CRAN Package Check Results for Maintainer ‘Tobias Schmidt <tobias.schmidt331 at gmail.com>’

Last updated on 2025-12-04 09:50:34 CET.

Package	ERROR	NOTE	OK
FastRet	2		11
metabodecon		3	10
toscmask			13
toscutil			13

Package FastRet

Current CRAN status: ERROR: 2, OK: 11

Version: 1.1.4
Check: tests
Result: ERROR Running ‘testthat.R’ [65s/112s] 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(FastRet) > > test_check("FastRet") Starting 2 test processes. Saving _problems/test-train_frm-gbtree-11.R Saving _problems/test-fit_gbtree-8.R Saving _problems/test-fit_gbtree-16.R > test-plot_frm.R: <1b>[1;30m2025-12-03 10:48:47.27<1b>[0m Starting training of a lasso model > test-plot_frm.R: <1b>[1;30m2025-12-03 10:48:47.27<1b>[0m Mocking is enabled. Returning 'mockdata/lasso_model.rds' > test-plot_frm.R: <1b>[1;30m2025-12-03 10:48:47.89<1b>[0m Starting training of a lasso model > test-plot_frm.R: <1b>[1;30m2025-12-03 10:48:47.89<1b>[0m Mocking is enabled. Returning 'mockdata/lasso_model.rds' > test-plot_frm.R: <1b>[1;30m2025-12-03 10:48:47.94<1b>[0m Starting model Adjustment > test-plot_frm.R: <1b>[1;30m2025-12-03 10:48:47.95<1b>[0m dim(original_data): 442 x 126 > test-adjust_frm.R: <1b>[1;30m2025-12-03 10:48:48.00<1b>[0m Starting model Adjustment > test-adjust_frm.R: <1b>[1;30m2025-12-03 10:48:48.00<1b>[0m dim(original_data): 442 x 126 > test-adjust_frm.R: <1b>[1;30m2025-12-03 10:48:48.00<1b>[0m dim(new_data): 25 x 3 > test-adjust_frm.R: <1b>[1;30m2025-12-03 10:48:48.00<1b>[0m predictors: 1, 2 > test-adjust_frm.R: <1b>[1;30m2025-12-03 10:48:48.00<1b>[0m nfolds: 5 > test-adjust_frm.R: <1b>[1;30m2025-12-03 10:48:48.00<1b>[0m Preprocessing data > test-adjust_frm.R: <1b>[1;30m2025-12-03 10:48:48.03<1b>[0m Formula: RT_ADJ ~ RT + I(RT^2) > test-adjust_frm.R: <1b>[1;30m2025-12-03 10:48:48.04<1b>[0m Estimating performance of adjusted model in CV > test-adjust_frm.R: <1b>[1;30m2025-12-03 10:48:48.21<1b>[0m Fitting adjustment model on full new data set > test-adjust_frm.R: <1b>[1;30m2025-12-03 10:48:48.22<1b>[0m Returning adjusted frm object > test-adjust_frm.R: <1b>[1;30m2025-12-03 10:48:48.22<1b>[0m Starting model Adjustment > test-adjust_frm.R: <1b>[1;30m2025-12-03 10:48:48.22<1b>[0m dim(original_data): 442 x 126 > test-adjust_frm.R: <1b>[1;30m2025-12-03 10:48:48.22<1b>[0m dim(new_data): 25 x 3 > test-adjust_frm.R: <1b>[1;30m2025-12-03 10:48:48.22<1b>[0m predictors: 1, 2, 3, 4, 5, 6 > test-adjust_frm.R: <1b>[1;30m2025-12-03 10:48:48.22<1b>[0m nfolds: 5 > test-adjust_frm.R: <1b>[1;30m2025-12-03 10:48:48.22<1b>[0m Preprocessing data > test-adjust_frm.R: <1b>[1;30m2025-12-03 10:48:48.25<1b>[0m Formula: RT_ADJ ~ RT + I(RT^2) + I(RT^3) + log(RT) + exp(RT) + sqrt(RT) > test-adjust_frm.R: <1b>[1;30m2025-12-03 10:48:48.26<1b>[0m Estimating performance of adjusted model in CV > test-adjust_frm.R: <1b>[1;30m2025-12-03 10:48:48.43<1b>[0m Fitting adjustment model on full new data set > test-adjust_frm.R: <1b>[1;30m2025-12-03 10:48:48.44<1b>[0m Returning adjusted frm object > test-selective_measuring.R: <1b>[1;30m2025-12-03 10:48:49.33<1b>[0m Starting Selective Measuring > test-selective_measuring.R: <1b>[1;30m2025-12-03 10:48:49.34<1b>[0m Preprocessing input data > test-selective_measuring.R: <1b>[1;30m2025-12-03 10:48:49.34<1b>[0m Mocking is enabled for 'preprocess_data'. Returning 'mockdata/RPCD_prepro.rds'. > test-selective_measuring.R: <1b>[1;30m2025-12-03 10:48:49.39<1b>[0m Standardizing features > test-selective_measuring.R: <1b>[1;30m2025-12-03 10:48:49.43<1b>[0m Training Ridge Regression model > test-selective_measuring.R: <1b>[1;30m2025-12-03 10:48:49.44<1b>[0m Fitting Ridge model > test-selective_measuring.R: <1b>[1;30m2025-12-03 10:48:51.27<1b>[0m End training > test-selective_measuring.R: <1b>[1;30m2025-12-03 10:48:51.27<1b>[0m Scaling features by coefficients of Ridge Regression model > test-selective_measuring.R: <1b>[1;30m2025-12-03 10:48:51.29<1b>[0m Applying PAM clustering > test-selective_measuring.R: <1b>[1;30m2025-12-03 10:48:52.16<1b>[0m Returning clustering results > test-plot_frm.R: <1b>[1;30m2025-12-03 10:48:47.95<1b>[0m dim(new_data): 25 x 3 > test-plot_frm.R: <1b>[1;30m2025-12-03 10:48:53.23<1b>[0m predictors: 1, 2, 3, 4, 5, 6 > test-plot_frm.R: <1b>[1;30m2025-12-03 10:48:53.23<1b>[0m nfolds: 5 > test-plot_frm.R: <1b>[1;30m2025-12-03 10:48:53.23<1b>[0m Preprocessing data > test-plot_frm.R: <1b>[1;30m2025-12-03 10:48:53.28<1b>[0m Formula: RT_ADJ ~ RT + I(RT^2) + I(RT^3) + log(RT) + exp(RT) + sqrt(RT) > test-plot_frm.R: <1b>[1;30m2025-12-03 10:48:53.29<1b>[0m Estimating performance of adjusted model in CV > test-plot_frm.R: <1b>[1;30m2025-12-03 10:48:53.69<1b>[0m Fitting adjustment model on full new data set > test-plot_frm.R: <1b>[1;30m2025-12-03 10:48:53.72<1b>[0m Returning adjusted frm object [ FAIL 3 | WARN 5 | SKIP 0 | PASS 19 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-train_frm-gbtree.R:5:5'): train_frm works if `method == "GBTree"` ── <subscriptOutOfBoundsError/error/condition> Error in `FUN(X[[i]], ...)`: subscript out of bounds Backtrace: ▆ 1. └─FastRet::train_frm(...) at test-train_frm-gbtree.R:5:5 2. └─base::lapply(tmp, "[[", 2) ── Error ('test-fit_gbtree.R:8:5'): fit.gbtrees works as expected ────────────── Error in `begin_iteration:end_iteration`: argument of length 0 Backtrace: ▆ 1. └─FastRet:::fit_gbtree(df, verbose = 0) at test-fit_gbtree.R:8:5 2. └─FastRet:::fit_gbtree_grid(...) 3. └─xgboost::xgb.train(...) ── Error ('test-fit_gbtree.R:16:5'): fit.gbtrees works for data from reverse phase column ── Error in `begin_iteration:end_iteration`: argument of length 0 Backtrace: ▆ 1. └─FastRet:::fit_gbtree(df, verbose = 0) at test-fit_gbtree.R:16:5 2. └─FastRet:::fit_gbtree_grid(...) 3. └─xgboost::xgb.train(...) [ FAIL 3 | WARN 5 | SKIP 0 | PASS 19 ] Error: ! Test failures. Execution halted Flavor: r-devel-linux-x86_64-fedora-clang

