From 96dbf26adfad7f43df3857d12afadf1c25778357 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 22 Jul 2022 15:29:08 +0200 Subject: Move logs into own directory to clean root --- .Rbuildignore | 7 +---- GNUmakefile | 18 ++++++------ build.log | 9 ------ check.log | 73 ------------------------------------------------- check_dev.log | 80 ------------------------------------------------------ log/build.log | 9 ++++++ log/check.log | 73 +++++++++++++++++++++++++++++++++++++++++++++++++ log/check_dev.log | 80 ++++++++++++++++++++++++++++++++++++++++++++++++++++++ log/test.log | 51 ++++++++++++++++++++++++++++++++++ log/test_dev.log | 54 ++++++++++++++++++++++++++++++++++++ log/tests_slow.log | 9 ++++++ test.log | 51 ---------------------------------- test_dev.log | 54 ------------------------------------ tests_slow.log | 9 ------ 14 files changed, 286 insertions(+), 291 deletions(-) delete mode 100644 build.log delete mode 100644 check.log delete mode 100644 check_dev.log create mode 100644 log/build.log create mode 100644 log/check.log create mode 100644 log/check_dev.log create mode 100644 log/test.log create mode 100644 log/test_dev.log create mode 100644 log/tests_slow.log delete mode 100644 test.log delete mode 100644 test_dev.log delete mode 100644 tests_slow.log diff --git a/.Rbuildignore b/.Rbuildignore index 208d9d46..3144040d 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -1,10 +1,5 @@ ^GNUmakefile$ -^build.log$ -^check.log$ -^check_dev.log$ -^test.log$ -^test_dev.log$ -^tests_slow.log$ +^log/.*.log$ ^test.R$ ^README.html$ ^mkin.Rcheck diff --git a/GNUmakefile b/GNUmakefile index 569e10ea..4ebb9d99 100644 --- a/GNUmakefile +++ b/GNUmakefile @@ -41,7 +41,7 @@ $(TGZ): $(pkgfiles) vignettes $(RM) -r vignettes/*.R $(RM) -r vignettes/web_only/*.R $(RM) Rplots.pdf - "$(RBIN)/R" CMD build . 2>&1 | tee build.log + "$(RBIN)/R" CMD build . 2>&1 | tee log/build.log roxygen: "$(RBIN)/Rscript" -e 'devtools::document()' @@ -64,10 +64,10 @@ quickinstall: build-no-vignettes "$(RBIN)/R" CMD INSTALL $(TGZVNR) check: roxygen build - _R_CHECK_CRAN_INCOMING_REMOTE_=false "$(RBIN)/R" CMD check --as-cran --no-tests $(TGZ) 2>&1 | tee check.log + _R_CHECK_CRAN_INCOMING_REMOTE_=false "$(RBIN)/R" CMD check --as-cran --no-tests $(TGZ) 2>&1 | tee log/check.log devcheck: roxygen build - _R_CHECK_CRAN_INCOMING_REMOTE_=false "$(RDEVBIN)/R" CMD check --as-cran --no-tests $(TGZ) 2>&1 | tee check_dev.log + _R_CHECK_CRAN_INCOMING_REMOTE_=false "$(RDEVBIN)/R" CMD check --as-cran --no-tests $(TGZ) 2>&1 | tee log/check_dev.log quickcheck: roxygen build-no-vignettes mv $(TGZVNR) $(TGZ) @@ -82,16 +82,16 @@ clean: $(RM) Rplots.pdf test: install - "$(RBIN)/Rscript" -e 'options(cli.dynamic = TRUE); devtools::test()' 2>&1 | tee test.log - sed -i -e "s/.*\r.*\r//" test.log + "$(RBIN)/Rscript" -e 'options(cli.dynamic = TRUE); devtools::test()' 2>&1 | tee log/test.log + sed -i -e "s/.*\r.*\r//" log/test.log devtest: devinstall - "$(RDEVBIN)/Rscript" -e 'options(cli.dynamic = TRUE); devtools::test()' 2>&1 | tee test_dev.log - sed -i -e "s/\r.*\r//" test_dev.log + "$(RDEVBIN)/Rscript" -e 'options(cli.dynamic = TRUE); devtools::test()' 2>&1 | tee log/test_dev.log + sed -i -e "s/\r.*\r//" log/test_dev.log slowtests: install - NOT_CRAN=true "$(RBIN)/Rscript" -e 'cli.dynamic = TRUE); library(mkin); testthat::test_dir("tests/testthat/slow")' 2>&1 | tee tests_slow.log - sed -i -e "s/\r.*\r//" tests_slow.log + NOT_CRAN=true "$(RBIN)/Rscript" -e 'cli.dynamic = TRUE); library(mkin); testthat::test_dir("tests/testthat/slow")' 2>&1 | tee log/tests_slow.log + sed -i -e "s/\r.