From 43af185533b11327368148a44e9295ea3eb3abb1 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 23 Nov 2023 06:17:28 +0100 Subject: Bump version, fix test from last commit, check and test --- log/build.log | 2 +- log/check.log | 29 +++++------ log/test.log | 161 +++++++++++++++++----------------------------------------- 3 files changed, 60 insertions(+), 132 deletions(-) (limited to 'log') diff --git a/log/build.log b/log/build.log index 6f7ac8ab..b4269860 100644 --- a/log/build.log +++ b/log/build.log @@ -7,5 +7,5 @@ * checking for empty or unneeded directories Removed empty directory ‘mkin/inst/rmarkdown/templates/hierarchical_kinetics_parent’ Removed empty directory ‘mkin/vignettes/web_only’ -* building ‘mkin_1.2.6.tar.gz’ +* building ‘mkin_1.2.7.tar.gz’ diff --git a/log/check.log b/log/check.log index 64457e57..26fdc5a0 100644 --- a/log/check.log +++ b/log/check.log @@ -1,17 +1,17 @@ -* using log directory ‘/home/agsad.admin.ch/f80868656/projects/mkin/mkin.Rcheck’ -* using R version 4.3.1 (2023-06-16) +* using log directory ‘/home/jranke/git/mkin/mkin.Rcheck’ +* using R version 4.3.2 (2023-10-31) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.3 LTS + gcc (Debian 12.2.0-14) 12.2.0 + GNU Fortran (Debian 12.2.0-14) 12.2.0 +* running under: Debian GNU/Linux 12 (bookworm) * using session charset: UTF-8 * using options ‘--no-tests --as-cran’ * checking for file ‘mkin/DESCRIPTION’ ... OK * checking extension type ... Package -* this is package ‘mkin’ version ‘1.2.5’ +* this is package ‘mkin’ version ‘1.2.7’ * package encoding: UTF-8 -* checking CRAN incoming feasibility ... [5s/26s] Note_to_CRAN_maintainers +* checking CRAN incoming feasibility ... [2s/15s] Note_to_CRAN_maintainers Maintainer: ‘Johannes Ranke ’ * checking package namespace information ... OK * checking package dependencies ... OK @@ -45,7 +45,7 @@ Maintainer: ‘Johannes Ranke ’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK -* checking R code for possible problems ... [14s/15s] OK +* checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK @@ -62,22 +62,17 @@ Maintainer: ‘Johannes Ranke ’ * checking sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK -* checking examples ... [20s/22s] OK +* checking examples ... [10s/10s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... SKIPPED * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK -* checking re-building of vignette outputs ... [17s/18s] OK +* checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK -* checking HTML version of manual ... NOTE -Skipping checking HTML validation: no command 'tidy' found +* 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 NOTE -See - ‘/home/agsad.admin.ch/f80868656/projects/mkin/mkin.Rcheck/00check.log’ -for details. - +Status: OK diff --git a/log/test.log b/log/test.log index 6d5bc470..a6ac83ed 100644 --- a/log/test.log +++ b/log/test.log @@ -1,117 +1,50 @@ ℹ Testing mkin -✔ | F W S OK | Context -✔ | 5 | AIC calculation -✔ | 5 | Analytical solutions for coupled models [1.5s] -✔ | 5 | Calculation of Akaike weights -✔ | 3 | Export dataset for reading into CAKE -✔ | 6 | Use of precompiled symbols in mkinpredict [3.1s] -✔ | 12 | Confidence intervals and p-values [0.4s] -✔ | 1 12 | Dimethenamid data from 2018 [13.2s] -──────────────────────────────────────────────────────────────────────────────── -Skip ('test_dmta.R:88:3'): Different backends get consistent results for SFO-SFO3+, dimethenamid data -Reason: Fitting this ODE model with saemix takes about 5 minutes on my new system -──────────────────────────────────────────────────────────────────────────────── -✔ | 14 | Error model fitting [2.5s] -✔ | 5 | Time step normalisation -✔ | 4 | Calculation of FOCUS chi2 error levels [0.3s] -✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.4s] -✔ | 4 | Test fitting the decline of metabolites from their maximum [0.2s] -✔ | 1 | Fitting the logistic model [0.1s] -✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [19.0s] -✖ | 1 2 15 | Nonlinear mixed-effects models [149.2s] -──────────────────────────────────────────────────────────────────────────────── -Failure ('test_mixed.R:21:3'): Print methods work -Results have changed from known value recorded in 'print_dfop_saem_1.txt'. - -old[13:23] vs new[13:23] - "" - "Fitted parameters:" - " estimate lower upper" -- "parent_0 99.92 98.77 101.06" -+ "parent_0 99.96 98.82 101.11" -- "log_k1 -2.72 -2.95 -2.50" -+ "log_k1 -2.71 -2.94 -2.49" -- "log_k2 -4.14 -4.27 -4.01" -+ "log_k2 -4.14 -4.26 -4.01" -- "g_qlogis -0.35 -0.53 -0.16" -+ "g_qlogis -0.36 -0.54 -0.17" -- "a.1 0.92 0.68 1.16" -+ "a.1 0.93 0.69 1.17" - "b.1 0.05 0.04 0.06" - "SD.log_k1 0.37 0.23 0.51" -and 1 more ... - -Skip ('test_mixed.R:80:3'): saemix results are reproducible for biphasic fits -Reason: Fitting with saemix takes around 10 minutes when using deSolve - -Skip ('test_mixed.R:133:3'): SFO-SFO saemix specific analytical solution work -Reason: This is seldom used, so save some time -──────────────────────────────────────────────────────────────────────────────── -✔ | 3 | Test dataset classes mkinds and mkindsg -✔ | 10 | Special cases of mkinfit calls [0.3s] -✔ | 3 | mkinfit features [0.5s] -✔ | 8 | mkinmod model generation and printing -✔ | 3 | Model predictions with mkinpredict [0.1s] -✖ | 3 9 | Multistart method for saem.mmkin models [23.2s] -──────────────────────────────────────────────────────────────────────────────── -Failure ('test_multistart.R:44:3'): multistart works for saem.mmkin models -Snapshot of `testcase` to 'multistart/mixed-model-fit-for-saem-object-with-mkin-transformations.svg' has changed -Run `testthat::snapshot_review('multistart/')` to review changes -Backtrace: - 1. vdiffr::expect_doppelganger(...) - at test_multistart.R:44:2 - 3. testthat::expect_snapshot_file(...) - -Failure ('test_multistart.R:55:3'): multistart works for saem.mmkin models -Snapshot of `testcase` to 'multistart/llhist-for-dfop-sfo-fit.svg' has changed -Run `testthat::snapshot_review('multistart/')` to review changes -Backtrace: - 1. vdiffr::expect_doppelganger("llhist for dfop sfo fit", llhist_dfop_sfo) - at test_multistart.R:55:2 - 3. testthat::expect_snapshot_file(...) - -Failure ('test_multistart.R:56:3'): multistart works for saem.mmkin models -Snapshot of `testcase` to 'multistart/parplot-for-dfop-sfo-fit.svg' has changed -Run `testthat::snapshot_review('multistart/')` to review changes -Backtrace: - 1. vdiffr::expect_doppelganger("parplot for dfop sfo fit", parplot_dfop_sfo) - at test_multistart.R:56:2 - 3. testthat::expect_snapshot_file(...) -──────────────────────────────────────────────────────────────────────────────── -✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.6s] -✔ | 9 | Nonlinear mixed-effects models with nlme [3.8s] -✖ | 1 14 | Plotting [4.7s] -──────────────────────────────────────────────────────────────────────────────── -Failure ('test_plot.R:55:3'): Plotting mkinfit, mmkin and mixed model objects is reproducible -Snapshot of `testcase` to 'plot/mixed-model-fit-for-nlme-object.svg' has changed -Run `testthat::snapshot_review('plot/')` to review changes -Backtrace: - 1. vdiffr::expect_doppelganger(...) - at test_plot.R:55:2 - 3. testthat::expect_snapshot_file(...) -──────────────────────────────────────────────────────────────────────────────── -✔ | 4 | Residuals extracted from mkinfit models -✔ | 1 36 | saemix parent models [31.4s] -──────────────────────────────────────────────────────────────────────────────── -Skip ('test_saemix_parent.R:143:3'): We can also use mkin solution methods for saem -Reason: This still takes almost 2.5 minutes although we do not solve ODEs -──────────────────────────────────────────────────────────────────────────────── -✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [0.5s] -✔ | 11 | Processing of residue series -✔ | 10 | Fitting the SFORB model [1.7s] -✔ | 1 | Summaries of old mkinfit objects -✔ | 5 | Summary -✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [0.8s] -✔ | 9 | Hypothesis tests [2.9s] -✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [0.7s] +✔ | F W S OK | Context +✔ | 5 | AIC calculation +✔ | 5 | Analytical solutions for coupled models [1.5s] +✔ | 5 | Calculation of Akaike weights +✔ | 3 | Export dataset for reading into CAKE +✔ | 6 | Use of precompiled symbols in mkinpredict [3.3s] +✔ | 12 | Confidence intervals and p-values +✔ | 1 12 | Dimethenamid data from 2018 [13.1s] +✔ | 14 | Error model fitting [2.5s] +✔ | 5 | Time step normalisation +✔ | 4 | Calculation of FOCUS chi2 error levels +✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) +✔ | 4 | Test fitting the decline of metabolites from their maximum +✔ | 1 | Fitting the logistic model +✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [20.4s] +✔ | 2 16 | Nonlinear mixed-effects models [149.9s] +✔ | 3 | Test dataset classes mkinds and mkindsg +✔ | 10 | Special cases of mkinfit calls +✔ | 3 | mkinfit features +✔ | 8 | mkinmod model generation and printing +✔ | 3 | Model predictions with mkinpredict +✔ | 12 | Multistart method for saem.mmkin models [23.0s] +✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.5s] +✔ | 9 | Nonlinear mixed-effects models with nlme [3.6s] +✔ | 15 | Plotting [4.8s] +✔ | 4 | Residuals extracted from mkinfit models +✔ | 1 38 | saemix parent models [35.2s] +✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper +✔ | 11 | Processing of residue series +✔ | 10 | Fitting the SFORB model [1.6s] +✔ | 1 | Summaries of old mkinfit objects +✔ | 5 | Summary +✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) +✔ | 9 | Hypothesis tests [2.8s] +✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 262.6 s - -── Skipped tests ────────────────────────────────────────────────────────────── -• Fitting this ODE model with saemix takes about 5 minutes on my new system (1) -• Fitting with saemix takes around 10 minutes when using deSolve (1) -• This is seldom used, so save some time (1) -• This still takes almost 2.5 minutes although we do not solve ODEs (1) - -[ FAIL 5 | WARN 0 | SKIP 4 | PASS 276 ] +Duration: 268.2 s + +── Skipped tests (4) ─────────────────────────────────────────────────────────── +• Fitting this ODE model with saemix takes about 5 minutes on my new system + (1): 'test_dmta.R:88:3' +• Fitting with saemix takes around 10 minutes when using deSolve (1): + 'test_mixed.R:80:3' +• This is seldom used, so save some time (1): 'test_mixed.R:133:3' +• This still takes almost 2.5 minutes although we do not solve ODEs (1): + 'test_saemix_parent.R:143:3' + +[ FAIL 0 | WARN 0 | SKIP 4 | PASS 283 ] -- cgit v1.2.1 From b07f9fcb7468ac1b5fab0924328fba36ae943be5 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sun, 26 Nov 2023 20:38:30 +0100 Subject: Deal with 'saem' fits failing when updating an 'mhmkin' object --- log/build.log | 2 +- log/check.log | 6 +++--- log/test.log | 24 ++++++++++++------------ 3 files changed, 16 insertions(+), 16 deletions(-) (limited to 'log') diff --git a/log/build.log b/log/build.log index b4269860..c2001830 100644 --- a/log/build.log +++ b/log/build.log @@ -7,5 +7,5 @@ * checking for empty or unneeded directories Removed empty directory ‘mkin/inst/rmarkdown/templates/hierarchical_kinetics_parent’ Removed empty directory ‘mkin/vignettes/web_only’ -* building ‘mkin_1.2.7.tar.gz’ +* building ‘mkin_1.2.8.tar.gz’ diff --git a/log/check.log b/log/check.log index 26fdc5a0..5e777a87 100644 --- a/log/check.log +++ b/log/check.log @@ -9,9 +9,9 @@ * using options ‘--no-tests --as-cran’ * checking for file ‘mkin/DESCRIPTION’ ... OK * checking extension type ... Package -* this is package ‘mkin’ version ‘1.2.7’ +* this is package ‘mkin’ version ‘1.2.8’ * package encoding: UTF-8 -* checking CRAN incoming feasibility ... [2s/15s] Note_to_CRAN_maintainers +* checking CRAN incoming feasibility ... [2s/14s] Note_to_CRAN_maintainers Maintainer: ‘Johannes Ranke ’ * checking package namespace information ... OK * checking package dependencies ... OK @@ -62,7 +62,7 @@ Maintainer: ‘Johannes Ranke ’ * checking sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK -* checking examples ... [10s/10s] OK +* checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... SKIPPED * checking for unstated dependencies in vignettes ... OK diff --git a/log/test.log b/log/test.log index a6ac83ed..9dc63675 100644 --- a/log/test.log +++ b/log/test.log @@ -4,39 +4,39 @@ ✔ | 5 | Analytical solutions for coupled models [1.5s] ✔ | 5 | Calculation of Akaike weights ✔ | 3 | Export dataset for reading into CAKE -✔ | 6 | Use of precompiled symbols in mkinpredict [3.3s] +✔ | 6 | Use of precompiled symbols in mkinpredict [3.2s] ✔ | 12 | Confidence intervals and p-values -✔ | 1 12 | Dimethenamid data from 2018 [13.1s] +✔ | 1 12 | Dimethenamid data from 2018 [13.8s] ✔ | 14 | Error model fitting [2.5s] ✔ | 5 | Time step normalisation ✔ | 4 | Calculation of FOCUS chi2 error levels ✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ✔ | 4 | Test fitting the decline of metabolites from their maximum ✔ | 1 | Fitting the logistic model -✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [20.4s] -✔ | 2 16 | Nonlinear mixed-effects models [149.9s] +✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [19.8s] +✔ | 2 16 | Nonlinear mixed-effects models [149.6s] ✔ | 3 | Test dataset classes mkinds and mkindsg ✔ | 10 | Special cases of mkinfit calls ✔ | 3 | mkinfit features ✔ | 8 | mkinmod model generation and printing ✔ | 3 | Model predictions with mkinpredict -✔ | 12 | Multistart method for saem.mmkin models [23.0s] -✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.5s] -✔ | 9 | Nonlinear mixed-effects models with nlme [3.6s] -✔ | 15 | Plotting [4.8s] +✔ | 12 | Multistart method for saem.mmkin models [23.6s] +✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.6s] +✔ | 9 | Nonlinear mixed-effects models with nlme [4.0s] +✔ | 15 | Plotting [4.7s] ✔ | 4 | Residuals extracted from mkinfit models -✔ | 1 38 | saemix parent models [35.2s] +✔ | 1 38 | saemix parent models [36.4s] ✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper ✔ | 11 | Processing of residue series -✔ | 10 | Fitting the SFORB model [1.6s] +✔ | 10 | Fitting the SFORB model [1.8s] ✔ | 1 | Summaries of old mkinfit objects ✔ | 5 | Summary ✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) -✔ | 9 | Hypothesis tests [2.8s] +✔ | 9 | Hypothesis tests [3.1s] ✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 268.2 s +Duration: 270.7 s ── Skipped tests (4) ─────────────────────────────────────────────────────────── • Fitting this ODE model with saemix takes about 5 minutes on my new system -- cgit v1.2.1 From e18c8da322ddb11105b7fdf93e9dd538673fb946 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sat, 