* using log directory ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/chemdeg.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc-13 (Debian 13.2.0-25) 13.2.0 GNU Fortran (Debian 13.2.0-25) 13.2.0 * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘chemdeg/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘chemdeg’ version ‘0.1.2’ * 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 serialization versions ... OK * checking whether package ‘chemdeg’ can be installed ... OK See 'https://www.r-project.org/nosvn/R.check/r-release-linux-x86_64/chemdeg-00install.html' 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 ... [6s/8s] OK * checking Rd files ... [1s/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/1s] 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 ... [1s/1s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [5s/7s] ERROR Running ‘testthat.R’ [5s/6s] 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/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > library(chemdeg) > > test_check("chemdeg") Reaction order estimated: 0 Reaction order estimated: 0 Reaction order estimated: 1 Reaction order estimated: 1 Kinetic model was not found in object. Probably the phasespace regression was not significant. Reaction order estimated: 1.5 Reaction order estimated: 1 Reaction order estimated: 1 Reaction order estimated: 1 Reaction order estimated: 0 Reaction order estimated: 1 Reaction order estimated: 1 Reaction order estimated: 0 Reaction order estimated: 1 Reaction order estimated: 1 Reaction order estimated: 1 Reaction order estimated: 1 Reaction order estimated: 0 Linear regression in the phase space: log(dx/dt)= -0.04 log(x) + ( -3.25 ) Estimate of n: Estimate Std. Error t value Pr(>|t|) -0.03946285 0.33112985 -0.11917637 0.91266817 Confidence interval of n: 2.5 % 97.5 % -1.093266 1.014340 Estimate of the intercept is significant; but the estimate of slope is not. The data are likely to be described by an 0-order kinetic model. Linear regression was performed (0-order kinetics). Estimated k value: Call: stats::lm(formula = y ~ t, data = list(t = dframe[[1]], y = dframe[[2]])) Residuals: 1 2 3 4 5 6 -0.009048 0.025238 -0.030476 0.023810 -0.011905 0.002381 Coefficients: Estimate Std. Error t value Pr(>|t|) (Intercept) 0.999048 0.017587 56.81 5.75e-07 *** t -0.041071 0.001452 -28.28 9.30e-06 *** --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 Residual standard error: 0.0243 on 4 degrees of freedom Multiple R-squared: 0.995, Adjusted R-squared: 0.9938 F-statistic: 799.9 on 1 and 4 DF, p-value: 9.3e-06 Confidence interval of k: 2.5 % 97.5 % 0.04510334 0.03703951 ----------------------------------------------------- Reaction order estimated: 1 Linear regression in the phase space: log(dx/dt)= 0.89 log(x) + ( -1.91 ) Estimate of n: Estimate Std. Error t value Pr(>|t|) 0.888563736 0.127851818 6.949949979 0.006110383 Confidence interval of n: 2.5 % 97.5 % 0.4816822 1.2954453 Statistical analysis indicates that an order 1 degradation kineitc model is likely to describe the data. The null hypothesis H0: "The process is described by an order 1kinetic model" cannot be rejected. Non-linear least squares regression was performed with an order 1 kinetic model: Estimate of k: Estimate Std. Error t value Pr(>|t|) k 0.1738856 0.002646756 65.69763 1.546955e-08 Waiting for profiling to be done... Confidence interval of k: 2.5% 97.5% 0.1673077 0.1808505 Goodness-of-fit: Value AIC: -36.613622360 AICc: -35.613622360 BIC: -37.030103421 RMSE: 0.008984573 Chi-sq_red: NA NB: Reduced Chi-squared is not calculated with unweighted data ----------------------------------------------------- Linear regression in the phase space: log(dx/dt)= -0.2 log(x) + ( -2.25 ) Estimate of n: Estimate Std. Error t value Pr(>|t|) -0.1972895 0.9500588 -0.2076603 0.8547198 Confidence interval of n: 2.5 % 97.5 % -4.285062 3.890483 The process is not appropriately described by a standard n-order kinetic model. Alternative