*\r//" log/tests_slow.log testcheck: roxygen test check diff --git a/build.log b/build.log deleted file mode 100644 index 5ac21b0d..00000000 --- a/build.log +++ /dev/null @@ -1,9 +0,0 @@ -* checking for file ‘./DESCRIPTION’ ... OK -* 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 -* building ‘mkin_1.1.2.tar.gz’ - diff --git a/check.log b/check.log deleted file mode 100644 index 8fce3fd1..00000000 --- a/check.log +++ /dev/null @@ -1,73 +0,0 @@ -* using log directory ‘/home/jranke/git/mkin/mkin.Rcheck’ -* using R version 4.2.1 (2022-06-23) -* using platform: x86_64-pc-linux-gnu (64-bit) -* 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 ‘1.1.2’ -* package encoding: UTF-8 -* checking CRAN incoming feasibility ... Note_to_CRAN_maintainers -Maintainer: ‘Johannes Ranke ’ -* 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 ‘mkin’ can be installed ... OK -* checking installed package size ... OK -* 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 R 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 contents of ‘data’ directory ... OK -* checking data for non-ASCII characters ... 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 ... 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 ... 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 - diff --git a/check_dev.log b/check_dev.log deleted file mode 100644 index bd2f319f..00000000 --- a/check_dev.log +++ /dev/null @@ -1,80 +0,0 @@ -* using log directory ‘/home/jranke/git/mkin/mkin.Rcheck’ -* using R Under development (unstable) (2020-11-11 r79413) -* using platform: x86_64-pc-linux-gnu (64-bit) -* 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 ‘0.9.50.4’ -* package encoding: UTF-8 -* checking CRAN incoming feasibility ... Note_to_CRAN_maintainers -Maintainer: ‘Johannes Ranke ’ -* 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 ‘mkin’ can be installed ... OK -* checking installed package size ... OK -* checking package directory ... 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 -* checking for left-over files ... OK -* checking index information ... OK -* checking package subdirectories ... OK -* checking R 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 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 ... NOTE -Rd file 'summary.saem.mmkin.Rd': - \examples lines wider than 100 characters: - f_mmkin_dfop_sfo <- mmkin(list(dfop_sfo), ds_syn_dfop_sfo, quiet = TRUE, error_model = "tc", cores = 5) - -These lines will be truncated in the PDF manual. -* 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 ... OK -* checking data for ASCII and uncompressed saves ... OK -* checking installed files from ‘inst/doc’ ... OK -* checking files in ‘vignettes’ ... OK -* checking examples ... 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 ... OK -* checking PDF version of manual ... OK -* checking for non-standard things in the check directory ... OK -* checking for detritus in the temp directory ... OK -* DONE - -Status: 2 NOTEs -See - ‘/home/jranke/git/mkin/mkin.Rcheck/00check.log’ -for details. - - diff --git a/log/build.log b/log/build.log new file mode 100644 index 00000000..5ac21b0d --- /dev/null +++ b/log/build.log @@ -0,0 +1,9 @@ +* checking for file ‘./DESCRIPTION’ ... OK +* 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 +* building ‘mkin_1.1.2.tar.gz’ + diff --git a/log/check.log b/log/check.log new file mode 100644 index 00000000..8fce3fd1 --- /dev/null +++ b/log/check.log @@ -0,0 +1,73 @@ +* using log directory ‘/home/jranke/git/mkin/mkin.Rcheck’ +* using