Move logs into own directory to clean root

6 files changed, 276 insertions, 0 deletions

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 <johannes.ranke@jrwb.de>’
+* 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 <jranke@uni-bremen.de>’
+* 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 ]