* using log directory ‘/srv/hornik/tmp/CRAN_pretest/CPxplorer.Rcheck’ * using R Under development (unstable) (2025-02-17 r87739) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.7 (1+b1) Debian flang-new version 19.1.7 (1+b1) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘CPxplorer/DESCRIPTION’ ... OK * this is package ‘CPxplorer’ version ‘0.9’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/5s] NOTE Maintainer: ‘Thanh Wang ’ New submission Possibly misspelled words in DESCRIPTION: PCAs (2:30, 10:49) deconvolution (11:58) spectrometric (11:5) The Title field should be in title case. Current version is: ‘Interactive tools for PCAs and analogues analysis and quantification’ In title case that is: ‘Interactive Tools for PCAs and Analogues Analysis and Quantification’ Size of tarball: 44998093 bytes * 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 ... WARNING Found the following files with non-portable file names: inst/Manuals/~$250217_CPxplorer_Manual.pptx inst/data/20241126_PCAs_OrebroDustIOFjos - ChainLength.xlsx inst/data/20241126_PCAs_OrebroDustIOFjos - ChainLength_TEST_singlechain.xlsx inst/data/NIST_Dust/CP calibration - multiple chains.xlsx These are not fully portable file names. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for sufficient/correct file permissions ... OK * checking serialization versions ... OK * checking whether package ‘CPxplorer’ can be installed ... [4s/4s] WARNING Found the following significant warnings: Warning: replacing previous import ‘ggplot2::last_plot’ by ‘plotly::last_plot’ when loading ‘CPxplorer’ Warning: replacing previous import ‘DT::dataTableOutput’ by ‘shiny::dataTableOutput’ when loading ‘CPxplorer’ Warning: replacing previous import ‘DT::renderDataTable’ by ‘shiny::renderDataTable’ when loading ‘CPxplorer’ See ‘/srv/hornik/tmp/CRAN_pretest/CPxplorer.Rcheck/00install.out’ for details. * checking package directory ... OK * checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... NOTE Missing dependency on R >= 4.1.0 because package code uses the pipe |> or function shorthand \(...) syntax added in R 4.1.0. File(s) using such syntax: ‘CPions.R’ ‘CPquant.R’ ‘plots.R’ ‘utils_CPions.R’ * checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file. Non-standard file/directory found at top level: ‘README.Rmd’ * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... WARNING Found the following non-empty subdirectories of ‘inst’ also used by R: inst/data It is recommended not to interfere with package subdirectories used by R. * 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 ... [6s/6s] NOTE CPions : server: no visible binding for global variable ‘m/z’ CPions : server: no visible binding for global variable ‘difflag’ CPions : server: no visible binding for global variable ‘difflead’ CPions : server: no visible binding for global variable ‘79Br’ CPions : server: no visible binding for global variable ‘81Br’ CPions : server: no visible binding for global variable ‘Molecule_Formula’ CPions : server: no visible binding for global variable ‘Compound_Class’ CPions : server: no visible binding for global variable ‘Molecule Name’ CPions : server: no visible binding for global variable ‘Rel_ab’ CPions : server: no visible binding for global variable ‘Molecule List Name’ CPions : server: no visible binding for global variable ‘Precursor Charge’ CPions : server: no visible binding for global variable ‘Label Type’ CPions : server: no visible binding for global variable ‘Explicit Retention Time’ CPions : server: no visible binding for global variable ‘Explicit Retention Time Window’ CPions : server: no visible binding for global variable ‘Note’ CPions : server: no visible binding for global variable ‘Adduct’ CPquant : server: no visible binding for global variable ‘Replicate Name’ CPquant : server: no visible binding for global variable ‘Sample Type’ CPquant : server: no visible binding for global variable ‘Molecule List’ CPquant : server: no visible binding for global variable ‘Mass Error PPM’ CPquant : server: no visible binding for global variable ‘Isotope Label Type’ CPquant : server: no visible