models should be evaluated. ----------------------------------------------------- Reaction order estimated: 1.4 Linear regression in the phase space: log(dx/dt)= 1.44 log(x) + ( -1.92 ) Estimate of n: Estimate Std. Error t value Pr(>|t|) 1.435918e+00 5.165275e-02 2.779944e+01 1.021746e-04 Confidence interval of n: 2.5 % 97.5 % 1.271536 1.600300 The confidence interval of n excludes integer-valued orders. The best estimate n= 1.4 was used to perform the regression. Non-linear least squares regression was performed with an order 1.4 kinetic model: Estimate of k: Estimate Std. Error t value Pr(>|t|) k 0.05819536 0.0006888422 84.48287 4.403611e-09 Waiting for profiling to be done... Confidence interval of k: 2.5% 97.5% 0.05645665 0.06001526 Goodness-of-fit: Value AIC: -13.205197 AICc: -12.205197 BIC: -13.621678 RMSE: 2.012016 Chi-sq_red: 6.166408 ----------------------------------------------------- Reaction order estimated: 0 Linear regression in the phase space: log(dx/dt)= 8.62 log(x) + ( -2.22 ) Estimate of n: Estimate Std. Error t value Pr(>|t|) 8.6222350 6.5703303 1.3122986 0.2807935 Confidence interval of n: 2.5 % 97.5 % -12.28749 29.53196 Estimate of the intercept is significant; but the estimate of slope is not. The data are likely to be described by an 0-order kinetic model. Estimates of model parameters are not significant. Alternative models should be evaluated. Linear regression in the phase space: log(dx/dt)= 8.62 log(x) + ( -2.22 ) Estimate of n: Estimate Std. Error t value Pr(>|t|) 8.6222350 6.5703303 1.3122986 0.2807935 Confidence interval of n: 2.5 % 97.5 % -12.28749 29.53196 Estimate of the intercept is significant; but the estimate of slope is not. The data are likely to be described by an 0-order kinetic model. Estimates of model parameters are not significant. Alternative models should be evaluated.Reaction order estimated: 1 Linear regression in the phase space: log(dx/dt)= 1.02 log(x) + ( -0.77 ) Estimate of n: Estimate Std. Error t value Pr(>|t|) 1.015092e+00 3.052917e-02 3.324993e+01 5.979796e-05 Confidence interval of n: 2.5 % 97.5 % 0.9179351 1.1122499 Statistical analysis indicates that an order 1 degradation kineitc model is likely to describe the data. The null hypothesis H0: "The process is described by an order 1kinetic model" cannot be rejected. Estimates of model parameters are not significant. Alternative models should be evaluated Linear regression in the phase space: log(dx/dt)= 1.02 log(x) + ( -0.77 ) Estimate of n: Estimate Std. Error t value Pr(>|t|) 1.015092e+00 3.052917e-02 3.324993e+01 5.979796e-05 Confidence interval of n: 2.5 % 97.5 % 0.9179351 1.1122499 Statistical analysis indicates that an order 1 degradation kineitc model is likely to describe the data. The null hypothesis H0: "The process is described by an order 1kinetic model" cannot be rejected. Estimates of model parameters are not significant. Alternative models should be evaluatedReaction order estimated: 1.4 Reaction order estimated: 1.4 Reaction order estimated: 0 Reaction order estimated: 0 NB: parameters of the regression are not significant! [ FAIL 3 | WARN 0 | SKIP 0 | PASS 137 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-det_order.R:228:3'): det_order works with 2-order model with unweighted data ── res[[6]] (`actual`) not equal to c(Order = 2) (`expected`). `actual`: NaN `expected`: 2 ── Failure ('test-det_order.R:229:3'): det_order works with 2-order model with unweighted data ── k_value(res) (`actual`) not equal to c(k = 0.5) (`expected`). `actual` is NULL `expected` is a double vector (0.5) ── Failure ('test-det_order.R:230:3'): det_order works with 2-order model with unweighted data ── res[[4]] is not an S3 object [ FAIL 3 | WARN 0 | SKIP 0 | PASS 137 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [5s/7s] OK * checking PDF version of manual ... [6s/8s] OK * checking HTML version of manual ... [1s/2s] OK * checking for non-standard things in the check directory ... OK * DONE Status: 1 ERROR