* using log directory ‘/srv/hornik/tmp/CRAN_pretest/PKbioanalysis.Rcheck’ * using R Under development (unstable) (2024-09-08 r87106) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 18.1.8 (9) Debian flang-new version 18.1.8 (9) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘PKbioanalysis/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘PKbioanalysis’ version ‘0.1.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/4s] NOTE Maintainer: ‘Omar Elashkar ’ New submission Possibly misspelled words in DESCRIPTION: PKbioanalysis (8:14, 10:56) bioanalysis (3:38) bioanalytical (8:95, 10:16) pharmacodynamic (8:79) pharmacokinetic (3:22, 8:63) Unknown, possibly misspelled, fields in DESCRIPTION: ‘Issues_url’ Found the following (possibly) invalid URLs: URL: https://github.com/OmarAshkar/BioanalyticR_private/actions/workflows/R-CMD-check.yaml From: README.md Status: 404 Message: Not Found URL: https://github.com/OmarAshkar/PKbioanalysis From: DESCRIPTION man/PKbioanalysis-package.Rd Status: 404 Message: Not Found URL: https://github.com/OmarAshkar/PKbioanalysis/issues From: DESCRIPTION man/PKbioanalysis-package.Rd Status: 404 Message: Not Found The Title field should be in title case. Current version is: ‘A package for pharmacokinetic bioanalysis design and exploration’ In title case that is: ‘A Package for Pharmacokinetic Bioanalysis Design and Exploration’ The Description field should not start with the package name, 'This package' or similar. * 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 ‘PKbioanalysis’ can be installed ... [5s/5s] 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 code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [1s/1s] OK * checking whether the package can be loaded with stated dependencies ... [1s/1s] OK * checking whether the package can be unloaded cleanly ... [1s/1s] OK * checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK * checking whether the namespace can be unloaded cleanly ... [1s/1s] OK * checking loading without being on the library search path ... [1s/1s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... WARNING build_injec_seq: function(plate, inlet_method, repeat_std, repeat_qc, repeat_analyte, blank_after_top_conc, blank_at_end, system_suitability, blank_every_n, inject_vol, descr, prefix, suffix, tray, explore_mode, conc_df) build_injec_seq.MultiPlate: function(plate, tray, ...) plot: function(x, ...) plot.PlateObj: function(plate, color, Instrument, caption, path) See section ‘Generic functions and methods’ in the ‘Writing R Extensions’ manual. * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [7s/7s] NOTE .add_every_n: no visible binding for global variable ‘grp’ .gen_edges: no visible binding for global variable ‘par_df’ .gen_edges: no visible global function definition for ‘colors’ .gen_edges: no visible binding for global variable ‘from’ .gen_edges: no visible binding for global variable ‘to’ .gen_graph: no visible binding for global variable ‘from’ .gen_graph: no visible binding for global variable ‘to’ .gen_graph: no visible binding for global variable ‘label’ .gen_graph: no visible binding for global variable ‘x’ .gen_nodes: no visible binding for global variable ‘par_df’ .gen_nodes: no visible binding for global variable ‘y’ .gen_nodes: no visible binding for global variable ‘name’ .gen_nodes: no visible binding for global variable ‘label’ .gen_nodes: no visible binding for global variable ‘x’ .last_qc: no visible binding for global variable ‘TYPE’ .last_qc: no visible binding for global variable ‘std_rep’ .last_std: no visible binding for global variable ‘TYPE’ .last_std: no visible binding for global variable ‘std_rep’ .multi_graph : : no visible binding for global variable ‘TYPE’ .parallel_dilution: no visible binding for global variable ‘TYPE’ .parallel_dilution: no visible binding for global variable ‘std_rep’ .parallel_dilution: no visible