- using R version 4.5.1 (2025-06-13)
- using platform: x86_64-apple-darwin20
- R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
- running under: macOS Ventura 13.3.1
- using session charset: UTF-8
- checking for file ‘fluxfixer/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘fluxfixer’ version ‘1.0.0’
- package encoding: UTF-8
- 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 whether package ‘fluxfixer’ can be installed ... [4s/7s] OK
See the install log for details.
- checking installed package size ... OK
- checking package directory ... 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 code files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... [0s/1s] OK
- checking whether the package can be loaded with stated dependencies ... [0s/1s] OK
- checking whether the package can be unloaded cleanly ... [0s/1s] OK
- checking whether the namespace can be loaded with stated dependencies ... [0s/1s] OK
- checking whether the namespace can be unloaded cleanly ... [0s/1s] OK
- checking loading without being on the library search path ... [0s/1s] 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 ... [4s/8s] OK
- checking Rd files ... [0s/1s] OK
- checking Rd metadata ... 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 ... [0s/1s] 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 ... [11s/17s] OK
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [201s/305s] ERROR
Running ‘testthat.R’ [200s/304s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(fluxfixer)
>
> test_check("fluxfixer")
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--- dTmax calculation by the MW and DR methods finished
Zero-flow condition estimation started
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--- dTmax calculation by the MW and DR methods finished
--- dTmax time series aggregation started
--- dTmax time series aggregation finished
Zero-flow condition estimation finished
--- MSE: Mean square error for out-of-bag data
--- Hyperparameter set: [m_try, min_nodesize, subsample]
--- MSE: 0.1155032912, Hyperparameter set: [2, 5, 0.1]
--- MSE: 0.1157711388, Hyperparameter set: [3, 5, 0.1]
Random forest outlier detection started
--- Hyperparameter optimization using grid search started
--- MSE: Mean square error for out-of-bag data
--- Hyperparameter set: [m_try, min_nodesize, subsample]
--- MSE: 0.116118315, Hyperparameter set: [2, 5, 0.1]
--- MSE: 0.1164037447, Hyperparameter set: [3, 5, 0.1]
--- Optimal hyperparameter set: [2, 5, 0.1]
--- Hyperparameter optimization using grid search finished
--- Random forest construction started
--- Random forest construction finished
Random forest outlier detection finished
Random forest-based gap-filling started
--- Hyperparameter optimization using grid search started
--- MSE: Mean square error for out-of-bag data
--- Hyperparameter set: [m_try, min_nodesize, subsample]
--- MSE: 0.1176580164, Hyperparameter set: [2, 5, 1]
--- MSE: 0.1187078861, Hyperparameter set: [3, 5, 1]
--- Optimal hyperparameter set: [2, 5, 1]
--- Hyperparameter optimization using grid search finished
--- Random forest construction started
--- Random forest construction finished
Random forest-based gap-filling finished
Saving _problems/test-remove_statistical_outlier-30.R
Z-score outlier detection started
--- 5 Z-score outliers were detected
--- 1 Z-score outlier was detected
--- No Z-score outlier was detected
Z-score outlier detection finished
Time series retrieval started
--- Signal damping correction was not applied
--- Detrending was not applied
Time series retrieval finished
*** Fluxfixer started running ***
Manual error value removal was not applied
Absolute limits test finished
Short-term drift correction finished
High frequency noise filtering was not applied
Z-score outlier detection started
--- 4 Z-score outliers were detected
--- No Z-score outlier was detected
Z-score outlier detection finished
Random forest outlier detection started
--- Hyperparameter optimization using grid search started
--- MSE: Mean square error for out-of-bag data
--- Hyperparameter set: [m_try, min_nodesize, subsample]
--- MSE: 0.0738723153, Hyperparameter set: [2, 5, 0.1]
--- MSE: 0.0728156744, Hyperparameter set: [3, 5, 0.1]
--- MSE: 0.0722560085, Hyperparameter set: [4, 5, 0.1]
--- MSE: 0.0722657316, Hyperparameter set: [5, 5, 0.1]
--- MSE: 0.072790208, Hyperparameter set: [6, 5, 0.1]
--- Optimal hyperparameter set: [4, 5, 0.1]
--- Hyperparameter optimization using grid search finished
--- Random forest construction started
--- Random forest construction finished
Random forest outlier detection finished
Reference value definition started
--- Reference average of target time series: 11.4773826234913
--- Reference standard deviation of target time series: 1.66431731873025
Reference value definition finished
Random forest-based gap-filling started
--- Hyperparameter optimization using grid search started
--- MSE: Mean square error for out-of-bag data
--- Hyperparameter set: [m_try, min_nodesize, subsample]
--- MSE: 0.0320510997, Hyperparameter set: [2, 5, 1]
--- MSE: 0.0322984728, Hyperparameter set: [3, 5, 1]
--- MSE: 0.0323055008, Hyperparameter set: [4, 5, 1]
--- MSE: 0.0325841009, Hyperparameter set: [5, 5, 1]
--- MSE: 0.0330064573, Hyperparameter set: [6, 5, 1]
--- Optimal hyperparameter set: [2, 5, 1]
--- Hyperparameter optimization using grid search finished
--- Random forest construction started
--- Random forest construction finished
Random forest-based gap-filling finished
Time series retrieval started
--- Signal damping correction was not applied
--- Detrending finished
Time series retrieval finished
Quality-control flag determination finished
Zero-flow condition estimation started
--- dTmax calculation by the SP method started
--- dTmax calculation by the SP method finished
--- dTmax time series aggregation started
--- dTmax time series aggregation finished
Zero-flow condition estimation finished
Fd calculation process started
--- Heartwood correction was not applied
--- Fd calculation by the SP method finished
Fd calculation process finished
*** Fluxfixer finished running successfully ***
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 48 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-remove_statistical_outlier.R:28:3'): modifying short-term drifts works ──
Error in `data.frame(time = vctr_time, dT = vctr_target, dT_mod = vctr_target)`: arguments imply differing number of rows: 299, 300
Backtrace:
▆
1. └─fluxfixer::modify_short_drift(...) at test-remove_statistical_outlier.R:28:3
2. └─base::data.frame(time = vctr_time, dT = vctr_target, dT_mod = vctr_target)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 48 ]
Error:
! Test failures.
Execution halted
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [13s/24s] OK
- checking PDF version of manual ... [7s/14s] OK
- DONE
Status: 1 ERROR
- using check arguments '--no-clean-on-error '