Version: 1.1.4
Check: tests
Result: ERROR Running ‘testthat.R’ [65s/142s] 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(FastRet) > > test_check("FastRet") Starting 2 test processes. Saving _problems/test-train_frm-gbtree-11.R Saving _problems/test-fit_gbtree-8.R Saving _problems/test-fit_gbtree-16.R > test-plot_frm.R: <1b>[1;30m2025-12-03 11:34:54.34<1b>[0m Starting training of a lasso model > test-plot_frm.R: <1b>[1;30m2025-12-03 11:34:54.35<1b>[0m Mocking is enabled. Returning 'mockdata/lasso_model.rds' > test-plot_frm.R: <1b>[1;30m2025-12-03 11:34:56.18<1b>[0m Starting training of a lasso model > test-plot_frm.R: <1b>[1;30m2025-12-03 11:34:56.18<1b>[0m Mocking is enabled. Returning 'mockdata/lasso_model.rds' > test-plot_frm.R: <1b>[1;30m2025-12-03 11:34:56.26<1b>[0m Starting model Adjustment > test-plot_frm.R: <1b>[1;30m2025-12-03 11:34:56.26<1b>[0m dim(original_data): 442 x 126 > test-plot_frm.R: <1b>[1;30m2025-12-03 11:34:56.26<1b>[0m dim(new_data): 25 x 3 > test-plot_frm.R: <1b>[1;30m2025-12-03 11:34:57.05<1b>[0m predictors: 1, 2, 3, 4, 5, 6 > test-plot_frm.R: <1b>[1;30m2025-12-03 11:34:57.05<1b>[0m nfolds: 5 > test-plot_frm.R: <1b>[1;30m2025-12-03 11:34:57.05<1b>[0m Preprocessing data > test-plot_frm.R: <1b>[1;30m2025-12-03 11:34:57.14<1b>[0m Formula: RT_ADJ ~ RT + I(RT^2) + I(RT^3) + log(RT) + exp(RT) + sqrt(RT) > test-plot_frm.R: <1b>[1;30m2025-12-03 11:34:57.16<1b>[0m Estimating performance of adjusted model in CV > test-plot_frm.R: <1b>[1;30m2025-12-03 11:34:57.66<1b>[0m Fitting adjustment model on full new data set > test-plot_frm.R: <1b>[1;30m2025-12-03 11:34:57.68<1b>[0m Returning adjusted frm object > test-adjust_frm.R: <1b>[1;30m2025-12-03 11:34:58.80<1b>[0m Starting model Adjustment > test-adjust_frm.R: <1b>[1;30m2025-12-03 11:34:58.82<1b>[0m dim(original_data): 442 x 126 > test-adjust_frm.R: <1b>[1;30m2025-12-03 11:34:58.82<1b>[0m dim(new_data): 25 x 3 > test-adjust_frm.R: <1b>[1;30m2025-12-03 11:34:58.82<1b>[0m predictors: 1, 2 > test-adjust_frm.R: <1b>[1;30m2025-12-03 11:34:58.82<1b>[0m nfolds: 5 > test-adjust_frm.R: <1b>[1;30m2025-12-03 11:34:58.82<1b>[0m Preprocessing data > test-adjust_frm.R: <1b>[1;30m2025-12-03 11:34:58.87<1b>[0m Formula: RT_ADJ ~ RT + I(RT^2) > test-adjust_frm.R: <1b>[1;30m2025-12-03 11:34:58.89<1b>[0m Estimating performance of adjusted model in CV > test-adjust_frm.R: <1b>[1;30m2025-12-03 11:34:59.24<1b>[0m Fitting adjustment model on full new data set > test-adjust_frm.R: <1b>[1;30m2025-12-03 11:34:59.27<1b>[0m Returning adjusted frm object > test-adjust_frm.R: <1b>[1;30m2025-12-03 11:34:59.27<1b>[0m Starting model Adjustment > test-adjust_frm.R: <1b>[1;30m2025-12-03 11:34:59.27<1b>[0m dim(original_data): 442 x 126 > test-adjust_frm.R: <1b>[1;30m2025-12-03 11:34:59.27<1b>[0m dim(new_data): 25 x 3 > test-adjust_frm.R: <1b>[1;30m2025-12-03 11:34:59.27<1b>[0m predictors: 1, 2, 3, 4, 5, 6 > test-adjust_frm.R: <1b>[1;30m2025-12-03 11:34:59.27<1b>[0m nfolds: 