binding for global variable ‘conc’ .parallel_dilution: no visible binding for global variable ‘SAMPLE_LOCATION’ .parallel_dilution: no visible binding for global variable ‘v1’ .parallel_dilution: no visible binding for global variable ‘v0’ add_qcs: no visible binding for global variable ‘TYPE’ add_qcs: no visible binding for global variable ‘std_rep’ add_qcs: no visible binding for global variable ‘conc’ add_qcs: no visible binding for global variable ‘plate_std’ build_injec_seq.PlateObj: no visible binding for global variable ‘SAMPLE_LOCATION’ build_injec_seq.PlateObj: no visible binding for global variable ‘TYPE’ build_injec_seq.PlateObj: no visible binding for global variable ‘std_rep’ build_injec_seq.PlateObj: no visible binding for global variable ‘conc’ build_injec_seq.PlateObj: no visible binding for global variable ‘value’ build_injec_seq.PlateObj: no visible binding for global variable ‘samples’ build_injec_seq.PlateObj : : no visible binding for global variable ‘conc’ combine_injec_lists: no visible binding for global variable ‘value’ download_sample_list: no visible binding for global variable ‘FILE_NAME’ download_sample_list: no visible binding for global variable ‘SAMPLE_LOCATION’ download_sample_list: no visible binding for global variable ‘FILE_TEXT’ download_sample_list: no visible binding for global variable ‘TYPE’ download_sample_list: no visible binding for global variable ‘INJ_VOL’ download_sample_list: no visible binding for global variable ‘CONC_A’ download_sample_list: no visible binding for global variable ‘Data file’ download_sample_list: no visible binding for global variable ‘Description’ download_sample_list: no visible binding for global variable ‘Vial’ download_sample_list: no visible binding for global variable ‘Volume’ download_sample_list : : no visible binding for global variable ‘wat’ export_integeration: no visible global function definition for ‘write.csv’ export_integeration: no visible binding for global variable ‘transition’ export_integeration: no visible binding for global variable ‘transition_id’ export_integeration: no visible binding for global variable ‘sample_id’ export_integeration: no visible binding for global variable ‘expected_peak_start’ export_integeration: no visible binding for global variable ‘expected_peak_end’ export_integeration: no visible binding for global variable ‘expected_peak_RT’ make_metabolic_study: no visible binding for global variable ‘cmpd’ plate_app : server: no visible binding for global variable ‘list_id’ plate_app : server : : no visible global function definition for ‘write.csv’ plate_app : server: no visible global function definition for ‘colorRampPalette’ plate_app : server: no visible binding for global variable ‘Index’ plate_app : server: no visible binding for global variable ‘FILE_NAME’ plate_app : server: no visible binding for global variable ‘FILE_TEXT’ plate_app : server: no visible binding for global variable ‘SAMPLE_LOCATION’ plate_app : server: no visible binding for global variable ‘INJ_VOL’ plate_app : server: no visible binding for global variable ‘conc’ plate_app : server: no visible binding for global variable ‘TYPE’ plate_app : server: no visible global function definition for ‘styleEqual’ plate_app : server: no visible binding for global variable ‘value’ plate_app : server: no visible binding for global variable ‘total_vol’ plate_app : server: no visible global function definition for ‘dataTableProxy’ plate_app : server: no visible global function definition for ‘editData’ plate_app : server: no visible binding for global variable ‘label’ plate_app : server : : no visible global function definition for ‘peaksobj’ plot.PlateObj: no visible binding for global variable ‘conc’ plot.PlateObj: no visible binding for global variable ‘value’ plot.PlateObj: no visible binding for global variable ‘time’ plot.PlateObj: no visible binding for