R version 4.2.1 (2022-06-23) +* using platform: x86_64-pc-linux-gnu (64-bit) +* 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 ‘1.1.2’ +* package encoding: UTF-8 +* checking CRAN incoming feasibility ... Note_to_CRAN_maintainers +Maintainer: ‘Johannes Ranke ’ +* 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 ‘mkin’ can be installed ... OK +* checking installed package size ... OK +* 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 R 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 contents of ‘data’ directory ... OK +* checking data for non-ASCII characters ... 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 ... 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 ... 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 + diff --git a/log/check_dev.log b/log/check_dev.log new file mode 100644 index 00000000..bd2f319f --- /dev/null +++ b/log/check_dev.log @@ -0,0 +1,80 @@ +* using log directory ‘/home/jranke/git/mkin/mkin.Rcheck’ +* using R Under development (unstable) (2020-11-11 r79413) +* using platform: x86_64-pc-linux-gnu (64-bit) +* 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 ‘0.9.50.4’ +* package encoding: UTF-8 +* checking CRAN incoming feasibility ... Note_to_CRAN_maintainers +Maintainer: ‘Johannes Ranke ’ +* 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 ‘mkin’ can be installed ... OK +* checking installed package size ... OK +* checking package directory ... 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 +* checking for left-over files ... OK +* checking index information ... OK +* checking package subdirectories ... OK +* checking R 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 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 ... NOTE +Rd file 'summary.saem.mmkin.Rd': + \examples lines wider than 100 characters: + f_mmkin_dfop_sfo <- mmkin(list(dfop_sfo), ds_syn_dfop_sfo, quiet = TRUE, error_model = "tc", cores = 5) + +These lines will be truncated in the PDF manual. +* 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 ... OK +* checking data for ASCII and uncompressed saves ... OK +* checking installed files from ‘inst/doc’ ... OK +* checking files in ‘vignettes’ ... OK +* checking examples ... 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 ... OK +* checking PDF version of manual ... OK +* checking for non-standard things in the check directory ... OK +* checking for detritus in the temp directory ... OK +* DONE + +Status: 2 NOTEs +See + ‘/home/jranke/git/mkin/mkin.Rcheck/00check.log’ +for details. + + diff --git a/log/test.log b/log/test.log new file mode 100644 index 00000000..266a566f --- /dev/null +++ b/log/test.log @@ -0,0 +1,51 @@ +ℹ Loading mkin +Loading required package: parallel +ℹ Testing mkin +✔ | F W S OK | Context +✔ | 5 | AIC calculation +✔ | 5 | Analytical solutions for coupled models [3.2s] +✔ | 5 | Calculation of Akaike weights +✔ | 3 | Export dataset for reading into CAKE +✔ | 12 | Confidence intervals and p-values [1.0s] +✔ | 1 12 | Dimethenamid data from 2018 [31.6s] +──────────────────────────────────────────────────────────────────────────────── +Skip (test_dmta.R:98:3): Different backends get consistent results for SFO-SFO3+, dimethenamid data +Reason: Fitting this ODE model with saemix takes about 15 minutes on my system +──────────────────────────────────────────────────────────────────────────────── +✔ | 14 | Error model fitting [5.1s] +✔ | 5 | Time step normalisation +✔ | 4 | Calculation of FOCUS chi2 error levels [0.6s] +✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.8s] +✔ | 4 | Test fitting the decline of metabolites from their maximum [0.3s] +✔ | 1 | Fitting the logistic model [0.2s] +✔ | 1 12 | Nonlinear mixed-effects models [0.2s] +──────────────────────────────────────────────────────────────────────────────── +Skip (test_mixed.R:68:3): saemix results are reproducible for biphasic fits +Reason: Fitting with saemix takes around 10 minutes when using deSolve +──────────────────────────────────────────────────────────────────────────────── +✔ | 3 | Test dataset classes mkinds and mkindsg +✔ | 10 | Special cases of mkinfit calls [0.4s] +✔ | 3 | mkinfit features [0.7s] +✔ | 8 | mkinmod model generation and printing [0.2s] +✔ | 3 | Model predictions with mkinpredict [0.4s] +✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.7s] +✔ | 9 | Nonlinear mixed-effects models with nlme [8.3s] +✔ | 16 | Plotting [10.6s] +✔ | 4 | Residuals extracted from mkinfit models +✔ | 25 | saemix parent models [172.9s] +✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.4s] +✔ | 7 | Fitting the SFORB model [3.7s] +✔ | 1 | Summaries of old mkinfit objects +✔ | 5 | Summary [0.2s] +✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.1s] +✔ | 9 | Hypothesis tests [7.8s] +✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s] + +══ Results ═════════════════════════════════════════════════════════════════════ +Duration: 255.9 s + +── Skipped tests ────────────────────────────────────────────────────────────── +• Fitting this ODE model with saemix takes about 15 minutes on my system (1) +• Fitting with saemix takes around 10 minutes when using deSolve (1) + +[ FAIL 0 | WARN 0 | SKIP 2 | PASS 225 ] diff --git a/log/test_dev.log b/log/test_dev.log new file mode 100644 index 00000000..24905a1a --- /dev/null +++ b/log/test_dev.log @@ -0,0 +1,54 @@ +ℹ Loading mkin +Loading required package: parallel +ℹ Testing mkin +✔ | F W S OK | Context +✔ | 5 | AIC calculation +✔ | 5 | Analytical solutions for coupled models [14.6s] +✔ | 5 | Calculation of Akaike weights +✔ | 2 | Export dataset for reading into CAKE +✔ | 12 | Confidence intervals and p-values [1.0s] +⠋ | 1 | Dimethenamid data from 2018 +✔ | 1 27 | Dimethenamid data from 2018 [116.1s] +──────────────────────────────────────────────────────────────────────────────── +Skip (test_dmta.R:164:3): Different backends get consistent results for SFO-SFO3+, dimethenamid data +Reason: Fitting this ODE model with saemix takes about 15 minutes on my system +──────────────────────────────────────────────────────────────────────────────── +✔ | 14 | Error model fitting [6.6s] +✔ | 5 | Time step normalisation +✔ | 4 | Calculation of FOCUS chi2 error levels [0.8s] +✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [3.5s] +✔ | 4 | Test fitting the decline of metabolites from their maximum [0.6s] +✔ | 1 | Fitting the logistic model [0.3s] +⠋ | 11 | Nonlinear mixed-effects models +✔ | 1 14 | Nonlinear mixed-effects models [1.3s] +──────────────────────────────────────────────────────────────────────────────── +Skip (test_mixed.R:68:3): saemix results are reproducible for biphasic fits +Reason: Fitting with saemix takes around 10 minutes when using deSolve +──────────────────────────────────────────────────────────────────────────────── +✔ | 3 | Test dataset classes mkinds and mkindsg +✔ | 10 | Special cases of mkinfit calls [0.6s] +✔ | 3 | mkinfit features [1.1s] +✔ | 8 | mkinmod model generation and printing [0.2s] +✔ | 3 | Model predictions with mkinpredict [0.3s] +✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.1s] +✔ | 9 | Nonlinear