27 Apr 2024 19:22:10 +0200 Subject: Fix bug in R/create_deg_func.R Closes #13 --- log/build.log | 2 +- log/check.log | 14 +++++++------- log/test.log | 29 +++++++++++++++-------------- 3 files changed, 23 insertions(+), 22 deletions(-) (limited to 'log') diff --git a/log/build.log b/log/build.log index c2001830..de7e4488 100644 --- a/log/build.log +++ b/log/build.log @@ -7,5 +7,5 @@ * checking for empty or unneeded directories Removed empty directory ‘mkin/inst/rmarkdown/templates/hierarchical_kinetics_parent’ Removed empty directory ‘mkin/vignettes/web_only’ -* building ‘mkin_1.2.8.tar.gz’ +* building ‘mkin_1.2.9.tar.gz’ diff --git a/log/check.log b/log/check.log index 5e777a87..58615282 100644 --- a/log/check.log +++ b/log/check.log @@ -1,6 +1,6 @@ * using log directory ‘/home/jranke/git/mkin/mkin.Rcheck’ -* using R version 4.3.2 (2023-10-31) -* using platform: x86_64-pc-linux-gnu (64-bit) +* using R version 4.4.0 (2024-04-24) +* using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Debian 12.2.0-14) 12.2.0 GNU Fortran (Debian 12.2.0-14) 12.2.0 @@ -9,9 +9,9 @@ * using options ‘--no-tests --as-cran’ * checking for file ‘mkin/DESCRIPTION’ ... OK * checking extension type ... Package -* this is package ‘mkin’ version ‘1.2.8’ +* this is package ‘mkin’ version ‘1.2.9’ * package encoding: UTF-8 -* checking CRAN incoming feasibility ... [2s/14s] Note_to_CRAN_maintainers +* checking CRAN incoming feasibility ... Note_to_CRAN_maintainers Maintainer: ‘Johannes Ranke ’ * checking package namespace information ... OK * checking package dependencies ... OK @@ -32,7 +32,7 @@ Maintainer: ‘Johannes Ranke ’ * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK -* checking R files for non-ASCII characters ... 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 @@ -62,11 +62,11 @@ Maintainer: ‘Johannes Ranke ’ * checking sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK -* checking examples ... OK +* checking examples ... [10s/10s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... SKIPPED * checking for unstated dependencies in vignettes ... OK -* checking package vignettes in ‘inst/doc’ ... OK +* checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * checking HTML version of manual ... OK diff --git a/log/test.log b/log/test.log index 9dc63675..e92a7409 100644 --- a/log/test.log +++ b/log/test.log @@ -4,39 +4,40 @@ ✔ | 5 | Analytical solutions for coupled models [1.5s] ✔ | 5 | Calculation of Akaike weights ✔ | 3 | Export dataset for reading into CAKE -✔ | 6 | Use of precompiled symbols in mkinpredict [3.2s] +✔ | 6 | Use of precompiled symbols in mkinpredict [3.1s] ✔ | 12 | Confidence intervals and p-values -✔ | 1 12 | Dimethenamid data from 2018 [13.8s] -✔ | 14 | Error model fitting [2.5s] +✔ | 1 12 | Dimethenamid data from 2018 [13.0s] +✔ | 14 | Error model fitting [2.6s] ✔ | 5 | Time step normalisation ✔ | 4 | Calculation of FOCUS chi2 error levels ✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ✔ | 4 | Test fitting the decline of metabolites from their maximum ✔ | 1 | Fitting the logistic model -✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [19.8s] -✔ | 2 16 | Nonlinear mixed-effects models [149.6s] +✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [19.7s] +✔ | 2 16 | Nonlinear mixed-effects models [144.7s] ✔ | 3 | Test dataset classes mkinds and mkindsg ✔ | 10 | Special cases of mkinfit calls ✔ | 3 | mkinfit features ✔ | 8 | mkinmod model generation and printing ✔ | 3 | Model predictions with mkinpredict -✔ | 12 | Multistart method for saem.mmkin models [23.6s] -✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.6s] -✔ | 9 | Nonlinear mixed-effects models with nlme [4.0s] -✔ | 