binding for global variable ‘Chromatogram Precursor M/Z’ CPquant : server: no visible binding for global variable ‘Analyte Concentration’ CPquant : server: no visible binding for global variable ‘Batch Name’ CPquant : server: no visible binding for global variable ‘Analyte_Concentration’ CPquant : server: no visible binding for global variable ‘Area’ CPquant : server: no visible binding for global variable ‘Molecule’ CPquant : server: no visible binding for global variable ‘C_homologue’ CPquant : server: no visible binding for global variable ‘Cl_homologue’ CPquant : server: no visible binding for global variable ‘Replicate_Name’ CPquant : server: no visible binding for global variable ‘Molecule_List’ CPquant : server: no visible binding for global variable ‘Isotope_Label_Type’ CPquant : server: no visible binding for global variable ‘Sample_Type’ CPquant : server: no visible binding for global variable ‘AverageBlank’ CPquant : server: no visible binding for global variable ‘Batch_Name’ CPquant : server: no visible binding for global variable ‘Quantification_Group’ CPquant : server: no visible binding for global variable ‘C_range’ CPquant : server: no visible binding for global variable ‘C_number’ CPquant : server: no visible binding for global variable ‘Cl_number’ CPquant : server: no visible binding for global variable ‘PCA’ CPquant : server: no visible binding for global variable ‘C_min’ CPquant : server: no visible binding for global variable ‘C_max’ CPquant : server: no visible binding for global variable ‘data’ CPquant : server: no visible binding for global variable ‘models’ CPquant : server: no visible binding for global variable ‘coef’ CPquant : server: no visible binding for global variable ‘rsquared’ CPquant : server: no visible binding for global variable ‘RF’ CPquant : server: no visible binding for global variable ‘intercept’ CPquant : server: no visible binding for global variable ‘Mass_Error_PPM’ CPquant : server: no visible binding for global variable ‘Chromatogram_Precursor_MZ’ CPquant : server: no visible binding for global variable ‘Relative_Area’ CPquant : server: no visible binding for global variable ‘Sum_RF_group’ CPquant : server: no visible binding for global variable ‘result’ CPquant : server: no visible binding for global variable ‘sum_Area’ CPquant : server: no visible binding for global variable ‘sum_deconv_RF’ CPquant : server : : no visible binding for global variable ‘Replicate_Name’ CPquant : server : : no visible binding for global variable ‘Sample_Type’ CPquant : server : : no visible binding for global variable ‘Concentration’ CPquant : server : : no visible binding for global variable ‘deconv_rsquared’ CPquant : server : : no visible binding for global variable ‘deconv_coef’ CPquant : server : : no visible binding for global variable ‘Batch_Name’ CPquant : server : : no visible binding for global variable ‘data’ CPquant : server : : no visible binding for global variable ‘deconv_resolved’ CPquant : server : : no visible binding for global variable ‘resolved_distribution’ CPquant : server : : no visible binding for global variable ‘Relative_Area’ CPquant : server : : no visible binding for global variable ‘Quantification_Group’ CPquant : server : : no visible binding for global variable ‘C_number’ CPquant : server : : no visible binding for global variable ‘Cl_number’ CPquant : server : : no visible binding for global variable ‘Area’ CPquant : server : : no visible binding for global variable ‘sum_Area’ CPquant : server : : no visible binding for global variable ‘sum_deconv_RF’ CPquant : server: no visible binding for global variable ‘Concentration’ CPquant : server: no visible binding for global variable ‘deconv_rsquared’ CPquant : server: no visible binding for global variable ‘IS’ CPquant : server: no visible binding for global variable ‘RS’ CPquant : server: no visible binding for global variable ‘RatioStd’ CPquant : server: no visible binding for global variable ‘RatioSample’ CPquant : server: no visible binding for global variable ‘Recovery’ CPquant : server: no visible binding for global variable ‘RecoveryPercentage’ CPquant : server: no visible global function definition for ‘sd’ CPquant : server: no visible binding for global variable ‘deconv_resolved’ calculate_haloperc: no visible binding for global variable ‘MW’ calculate_haloperc: no visible binding for global variable ‘Count’ calculate_haloperc: no visible binding for global variable ‘Halogen’ calculate_haloperc: no visible binding for global variable ‘MW_atoms’ generateInput_Envipat_BCA: no visible binding for global variable ‘Cl’ generateInput_Envipat_BCA: no visible binding for global variable ‘Br’ generateInput_Envipat_BCA: no visible binding for global variable ‘C’ generateInput_Envipat_BCA: no visible binding for global variable ‘H’ generateInput_Envipat_BCA: no visible binding for global variable ‘Molecule_Formula’ generateInput_Envipat_BCA: no visible binding for global variable ‘Halo_perc’ generateInput_Envipat_BCA: no visible binding for global variable ‘Charge’ generateInput_Envipat_BCA: no visible binding for global variable ‘Adduct’ generateInput_Envipat_BCA: no visible binding for global variable ‘Adduct_Formula’ generateInput_Envipat_advanced: no visible binding for global variable ‘Adduct_Annotation’ generateInput_Envipat_advanced: no visible binding for global variable ‘Cl’ generateInput_Envipat_advanced: no visible binding for global variable ‘H’ generateInput_Envipat_advanced: no visible binding for global variable ‘Compound_Class’ generateInput_Envipat_advanced: no visible binding for global variable ‘Br’ generateInput_Envipat_advanced: no visible binding for global variable ‘C’ generateInput_Envipat_advanced: no visible binding for global variable ‘S’ generateInput_Envipat_advanced: no visible binding for global variable ‘O’ generateInput_Envipat_advanced: no visible binding for global variable ‘Molecule_Formula’ generateInput_Envipat_advanced: no visible binding for global variable ‘Molecule_Halo_perc’ generateInput_Envipat_advanced: no visible binding for global variable ‘Adduct_Formula’ generateInput_Envipat_normal: no visible binding for global variable ‘Cl’ generateInput_Envipat_normal: no visible binding for global variable ‘H’ generateInput_Envipat_normal: no visible binding for global variable ‘Molecule_Formula’ generateInput_Envipat_normal: no visible binding for global variable ‘Halo_perc’ generateInput_Envipat_normal: no visible binding for global variable ‘Charge’ generateInput_Envipat_normal: no visible binding for global variable ‘Adduct’ generateInput_Envipat_normal: no visible binding for global variable ‘Adduct_Formula’ generateInput_Envipat_normal: no visible binding for global variable ‘C’ getAdduct_BCA: no visible binding for global variable ‘H’ getAdduct_BCA : getisotopes: no visible binding for global variable ‘isotopes’ getAdduct_BCA: no visible binding for global variable ‘abundance’ getAdduct_BCA: no visible binding for global variable ‘m/z’ getAdduct_BCA: no visible binding for global variable ‘12C’ getAdduct_BCA: no visible binding for global variable ‘13C’ getAdduct_BCA: no visible binding for global variable ‘1H’ getAdduct_BCA: no visible binding for global variable ‘2H’ getAdduct_BCA: no visible binding for global variable ‘35Cl’ getAdduct_BCA: no visible binding for global variable ‘37Cl’ getAdduct_BCA: no visible binding for global variable ‘79Br’ getAdduct_BCA: no visible binding for global variable ‘81Br’ getAdduct_BCA: no visible binding for global variable ‘Isotopologue’ getAdduct_BCA: no visible binding for global variable ‘Adduct’ getAdduct_BCA: no visible binding for global variable ‘Isotope_Formula’ getAdduct_BCA: no visible binding for global variable ‘Rel_ab’ getAdduct_advanced: no visible binding for global variable ‘H’ getAdduct_advanced : getisotopes: no visible binding for global variable ‘isotopes’ getAdduct_advanced: no visible binding for global variable ‘abundance’ getAdduct_advanced: no visible binding for global variable ‘m/z’ getAdduct_advanced: no visible binding for global variable ‘12C’ getAdduct_advanced: no visible binding for global variable ‘13C’ getAdduct_advanced: no visible binding for global variable ‘1H’ getAdduct_advanced: no