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 --- 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 ++++++ 6 files changed, 276 insertions(+) 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 (limited to 'log') 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 ] -- cgit v1.2.1