15 | Plotting [4.7s] +✔ | 12 | Multistart method for saem.mmkin models [23.3s] +✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.5s] +✔ | 9 | Nonlinear mixed-effects models with nlme [3.7s] +✔ | 15 | Plotting [4.5s] ✔ | 4 | Residuals extracted from mkinfit models -✔ | 1 38 | saemix parent models [36.4s] +✔ | 1 38 | saemix parent models [34.8s] ✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper ✔ | 11 | Processing of residue series -✔ | 10 | Fitting the SFORB model [1.8s] +✔ | 10 | Fitting the SFORB model [1.7s] ✔ | 1 | Summaries of old mkinfit objects ✔ | 5 | Summary ✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) -✔ | 9 | Hypothesis tests [3.1s] +✔ | 9 | Hypothesis tests [2.9s] ✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) +✔ | 2 | water-sediment ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 270.7 s +Duration: 262.3 s ── Skipped tests (4) ─────────────────────────────────────────────────────────── • Fitting this ODE model with saemix takes about 5 minutes on my new system @@ -47,4 +48,4 @@ Duration: 270.7 s • This still takes almost 2.5 minutes although we do not solve ODEs (1): 'test_saemix_parent.R:143:3' -[ FAIL 0 | WARN 0 | SKIP 4 | PASS 283 ] +[ FAIL 0 | WARN 0 | SKIP 4 | PASS 285 ] -- cgit v1.2.1 From 272b3863d1463dfaf62c6e06ea22610c0540237f Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sun, 28 Jul 2024 09:25:18 +0200 Subject: Make sure test work on my desktop, skip more tests on travis --- log/test.log | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) (limited to 'log') diff --git a/log/test.log b/log/test.log index e92a7409..0bd7338d 100644 --- a/log/test.log +++ b/log/test.log @@ -6,26 +6,26 @@ ✔ | 3 | Export dataset for reading into CAKE ✔ | 6 | Use of precompiled symbols in mkinpredict [3.1s] ✔ | 12 | Confidence intervals and p-values -✔ | 1 12 | Dimethenamid data from 2018 [13.0s] +✔ | 1 12 | Dimethenamid data from 2018 [13.3s] ✔ | 14 | Error model fitting [2.6s] ✔ | 5 | Time step normalisation ✔ | 4 | Calculation of FOCUS chi2 error levels ✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ✔ | 4 | Test fitting the decline of metabolites from their maximum ✔ | 1 | Fitting the logistic model -✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [19.7s] -✔ | 2 16 | Nonlinear mixed-effects models [144.7s] +✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [19.1s] +✔ | 2 16 | Nonlinear mixed-effects models [148.9s] ✔ | 3 | Test dataset classes mkinds and mkindsg ✔ | 10 | Special cases of mkinfit calls ✔ | 3 | mkinfit features ✔ | 8 | mkinmod model generation and printing ✔ | 3 | Model predictions with mkinpredict -✔ | 12 | Multistart method for saem.mmkin models [23.3s] +✔ | 12 | Multistart method for saem.mmkin models [23.1s] ✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.5s] -✔ | 9 | Nonlinear mixed-effects models with nlme [3.7s] -✔ | 15 | Plotting [4.5s] +✔ | 9 | Nonlinear mixed-effects models with nlme [3.8s] +✔ | 15 | Plotting [4.6s] ✔ | 4 | Residuals extracted from mkinfit models -✔ | 1 38 | saemix parent models [34.8s] +✔ | 1 38 | saemix parent models [35.5s] ✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper ✔ | 11 | Processing of residue series ✔ | 10 | Fitting the SFORB model [1.7s] @@ -37,7 +37,7 @@ ✔ | 2 | water-sediment ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 262.3 s +Duration: 267.0 s ── Skipped tests (4) ─────────────────────────────────────────────────────────── • Fitting this ODE model with saemix takes about 5 minutes on my new system -- cgit v1.2.1 From e5aea600fd957955fc3e8e41dbc93bf4f65af803 Mon Sep 17 00:00:00 2001 From: Ranke Johannes Date: Thu, 19 Dec 2024 10:59:44 +0100 Subject: Support