_result[["alpha"]] (`actual`) not equal to 0.35079243 (`expected`).        `actual`: 0.350792437   `expected`: 0.350792430   ── Failure ('test-platt_etr_I.R:49:5'): test-platt_etr_I generate regression modified 20240925.csv ──   model_result[["beta"]] (`actual`) not equal to 0.05625881 (`expected`).        `actual`: 0.056258772   `expected`: 0.056258810   ── Failure ('test-platt_etr_I.R:51:5'): test-platt_etr_I generate regression modified 20240925.csv ──   model_result[["etrmax_without_photoinhibition"]] (`actual`) not equal to 242.02871 (`expected`).        `actual`: 242.028655   `expected`: 242.028710   ── Failure ('test-platt_etr_I.R:52:5'): test-platt_etr_I generate regression modified 20240925.csv ──   model_result[["ik_with_photoinhibition"]] (`actual`) not equal to 432.8934096 (`expected`).        `actual`: 432.8934027   `expected`: 432.8934096   ── Failure ('test-platt_etr_I.R:53:5'): test-platt_etr_I generate regression modified 20240925.csv ──   model_result[["ik_without_photoinhibition"]] (`actual`) not equal to 689.94849 (`expected`).        `actual`: 689.94833   `expected`: 689.94849   ── Failure ('test-platt_etr_I.R:54:5'): test-platt_etr_I generate regression modified 20240925.csv ──   model_result[["im_with_photoinhibition"]] (`actual`) not equal to 1365.3918 (`expected`).        `actual`: 1365.391883   `expected`: 1365.391800   ── Failure ('test-platt_etr_I.R:56:5'): test-platt_etr_I generate regression modified 20240925.csv ──   model_result[["ib"]] (`actual`) not equal to 4302.05878 (`expected`).        `actual`: 4302.0607   `expected`: 4302.0588   ── Failure ('test-platt_etr_I.R:57:5'): test-platt_etr_I generate regression modified 20240925.csv ──   model_result[["etrmax_with_without_ratio"]] (`actual`) not equal to 1.593806867 (`expected`).        `actual`: 1.59380652   `expected`: 1.59380687   ── Failure ('test-vollenweider_etr_I.R:9:5'): test-vollenweider_etr_I generate regression 20240925.csv ──   model_result[["sdiff"]] (`actual`) not equal to 57.4445851 (`expected`).        `actual`: 57.444548   `expected`: 57.444585   ── Failure ('test-vollenweider_etr_I.R:10:5'): test-vollenweider_etr_I generate regression 20240925.csv ──   model_result[["pmax"]] (`actual`) not equal to 165.46686 (`expected`).        `actual`: 165.466889   `expected`: 165.466860   ── Failure ('test-vollenweider_etr_I.R:13:5'): test-vollenweider_etr_I generate regression 20240925.csv ──   model_result[["n"]] (`actual`) not equal to 34.8365884 (`expected`).        `actual`: 37.6   `expected`: 34.8   ── Failure ('test-vollenweider_etr_I.R:14:5'): test-vollenweider_etr_I generate regression 20240925.csv ──   model_result[["ik"]] (`actual`) not equal to 536.24749 (`expected`).        `actual`: 536.24763   `expected`: 536.24749   ── Failure ('test-vollenweider_etr_I.R:15:5'): test-vollenweider_etr_I generate regression 20240925.csv ──   model_result[["popt"]] (`actual`) not equal to 153.09957 (`expected`).        `actual`: 153.09935   `expected`: 153.09957   ── Failure ('test-vollenweider_etr_I.R:16:5'): test-vollenweider_etr_I generate regression 20240925.csv ──   model_result[["iik"]] (`actual`) not equal to 496.16738 (`expected`).        `actual`: 496.16673   `expected`: 496.16738   ── Failure ('test-vollenweider_etr_I.R:17:5'): test-vollenweider_etr_I generate regression 20240925.csv ──   model_result[["pmax_popt_and_ik_iik_ratio"]] (`actual`) not equal to 1.08077941 (`expected`).        `actual`: 1.0807811   `expected`: 1.0807794   ── Failure ('test-vollenweider_etr_I.R:60:5'): test-vollenweider_etr_I generate regression modified 20240925.csv ──   model_result[["sdiff"]] (`actual`) not equal to 57.4445851 (`expected`).        `actual`: 57.444548   `expected`: 57.444585   ── Failure ('test-vollenweider_etr_I.R:61:5'): test-vollenweider_etr_I generate regression modified 20240925.csv ──   model_result[["a"]] (`actual`) not equal to 165.46686 (`expected`).        `actual`: 165.466889   `expected`: 165.466860   ── Failure ('test-vollenweider_etr_I.R:64:5'): test-vollenweider_etr_I generate regression modified 20240925.csv ──   model_result[["d"]] (`actual`) not equal to 34.8365884 (`expected`).        `actual`: 37.6   `expected`: 34.8   ── Failure ('test-vollenweider_etr_I.R:65:5'): test-vollenweider_etr_I generate regression modified 20240925.csv ──   model_result[["alpha"]] (`actual`) not equal to 0.30856436 (`expected`).        `actual`: 0.308564323   `expected`: 0.308564360   ── Failure ('test-vollenweider_etr_I.R:67:5'): test-vollenweider_etr_I generate regression modified 20240925.csv ──   model_result[["etrmax_with_photoinhibition"]] (`actual`) not equal to 153.09957 (`expected`).        `actual`: 153.09935   `expected`: 153.09957   ── Failure ('test-vollenweider_etr_I.R:68:5'): test-vollenweider_etr_I generate regression modified 20240925.csv ──   model_result[["etrmax_without_photoinhibition"]] (`actual`) not equal to 165.46686 (`expected`).        `actual`: 165.466889   `expected`: 165.466860   ── Failure ('test-vollenweider_etr_I.R:69:5'): test-vollenweider_etr_I generate regression modified 20240925.csv ──   model_result[["ik_with_photoinhibition"]] (`actual`) not equal to 496.16738 (`expected`).        `actual`: 496.16673   `expected`: 496.16738   ── Failure ('test-vollenweider_etr_I.R:70:5'): test-vollenweider_etr_I generate regression modified 20240925.csv ──   model_result[["ik_without_photoinhibition"]] (`actual`) not equal to 536.24749 (`expected`).        `actual`: 536.24763   `expected`: 536.24749   ── Failure ('test-vollenweider_etr_I.R:74:5'): test-vollenweider_etr_I generate regression modified 20240925.csv ──   model_result[["etrmax_with_without_ratio"]] (`actual`) not equal to 1.08077941 (`expected`).        `actual`: 1.0807811   `expected`: 1.0807794   ── Failure ('test-vollenweider_etr_II.R:9:5'): test-vollenweider_etr_II generate regression 20240925.csv ──   model_result[["sdiff"]] (`actual`) not equal to 2.5104818 (`expected`).        `actual`: 2.480   `expected`: 2.510   ── Failure ('test-vollenweider_etr_II.R:10:5'): test-vollenweider_etr_II generate regression 20240925.csv ──   model_result[["pmax"]] (`actual`) not equal to 53.404027 (`expected`).        `actual`: 53.458   `expected`: 53.404   ── Failure ('test-vollenweider_etr_II.R:13:5'): test-vollenweider_etr_II generate regression 20240925.csv ──   model_result[["n"]] (`actual`) not equal to 2.34641 (`expected`).        `actual`: 2.19   `expected`: 2.35   ── Failure ('test-vollenweider_etr_II.R:14:5'): test-vollenweider_etr_II generate regression 20240925.csv ──   model_result[["ik"]] (`actual`) not equal to 351.3752 (`expected`).        `actual`: 351.82   `expected`: 351.38   ── Failure ('test-vollenweider_etr_II.R:15:5'): test-vollenweider_etr_II generate regression 20240925.csv ──   model_result[["popt"]] (`actual`) not equal to 44.16714 (`expected`).        `actual`: 44.1710   `expected`: 44.1671   ── Failure ('test-vollenweider_etr_II.R:16:5'): test-vollenweider_etr_II generate regression 20240925.csv ──   model_result[["iik"]] (`actual`) not equal to 290.60051 (`expected`).        `actual`: 290.71   `expected`: 290.60   ── Failure ('test-vollenweider_etr_II.R:17:5'): test-vollenweider_etr_II generate regression 20240925.csv ──   model_result[["pmax_popt_and_ik_iik_ratio"]] (`actual`) not equal to 1.209134835 (`expected`).        `actual`: 1.2102   `expected`: 1.2091   ── Failure ('test-vollenweider_etr_II.R:60:5'): test-vollenweider_etr_II generate regression modified 20240925.csv ──   model_result[["sdiff"]] (`actual`) not equal to 2.5104818 (`expected`).        `actual`: 2.480   `expected`: 2.510   ── Failure ('test-vollenweider_etr_II.R:61:5'): test-vollenweider_etr_II generate regression modified 20240925.csv ──   model_result[["a"]] (`actual`) not equal to 53.404027 (`expected`).        `actual`: 53.458   `expected`: 53.404   ── Failure ('test-vollenweider_etr_II.R:64:5'): test-vollenweider_etr_II generate regression modified 20240925.csv ──   model_result[["d"]] (`actual`) not equal to 2.34641 (`expected`).        `actual`: 2.19   `expected`: 2.35   ── Failure ('test-vollenweider_etr_II.R:65:5'): test-vollenweider_etr_II generate regression modified 20240925.csv ──   model_result[["alpha"]] (`actual`) not equal to 0.15198576 (`expected`).        `actual`: 0.151944   `expected`: 0.151986   ── Failure ('test-vollenweider_etr_II.R:67:5'): test-vollenweider_etr_II generate regression modified 20240925.csv ──   model_result[["etrmax_with_photoinhibition"]] (`actual`) not equal to 44.16714 (`expected`).        `actual`: 44.1710   `expected`: 44.1671   ── Failure ('test-vollenweider_etr_II.R:68:5'): test-vollenweider_etr_II generate regression modified 20240925.csv ──   model_result[["etrmax_without_photoinhibition"]] (`actual`) not equal to 53.404027 (`expected`).        `actual`: 53.458   `expected`: 53.404   ── Failure ('test-vollenweider_etr_II.R:69:5'): test-vollenweider_etr_II generate regression modified 20240925.csv ──   model_result[["ik_with_photoinhibition"]] (`actual`) not equal to 290.60051 (`expected`).        `actual`: 290.71   `expected`: 290.60   ── Failure ('test-vollenweider_etr_II.R:70:5'): test-vollenweider_etr_II generate regression modified 20240925.csv ──   model_result[["ik_without_photoinhibition"]] (`actual`) not equal to 351.3752 (`expected`).        `actual`: 351.82   `expected`: 351.38   ── Failure ('test-vollenweider_etr_II.R:71:5'): test-vollenweider_etr_II generate regression modified 20240925.csv ──   model_result[["im_with_photoinhibition"]] (`actual`) not equal to 757 (`expected`).        `actual`: 756.0   `expected`: 757.0   ── Failure ('test-vollenweider_etr_II.R:74:5'): test-vollenweider_etr_II generate regression modified 20240925.csv ──   model_result[["etrmax_with_without_ratio"]] (`actual`) not equal to 1.209134835 (`expected`).        `actual`: 1.2102   `expected`: 1.2091      [ FAIL 51 | WARN 16 | SKIP 0 | PASS 149 ]   Error: Test failures   Execution halted
• checking PDF version of manual ... OK
• checking HTML version of manual ... OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE

Status: 1 ERROR