* using log directory ‘/srv/hornik/tmp/CRAN_pretest/PKbioanalysis.Rcheck’ * using R Under development (unstable) (2024-09-09 r87107) * 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/3s] NOTE Maintainer: ‘Omar Elashkar ’ New submission Possibly misspelled words in DESCRIPTION: Bioanalysis (3:38) PKbioanalysis (11:19) Pharmacokinetic (3:22) bioanalytical (9:55, 10:77) pharmacodynamic (9:39) pharmacokinetic (9:23) 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 * 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 ... OK * 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 ... OK * 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] OK Running ‘testthat.R’ [5s/5s] * 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: 2 NOTEs