observed data as tibble Closes #14 --- log/build.log | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) (limited to 'log') diff --git a/log/build.log b/log/build.log index de7e4488..ce7cc8e1 100644 --- a/log/build.log +++ b/log/build.log @@ -5,7 +5,8 @@ * creating vignettes ... OK * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories -Removed empty directory ‘mkin/inst/rmarkdown/templates/hierarchical_kinetics_parent’ Removed empty directory ‘mkin/vignettes/web_only’ * building ‘mkin_1.2.9.tar.gz’ +Warning: invalid uid value replaced by that for user 'nobody' +Warning: invalid gid value replaced by that for user 'nobody' -- cgit v1.2.1 From 328d1173db2395c1a5705b5f0980e2956db8be1f Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 13 Feb 2025 12:43:29 +0100 Subject: Update wordlist, bump date and simplify DESCRIPTION Also, the R-Universe URL that the badge points to is updated --- log/check.log | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) (limited to 'log') diff --git a/log/check.log b/log/check.log index 58615282..3eec3f96 100644 --- a/log/check.log +++ b/log/check.log @@ -1,5 +1,5 @@ * using log directory ‘/home/jranke/git/mkin/mkin.Rcheck’ -* using R version 4.4.0 (2024-04-24) +* using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Debian 12.2.0-14) 12.2.0 @@ -21,11 +21,11 @@ Maintainer: ‘Johannes Ranke ’ * 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 ‘mkin’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK -* checking for future file timestamps ... OK +* checking for future file timestamps ... NOTE +unable to verify current time * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK @@ -62,17 +62,20 @@ Maintainer: ‘Johannes Ranke ’ * checking sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK -* checking examples ... [10s/10s] OK +* checking examples ... [11s/12s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... SKIPPED * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK -* checking re-building of vignette outputs ... OK +* checking re-building of vignette outputs ... [13s/11s] OK * 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: OK +Status: 1 NOTE +See + ‘/home/jranke/git/mkin/mkin.Rcheck/00check.log’ +for details. -- cgit v1.2.1 From 53391cdce906364ace5dfeb1380716425c60ee04 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 13 Feb 2025 14:50:06 +0100 Subject: Update docs --- log/build.log | 9 +-------- 1 file changed, 1 insertion(+), 8 deletions(-) (limited to 'log') diff --git a/log/build.log b/log/build.log index ce7cc8e1..a02e93ae 100644 --- a/log/build.log +++ b/log/build.log @@ -2,11 +2,4 @@ * preparing ‘mkin’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes -* creating vignettes ... OK -* checking for LF line-endings in source and make files and shell scripts -* checking for empty or unneeded directories -Removed empty directory ‘mkin/vignettes/web_only’ -* building ‘mkin_1.2.9.tar.gz’ -Warning: invalid uid value replaced by that for user 'nobody' -Warning: invalid gid value replaced by that for user 'nobody' - +* creating vignettes ... \ No newline at end of file -- cgit v1.2.1 From 6476f5f49b373cd4cf05f2e73389df83e437d597 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 13 Feb 2025 16:30:31 +0100 Subject: Axis legend formatting, update vignettes --- log/build.log | 8 +++++++- log/check.log | 4 ++-- log/test.log | 22 +++++++++++----------- 3 files changed, 20 insertions(+), 14 deletions(-) (limited to 'log') diff --git a/log/build.log b/log/build.log index a02e93ae..de7e4488 100644 --- a/log/build.log +++ b/log/build.log @@ -2,4 +2,10 @@ * preparing ‘mkin’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes -* creating