global variable ‘SAMPLE_LOCATION’ print.InjecListObj: no visible binding for global variable ‘INJ_VOL’ print.InjecListObj: no visible binding for global variable ‘SAMPLE_LOCATION’ print.InjecListObj: no visible binding for global variable ‘total_volume’ write_injec_seq: no visible binding for global variable ‘FILE_NAME’ write_injec_seq: no visible binding for global variable ‘index’ Undefined global functions or variables: CONC_A Data file Description FILE_NAME FILE_TEXT INJ_VOL Index SAMPLE_LOCATION TYPE Vial Volume cmpd colorRampPalette colors conc dataTableProxy editData expected_peak_RT expected_peak_end expected_peak_start from grp index label list_id name par_df peaksobj plate_std sample_id samples std_rep styleEqual time to total_vol total_volume transition transition_id v0 v1 value wat write.csv x y Consider adding importFrom("base", "file") importFrom("grDevices", "colorRampPalette", "colors") importFrom("stats", "time") importFrom("utils", "write.csv") to your NAMESPACE file. Found the following assignments to the global environment: File ‘PKbioanalysis/R/plate_app.R’: assign("plat", reuse_plate(id, input$refill_gaps), envir = .GlobalEnv) * checking Rd files ... [0s/0s] 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 ... WARNING Documented arguments not in \usage in Rd file 'dot-injecList.Rd': ‘m’ Undocumented arguments in Rd file 'dot-plate.Rd' ‘plate_id’ ‘last_modified’ ‘descr’ Undocumented arguments in Rd file 'dot-retrieve_plate.Rd' ‘id_full’ Documented arguments not in \usage in Rd file 'plate_app.Rd': ‘chrom_res’ Undocumented arguments in Rd file 'plot.PlateObj.Rd' ‘path’ Documented arguments not in \usage in Rd file 'plot.PlateObj.Rd': ‘path.’ Undocumented arguments in Rd file 'print.PlateObj.Rd' ‘...’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [3s/3s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [5s/5s] ERROR Running ‘testthat.R’ [5s/5s] 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(PKbioanalysis) > > test_check("PKbioanalysis") 96 Well Plate Active Rows: A B C D E F G H Last Fill: A,1 Remaining Empty Spots: 96 Description: Last Modified: 2024-09-10 00:21:47.722773 Plate ID: 1_1 Registered: FALSE 96 Well Plate Active Rows: A B C D E F G H Last Fill: A,1 Remaining Empty Spots: 96 Description: Last Modified: 2024-09-10 00:21:47.814495 Plate ID: 1_1 Registered: FALSE 96 Well Plate Active Rows: A B C D E F G H Last Fill: A,1 Remaining Empty Spots: 96 Description: Last Modified: 2024-09-10 00:21:47.836555 Plate ID: 1_1 Registered: FALSE 96 Well Plate Active Rows: A B C D E F G H Last Fill: A,1 Remaining Empty Spots: 96 Description: Last Modified: 2024-09-10 00:21:47.894842 Plate ID: 1_1 Registered: FALSE 96 Well Plate Active Rows: A B C D E F G H Last Fill: A,1 Remaining Empty Spots: 96 Description: Last Modified: 2024-09-10 00:21:47.952961 Plate ID: 1_1 Registered: FALSE 96 Well Plate Active Rows: A B C D E F G H Last Fill: A,1 Remaining Empty Spots: 96 Description: Last Modified: 2024-09-10 00:21:48.023134 Plate ID: 1_1 Registered: FALSE 96 Well Plate Active Rows: A B C D E F G H Last Fill: A,1 Remaining Empty Spots: 96 Description: Last Modified: 2024-09-10 00:21:48.092779 Plate ID: 1_1 Registered: FALSE Plate not registered. To register, use register_plate() 96 Well Plate Active Rows: A B C D E F G H Last Fill: A,1 Remaining Empty Spots: 96 Description: Last Modified: 2024-09-10 00:21:48.173419 Plate ID: 1_1 Registered: FALSE 96 Well Plate Active Rows: A B C D E F G H Last Fill: A,1 Remaining Empty Spots: 96 Description: Last Modified: 2024-09-10 00:21:48.206108 Plate ID: 1_1 Registered: FALSE 96 Well Plate Active Rows: A B C D E F G H Last Fill: A,1 Remaining Empty Spots: 96 Description: Last Modified: 2024-09-10 00:21:48.248241 Plate ID: 1_1 Registered: FALSE 96 Well Plate Active Rows: A B C D E F G H Last Fill: A,1 Remaining Empty Spots: 96 Description: Last Modified: 2024-09-10 