mixed-effects models with nlme [8.7s] +✔ | 16 | Plotting [1.4s] +✔ | 4 | Residuals extracted from mkinfit models +✔ | 23 | saemix parent models [28.4s] +✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [12.0s] +✔ | 7 | Fitting the SFORB model [16.9s] +✔ | 1 | Summaries of old mkinfit objects +✔ | 4 | Summary [0.1s] +✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [18.1s] +✔ | 9 | Hypothesis tests [78.9s] +✔ | 2 | tffm0 +✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.0s] + +══ Results ═════════════════════════════════════════════════════════════════════ +Duration: 315.9 s + +── Skipped tests ────────────────────────────────────────────────────────────── +• Fitting this ODE model with saemix takes about 15 minutes on my system (1) +• Fitting with saemix takes around 10 minutes when using deSolve (1) + +[ FAIL 0 | WARN 0 | SKIP 2 | PASS 240 ] diff --git a/log/tests_slow.log b/log/tests_slow.log new file mode 100644 index 00000000..b5b646b6 --- /dev/null +++ b/log/tests_slow.log @@ -0,0 +1,9 @@ +Loading required package: parallel +✔ | OK F W S | Context +✔ | 21 | Fitting of parent only models [24.2 s] +✔ | 15 | Roundtripping error model parameters [51.5 s] + +══ Results ═════════════════════════════════════════════════════════════════════ +Duration: 75.7 s + +[ FAIL 0 | WARN 0 | SKIP 0 | PASS 36 ] diff --git a/test.log b/test.log deleted file mode 100644 index 266a566f..00000000 --- a/test.log +++ /dev/null @@ -1,51 +0,0 @@ -ℹ Loading mkin -Loading required package: parallel -ℹ Testing mkin -✔ | F W S OK | Context -✔ | 5 | AIC calculation -✔ | 5 | Analytical solutions for coupled models [3.2s] -✔ | 5 | Calculation of Akaike weights -✔ | 3 | Export dataset for reading into CAKE -✔ | 12 | Confidence intervals and p-values [1.0s] -✔ | 1 12 | Dimethenamid data from 2018 [31.6s] -──────────────────────────────────────────────────────────────────────────────── -Skip (test_dmta.R:98:3): Different backends get consistent results for SFO-SFO3+, dimethenamid data -Reason: Fitting this ODE model with saemix takes about 15 minutes on my system -──────────────────────────────────────────────────────────────────────────────── -✔ | 14 | Error model fitting [5.1s] -✔ | 5 | Time step normalisation -✔ | 4 | Calculation of FOCUS chi2 error levels [0.6s] -✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.8s] -✔ | 4 | Test fitting the decline of metabolites from their maximum [0.3s] -✔ | 1 | Fitting the logistic model [0.2s] -✔ | 1 12 | Nonlinear mixed-effects models [0.2s] -──────────────────────────────────────────────────────────────────────────────── -Skip (test_mixed.R:68:3): saemix results are reproducible for biphasic fits -Reason: Fitting with saemix takes around 10 minutes when using deSolve -──────────────────────────────────────────────────────────────────────────────── -✔ | 3 | Test dataset classes mkinds and mkindsg -✔ | 10 | Special cases of mkinfit calls [0.4s] -✔ | 3 | mkinfit features [0.7s] -✔ | 8 | mkinmod model generation and printing [0.2s] -✔ | 3 | Model predictions with mkinpredict [0.4s] -✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.7s] -✔ | 9 | Nonlinear mixed-effects models with nlme [8.3s] -✔ | 16 | Plotting [10.6s] -✔ | 4 | Residuals extracted from mkinfit models -✔ | 25 | saemix parent models [172.9s] -✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.4s] -✔ | 7 | Fitting the SFORB model [3.7s] -✔ | 1 | Summaries of old mkinfit objects -✔ | 5 | Summary [0.2s] -✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.1s] -✔ | 9 | Hypothesis tests [7.8s] -✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s] - -══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 255.9 s - -── Skipped tests ────────────────────────────────────────────────────────────── -• Fitting this ODE model with saemix takes about 15 minutes on my system (1) -• Fitting with saemix takes around 10 minutes when using deSolve (1) - -[ FAIL 0 | WARN 0 | SKIP 2 | PASS 225 ] diff --git a/test_dev.log b/test_dev.log deleted file mode 100644 index 24905a1a..00000000 --- a/test_dev.log +++ /dev/null @@ -1,54 +0,0 @@ -ℹ Loading mkin -Loading required package: parallel -ℹ Testing mkin -✔ | F W S OK | Context -✔ | 5 | AIC calculation -✔ | 5 | Analytical solutions for coupled models [14.6s] -✔ | 5 | Calculation of Akaike weights -✔ | 2 | Export dataset for reading into CAKE -✔ | 12 | Confidence intervals and p-values [1.0s] -⠋ | 1 | Dimethenamid data from 2018 -✔ | 1 27 | Dimethenamid data from 2018 [116.1s] -──────────────────────────────────────────────────────────────────────────────── -Skip (test_dmta.R:164:3): Different backends get consistent results for SFO-SFO3+, dimethenamid data -Reason: Fitting this ODE model with saemix takes about 15 minutes on my system -──────────────────────────────────────────────────────────────────────────────── -✔ | 14 | Error model fitting [6.6s] -✔ | 5 | Time step normalisation -✔ | 4 | Calculation of FOCUS chi2 error levels [0.8s] -✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [3.5s] -✔ | 4 | Test fitting the decline of metabolites from their maximum [0.6s] -✔ | 1 | Fitting the logistic model [0.3s] -⠋ | 11 | Nonlinear mixed-effects models -✔ | 1 14 | Nonlinear mixed-effects models [1.3s] -──────────────────────────────────────────────────────────────────────────────── -Skip (test_mixed.R:68:3): saemix results are reproducible for biphasic fits -Reason: Fitting with saemix takes around 10 minutes when using deSolve -──────────────────────────────────────────────────────────────────────────────── -✔ | 3 | Test dataset classes mkinds and mkindsg -✔ | 10 | Special cases of mkinfit calls [0.6s] -✔ | 3 | mkinfit features [1.1s] -✔ | 8 | mkinmod model generation and printing [0.2s] -✔ | 3 | Model predictions with mkinpredict [0.3s] -✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.1s] -✔ | 9 | Nonlinear mixed-effects models with nlme [8.7s] -✔ | 16 | Plotting [1.4s] -✔ | 4 | Residuals extracted from mkinfit models -✔ | 23 | saemix parent models [28.4s] -✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [12.0s] -✔ | 7 | Fitting the SFORB model [16.9s] -✔ | 1 | Summaries of old mkinfit objects -✔ | 4 | Summary [0.1s] -✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [18.1s] -✔ | 9 | Hypothesis tests [78.9s] -✔ | 2 | tffm0 -✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.0s] - -══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 315.9 s - -── Skipped tests ────────────────────────────────────────────────────────────── -• Fitting this ODE model with saemix takes about 15 minutes on my system (1) -• Fitting with saemix takes around 10 minutes when using deSolve (1) - -[ FAIL 0 | WARN 0 | SKIP 2 | PASS 240 ] diff --git a/tests_slow.log b/tests_slow.log deleted file mode 100644 index b5b646b6..00000000 --- a/tests_slow.log +++ /dev/null @@ -1,9 +0,0 @@ -Loading required package: parallel -✔ | OK F W S | Context -✔ | 21 | Fitting of parent only models [24.2 s] -✔ | 15 | Roundtripping error model parameters [51.5 s] - -══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 75.7 s - -[ FAIL 0 | WARN 0 | SKIP 0 | PASS 36 ] -- cgit v1.2.1