vignettes ... \ No newline at end of file +* creating vignettes ... OK +* checking for LF line-endings in source and make files and shell scripts +* checking for empty or unneeded directories +Removed empty directory ‘mkin/inst/rmarkdown/templates/hierarchical_kinetics_parent’ +Removed empty directory ‘mkin/vignettes/web_only’ +* building ‘mkin_1.2.9.tar.gz’ + diff --git a/log/check.log b/log/check.log index 3eec3f96..0c54a49d 100644 --- a/log/check.log +++ b/log/check.log @@ -62,12 +62,12 @@ unable to verify current time * checking sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK -* checking examples ... [11s/12s] OK +* checking examples ... [10s/10s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... SKIPPED * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK -* checking re-building of vignette outputs ... [13s/11s] OK +* checking re-building of vignette outputs ... [13s/10s] OK * checking PDF version of manual ... OK * checking HTML version of manual ... OK * checking for non-standard things in the check directory ... OK diff --git a/log/test.log b/log/test.log index 0bd7338d..746f0458 100644 --- a/log/test.log +++ b/log/test.log @@ -1,31 +1,31 @@ ℹ Testing mkin ✔ | F W S OK | Context ✔ | 5 | AIC calculation -✔ | 5 | Analytical solutions for coupled models [1.5s] +✔ | 5 | Analytical solutions for coupled models [1.6s] ✔ | 5 | Calculation of Akaike weights ✔ | 3 | Export dataset for reading into CAKE -✔ | 6 | Use of precompiled symbols in mkinpredict [3.1s] +✔ | 6 | Use of precompiled symbols in mkinpredict [3.3s] ✔ | 12 | Confidence intervals and p-values ✔ | 1 12 | Dimethenamid data from 2018 [13.3s] -✔ | 14 | Error model fitting [2.6s] +✔ | 14 | Error model fitting [2.7s] ✔ | 5 | Time step normalisation ✔ | 4 | Calculation of FOCUS chi2 error levels ✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ✔ | 4 | Test fitting the decline of metabolites from their maximum ✔ | 1 | Fitting the logistic model -✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [19.1s] -✔ | 2 16 | Nonlinear mixed-effects models [148.9s] +✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [19.7s] +✔ | 2 16 | Nonlinear mixed-effects models [148.2s] ✔ | 3 | Test dataset classes mkinds and mkindsg ✔ | 10 | Special cases of mkinfit calls ✔ | 3 | mkinfit features ✔ | 8 | mkinmod model generation and printing ✔ | 3 | Model predictions with mkinpredict -✔ | 12 | Multistart method for saem.mmkin models [23.1s] -✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.5s] -✔ | 9 | Nonlinear mixed-effects models with nlme [3.8s] +✔ | 12 | Multistart method for saem.mmkin models [23.7s] +✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.6s] +✔ | 9 | Nonlinear mixed-effects models with nlme [4.2s] ✔ | 15 | Plotting [4.6s] ✔ | 4 | Residuals extracted from mkinfit models -✔ | 1 38 | saemix parent models [35.5s] +✔ | 1 38 | saemix parent models [35.9s] ✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper ✔ | 11 | Processing of residue series ✔ | 10 | Fitting the SFORB model [1.7s] @@ -37,14 +37,14 @@ ✔ | 2 | water-sediment ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 267.0 s +Duration: 268.8 s ── Skipped tests (4) ─────────────────────────────────────────────────────────── • Fitting this ODE model with saemix takes about 5 minutes on my new system (1): 'test_dmta.R:88:3' • Fitting with saemix takes around 10 minutes when using deSolve (1): 'test_mixed.R:80:3' -• This is seldom used, so save some time (1): 'test_mixed.R:133:3' +• This is seldom used, so save some time (1): 'test_mixed.R:135:3' • This still takes almost 2.5 minutes although we do not solve ODEs (1): 'test_saemix_parent.R:143:3' -- cgit v1.2.1