00:21:48.275591 Plate ID: 1_1 Registered: FALSE 96 Well Plate Active Rows: A B C D E F G H Last Fill: A,1 Remaining Empty Spots: 96 Description: Last Modified: 2024-09-10 00:21:48.433245 Plate ID: 1_1 Registered: FALSE 96 Well Plate Active Rows: A B C D E F G H Last Fill: A,1 Remaining Empty Spots: 96 Description: Last Modified: 2024-09-10 00:21:48.464609 Plate ID: 1_1 Registered: FALSE 96 Well Plate Active Rows: A B C D E F G H Last Fill: A,1 Remaining Empty Spots: 96 Description: Last Modified: 2024-09-10 00:21:48.519949 Plate ID: 1_1 Registered: FALSE 96 Well Plate Active Rows: A B C D E F G H Last Fill: A,1 Remaining Empty Spots: 96 Description: Last Modified: 2024-09-10 00:21:48.549365 Plate ID: 1_1 Registered: FALSE 96 Well Plate Active Rows: H Last Fill: H,4 Remaining Empty Spots: 8 Description: Last Modified: 2024-09-10 00:21:48.6015 Plate ID: 1_1 Registered: FALSE 96 Well Plate Active Rows: A B C D E F G H Last Fill: A,1 Remaining Empty Spots: 96 Description: Last Modified: 2024-09-10 00:21:48.651567 Plate ID: 1_1 Registered: FALSE Plate not registered. To register, use register_plate() 96 Well Plate Active Rows: A B C D E F G H Last Fill: A,1 Remaining Empty Spots: 96 Description: Last Modified: 2024-09-10 00:21:48.702571 Plate ID: 1_1 Registered: FALSE Plate not registered. To register, use register_plate() 96 Well Plate Active Rows: A B C D E F G H Last Fill: A,1 Remaining Empty Spots: 96 Description: Last Modified: 2024-09-10 00:21:48.751713 Plate ID: 1_1 Registered: FALSE Plate not registered. To register, use register_plate() 96 Well Plate Active Rows: A B C D E F G H Last Fill: A,1 Remaining Empty Spots: 96 Description: Last Modified: 2024-09-10 00:21:48.804812 Plate ID: 1_1 Registered: FALSE Plate not registered. To register, use register_plate() 96 Well Plate Active Rows: A B C D E F G H Last Fill: A,1 Remaining Empty Spots: 96 Description: Last Modified: 2024-09-10 00:21:48.854096 Plate ID: 1_1 Registered: FALSE 96 Well Plate Active Rows: A B C D E F G H Last Fill: A,1 Remaining Empty Spots: 96 Description: Last Modified: 2024-09-10 00:21:48.881461 Plate ID: 1_1 Registered: FALSE 96 Well Plate Active Rows: A B C D E F G H Last Fill: A,1 Remaining Empty Spots: 96 Description: Last Modified: 2024-09-10 00:21:49.00899 Plate ID: 1_1 Registered: FALSE 96 Well Plate Active Rows: A B C D E F G H Last Fill: A,1 Remaining Empty Spots: 96 Description: Last Modified: 2024-09-10 00:21:49.137725 Plate ID: 1_1 Registered: FALSE 96 Well Plate Active Rows: A B C D E F G H Last Fill: A,1 Remaining Empty Spots: 96 Description: Last Modified: 2024-09-10 00:21:49.264261 Plate ID: 1_1 Registered: FALSE 96 Well Plate Active Rows: A B C D E F G H Last Fill: A,1 Remaining Empty Spots: 96 Description: Last Modified: 2024-09-10 00:21:49.392085 Plate ID: 1_1 Registered: FALSE 96 Well Plate Active Rows: A B C D E F G H Last Fill: A,1 Remaining Empty Spots: 96 Description: Last Modified: 2024-09-10 00:21:49.518441 Plate ID: 1_1 Registered: FALSE 96 Well Plate Active Rows: A B C D E F G H Last Fill: A,1 Remaining Empty Spots: 96 Description: Last Modified: 2024-09-10 00:21:49.643819 Plate ID: 1_1 Registered: FALSE 96 Well Plate Active Rows: A B C D E F G H Last Fill: A,1 Remaining Empty Spots: 96 Description: Last Modified: 2024-09-10 00:21:49.767193 Plate ID: 1_1 Registered: FALSE Plate not registered. To register, use register_plate() Plate not registered. To register, use register_plate() Plate not registered. To register, use register_plate() Plate not registered. To register, use register_plate() Plate not registered. To register, use register_plate() 96 Well Plate Active Rows: A B C D E F G H Last Fill: A,1 Remaining Empty Spots: 96 Description: Last Modified: 2024-09-10 00:21:49.966734 Plate ID: 1_1 Registered: FALSE 96 Well Plate Active Rows: A B C D E F G H Last Fill: A,1 Remaining Empty Spots: 96 Description: Last Modified: 2024-09-10 