5 > test-adjust_frm.R: <1b>[1;30m2025-12-03 11:34:59.27<1b>[0m Preprocessing data > test-adjust_frm.R: <1b>[1;30m2025-12-03 11:34:59.35<1b>[0m Formula: RT_ADJ ~ RT + I(RT^2) + I(RT^3) + log(RT) + exp(RT) + sqrt(RT) > test-adjust_frm.R: <1b>[1;30m2025-12-03 11:34:59.37<1b>[0m Estimating performance of adjusted model in CV > test-adjust_frm.R: <1b>[1;30m2025-12-03 11:35:00.33<1b>[0m Fitting adjustment model on full new data set > test-adjust_frm.R: <1b>[1;30m2025-12-03 11:35:00.37<1b>[0m Returning adjusted frm object > test-selective_measuring.R: <1b>[1;30m2025-12-03 11:35:01.45<1b>[0m Starting Selective Measuring > test-selective_measuring.R: <1b>[1;30m2025-12-03 11:35:01.45<1b>[0m Preprocessing input data > test-selective_measuring.R: <1b>[1;30m2025-12-03 11:35:01.45<1b>[0m Mocking is enabled for 'preprocess_data'. Returning 'mockdata/RPCD_prepro.rds'. > test-selective_measuring.R: <1b>[1;30m2025-12-03 11:35:01.48<1b>[0m Standardizing features > test-selective_measuring.R: <1b>[1;30m2025-12-03 11:35:01.52<1b>[0m Training Ridge Regression model > test-selective_measuring.R: <1b>[1;30m2025-12-03 11:35:01.53<1b>[0m Fitting Ridge model > test-selective_measuring.R: <1b>[1;30m2025-12-03 11:35:04.75<1b>[0m End training > test-selective_measuring.R: <1b>[1;30m2025-12-03 11:35:04.76<1b>[0m Scaling features by coefficients of Ridge Regression model > test-selective_measuring.R: <1b>[1;30m2025-12-03 11:35:05.04<1b>[0m Applying PAM clustering > test-selective_measuring.R: <1b>[1;30m2025-12-03 11:35:10.56<1b>[0m Returning clustering results [ FAIL 3 | WARN 5 | SKIP 0 | PASS 19 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-train_frm-gbtree.R:5:5'): train_frm works if `method == "GBTree"` ── <subscriptOutOfBoundsError/error/condition> Error in `FUN(X[[i]], ...)`: subscript out of bounds Backtrace: ▆ 1. └─FastRet::train_frm(...) at test-train_frm-gbtree.R:5:5 2. └─base::lapply(tmp, "[[", 2) ── Error ('test-fit_gbtree.R:8:5'): fit.gbtrees works as expected ────────────── Error in `begin_iteration:end_iteration`: argument of length 0 Backtrace: ▆ 1. └─FastRet:::fit_gbtree(df, verbose = 0) at test-fit_gbtree.R:8:5 2. └─FastRet:::fit_gbtree_grid(...) 3. └─xgboost::xgb.train(...) ── Error ('test-fit_gbtree.R:16:5'): fit.gbtrees works for data from reverse phase column ── Error in `begin_iteration:end_iteration`: argument of length 0 Backtrace: ▆ 1. └─FastRet:::fit_gbtree(df, verbose = 0) at test-fit_gbtree.R:16:5 2. └─FastRet:::fit_gbtree_grid(...) 3. └─xgboost::xgb.train(...) [ FAIL 3 | WARN 5 | SKIP 0 | PASS 19 ] Error: ! Test failures. Execution halted Flavor: r-devel-linux-x86_64-fedora-gcc

Package metabodecon

Current CRAN status: NOTE: 3, OK: 10

Version: 1.6.2
Check: package dependencies
Result: NOTE Package suggested but not available for checking: ‘mdrb’ Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64

Package toscmask

Current CRAN status: OK: 13

Package toscutil

Current CRAN status: OK: 13