mkin/tests/testthat, branch v1.2.1Fitting kinetic models to chemical degradation data (also on github)https://erac.jrwb.de/mkin/atom?h=v1.2.12022-11-18T23:17:33ZConfirm which test fail on R-devel2022-11-18T23:17:33ZJohannes Rankejranke@uni-bremen.de2022-11-18T23:17:33Zurn:sha1:64e245a16ec22cf864fcb5bae3b4b2fb2eee5905Move two saem fits from setup script to skipped tests2022-11-18T21:11:02ZJohannes Rankejranke@uni-bremen.de2022-11-18T21:11:02Zurn:sha1:5ec8e1bad1aa7d79ee9c19bdd50be07f81a14278
Save winbuilder/CRAN check time...
Use cluster with two cores to reduce windows check time2022-11-18T19:35:06ZJohannes Rankejranke@uni-bremen.de2022-11-18T19:35:06Zurn:sha1:b6b7e387261e5483f1bdfafaaa975e2f24c6567cMake mixed model test data permanent to ensure reproducibility2022-11-18T18:14:47ZJohannes Rankejranke@uni-bremen.de2022-11-18T18:14:47Zurn:sha1:5364f037a72863ef5ba81e14ba4417f68fd389f9
To ensure that tests on different platforms work on the same data, the
mixed modelling test data previosly generated in
tests/testthat/setup_script.R were generated once using the script in
inst/dataset/generation/ds_mixed.R, and are now distributed with the
package.
Round parameters with signif() before printing2022-11-18T10:31:49ZJohannes Rankejranke@uni-bremen.de2022-11-18T09:09:28Zurn:sha1:a14237fc1580b09f8772cd3330b0a445785e48ac
This will hopefully make the test pass on all relevant platforms.
Pass error.init to saemix_model, show in parplot2022-11-18T07:37:40ZJohannes Rankejranke@uni-bremen.de2022-11-18T07:37:40Zurn:sha1:df0cff4b829f1abf62f037591a24a8019174dd0a
Due to an oversight, error.init was not really passed to saemix_model in
saem.mmkin. The new initial values were reverted to c(1, 1), in order to
avoid changing the test results. Initial values for error model
parameters are now shown in parplot.multistart.
Avoid ill-determined fit, it is platform dependent2022-11-18T05:50:00ZJohannes Rankejranke@uni-bremen.de2022-11-18T05:50:00Zurn:sha1:1ba099d12ece70f77737505c41eaa7fd1c701140
The previous test lead to an error on the Fedora test systems (gcc and
clang) on CRAN:
...
Results have changed from known value recorded in 'print_dfop_saemix_1.txt'.
old[13:24] vs new[13:24]
""
"Fitted parameters:"
" estimate lower upper"
- "parent_0 100.09 98.94 101.25"
+ "parent_0 100.17 99.01 101.33"
- "log_k1 -2.68 -2.91 -2.45"
+ "log_k1 -2.66 -2.89 -2.43"
"log_k2 -4.12 -4.24 -4.00"
- "g_qlogis -0.41 -0.63 -0.20"
+ "g_qlogis -0.43 -0.65 -0.21"
- "a.1 0.91 0.67 1.15"
+ "a.1 0.91 0.67 1.16"
"b.1 0.05 0.04 0.06"
- "SD.log_k1 0.36 0.21 0.50"
+ "SD.log_k1 0.35 0.21 0.50"
and 2 more ...
Typo that did not affect test results2022-11-18T03:49:20ZJohannes Rankejranke@uni-bremen.de2022-11-18T03:49:20Zurn:sha1:549baaa3cef90ee9f256b14531d4de40d5131dc0Reduce testing on CRAN servers2022-11-16T21:44:34ZJohannes Rankejranke@uni-bremen.de2022-11-16T21:44:34Zurn:sha1:90354f5cd9e095f9ef98424689a2716770b248d4Address platform dependence that surfaced on winbuilder2022-11-16T12:52:08ZJohannes Rankejranke@uni-bremen.de2022-11-16T12:50:54Zurn:sha1:5889cd78376e244f38e6c5acba8ffbc46e18f803