00:21:50.096907 Plate ID: 1_1 Registered: FALSE 96 Well Plate Active Rows: A B C D E F G H Last Fill: A,1 Remaining Empty Spots: 96 Description: Last Modified: 2024-09-10 00:21:50.230128 Plate ID: 1_1 Registered: FALSE 96 Well Plate Active Rows: A B C D E F G H Last Fill: A,1 Remaining Empty Spots: 96 Description: Last Modified: 2024-09-10 00:21:50.357336 Plate ID: 1_1 Registered: FALSE 96 Well Plate Active Rows: A B C D E F G H Last Fill: A,1 Remaining Empty Spots: 96 Description: Last Modified: 2024-09-10 00:21:50.485133 Plate ID: 1_1 Registered: FALSE 96 Well Plate Active Rows: A B C D E F G H Last Fill: A,1 Remaining Empty Spots: 96 Description: Last Modified: 2024-09-10 00:21:50.612277 Plate ID: 1_1 Registered: FALSE 96 Well Plate Active Rows: A B C D E F G H Last Fill: A,1 Remaining Empty Spots: 96 Description: Last Modified: 2024-09-10 00:21:50.761787 Plate ID: 1_1 Registered: FALSE 96 Well Plate Active Rows: A B C D E F G H Last Fill: A,1 Remaining Empty Spots: 96 Description: Last Modified: 2024-09-10 00:21:50.888149 Plate ID: 1_1 Registered: FALSE 96 Well Plate Active Rows: A B C D E F G H Last Fill: A,1 Remaining Empty Spots: 96 Description: Last Modified: 2024-09-10 00:21:50.967687 Plate ID: 1_1 Registered: FALSE Plate not registered. To register, use register_plate() [ FAIL 6 | WARN 11 | SKIP 0 | PASS 37 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-injec_list.R:10:3'): save_injecseq_csv ───────────────────────── Error in `gzfile(file, mode)`: cannot open the connection Backtrace: ▆ 1. ├─PKbioanalysis::register_plate(...) at test-injec_list.R:10:3 2. └─PKbioanalysis:::register_plate.PlateObj(...) 3. └─PKbioanalysis:::.register_plate_logic(plate) 4. └─base::saveRDS(plate, save_path) 5. └─base::gzfile(file, mode) ── Error ('test-injec_list.R:29:3'): multiple_plates ─────────────────────────── Error in `gzfile(file, mode)`: cannot open the connection Backtrace: ▆ 1. ├─PKbioanalysis::register_plate(...) at test-injec_list.R:29:3 2. └─PKbioanalysis:::register_plate.PlateObj(...) 3. └─PKbioanalysis:::.register_plate_logic(plate) 4. └─base::saveRDS(plate, save_path) 5. └─base::gzfile(file, mode) ── Error ('test-injec_list.R:47:3'): exploratory_samples_added ───────────────── Error in `gzfile(file, mode)`: cannot open the connection Backtrace: ▆ 1. ├─PKbioanalysis::register_plate(...) at test-injec_list.R:47:3 2. └─PKbioanalysis:::register_plate.PlateObj(...) 3. └─PKbioanalysis:::.register_plate_logic(plate) 4. └─base::saveRDS(plate, save_path) 5. └─base::gzfile(file, mode) ── Error ('test-injec_list.R:63:3'): writing_increment_id ────────────────────── Error in `gzfile(file, mode)`: cannot open the connection Backtrace: ▆ 1. ├─PKbioanalysis::register_plate(...) at test-injec_list.R:63:3 2. └─PKbioanalysis:::register_plate.PlateObj(...) 3. └─PKbioanalysis:::.register_plate_logic(plate) 4. └─base::saveRDS(plate, save_path) 5. └─base::gzfile(file, mode) ── Error ('test-plate.R:13:3'): plate_registration ───────────────────────────── Error in `gzfile(file, mode)`: cannot open the connection Backtrace: ▆ 1. ├─PKbioanalysis::register_plate(x) at test-plate.R:13:3 2. └─PKbioanalysis:::register_plate.PlateObj(x) 3. └─PKbioanalysis:::.register_plate_logic(plate) 4. └─base::saveRDS(plate, save_path) 5. └─base::gzfile(file, mode) ── Error ('test-plate.R:22:3'): reuse_plate ──────────────────────────────────── Error in `gzfile(file, mode)`: cannot open the connection Backtrace: ▆ 1. ├─PKbioanalysis::register_plate(...) at test-plate.R:22:3 2. └─PKbioanalysis:::register_plate.PlateObj(...) 3. └─PKbioanalysis:::.register_plate_logic(plate) 4. └─base::saveRDS(plate, save_path) 5. └─base::gzfile(file, mode) [ FAIL 6 | WARN 11 | SKIP 0 | PASS 37 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [15s/15s] OK * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [0s/0s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 2 WARNINGs, 2 NOTEs