visible binding for global variable ‘2H’ getAdduct_advanced: no visible binding for global variable ‘35Cl’ getAdduct_advanced: no visible binding for global variable ‘37Cl’ getAdduct_advanced: no visible binding for global variable ‘79Br’ getAdduct_advanced: no visible binding for global variable ‘81Br’ getAdduct_advanced: no visible binding for global variable ‘16O’ getAdduct_advanced: no visible binding for global variable ‘17O’ getAdduct_advanced: no visible binding for global variable ‘18O’ getAdduct_advanced: no visible binding for global variable ‘32S’ getAdduct_advanced: no visible binding for global variable ‘33S’ getAdduct_advanced: no visible binding for global variable ‘34S’ getAdduct_advanced: no visible binding for global variable ‘36S’ getAdduct_advanced: no visible binding for global variable ‘Isotopologue’ getAdduct_advanced: no visible binding for global variable ‘Adduct_Isotopologue’ getAdduct_advanced: no visible binding for global variable ‘Isotope_Formula’ getAdduct_advanced: no visible binding for global variable ‘Rel_ab’ getAdduct_normal: no visible binding for global variable ‘H’ getAdduct_normal : getisotopes: no visible binding for global variable ‘isotopes’ getAdduct_normal: no visible binding for global variable ‘abundance’ getAdduct_normal: no visible binding for global variable ‘m/z’ getAdduct_normal: no visible binding for global variable ‘12C’ getAdduct_normal: no visible binding for global variable ‘13C’ getAdduct_normal: no visible binding for global variable ‘1H’ getAdduct_normal: no visible binding for global variable ‘2H’ getAdduct_normal: no visible binding for global variable ‘35Cl’ getAdduct_normal: no visible binding for global variable ‘37Cl’ getAdduct_normal: no visible binding for global variable ‘79Br’ getAdduct_normal: no visible binding for global variable ‘81Br’ getAdduct_normal: no visible binding for global variable ‘Isotopologue’ getAdduct_normal: no visible binding for global variable ‘Adduct’ getAdduct_normal: no visible binding for global variable ‘Isotope_Formula’ getAdduct_normal: no visible binding for global variable ‘Rel_ab’ plot_calibration_curves: no visible binding for global variable ‘RF’ plot_calibration_curves: no visible binding for global variable ‘data’ plot_calibration_curves: no visible binding for global variable ‘Molecule’ plot_calibration_curves: no visible binding for global variable ‘C_number’ plot_calibration_curves: no visible binding for global variable ‘Cl_number’ plot_calibration_curves: no visible binding for global variable ‘Quantification_Group’ plot_homologue_group_pattern_comparison: no visible binding for global variable ‘Replicate_Name’ plot_homologue_group_pattern_comparison: no visible binding for global variable ‘Molecule’ plot_homologue_group_pattern_comparison: no visible binding for global variable ‘C_number’ plot_homologue_group_pattern_comparison: no visible binding for global variable ‘Cl_number’ plot_quanqualratio: no visible binding for global variable ‘Replicate_Name’ plot_quanqualratio: no visible binding for global variable ‘Molecule’ plot_quanqualratio: no visible binding for global variable ‘Isotope_Label_Type’ plot_quanqualratio: no visible binding for global variable ‘Area’ plot_quanqualratio: no visible binding for global variable ‘Quan_Area’ plot_quanqualratio: no visible binding for global variable ‘Chromatogram_Precursor_MZ’ plot_quanqualratio: no visible binding for global variable ‘QuanMZ’ plot_quanqualratio: no visible binding for global variable ‘Sample_Type’ plot_quanqualratio: no visible binding for global variable ‘Molecule_List’ plot_quanqualratio: no visible binding for global variable ‘QuanQualMZ’ plot_quanqualratio: no visible binding for global variable ‘QuanQualRatio’ plot_sample_contribution: no visible binding for global variable ‘deconv_coef’ plot_sample_contribution: no visible binding for global variable ‘Batch_Name’ plot_sample_contribution: no visible binding for global variable ‘Replicate_Name’ plot_skyline_output: no visible binding for global variable ‘Isotope_Label_Type’ plot_skyline_output: no visible binding for global variable ‘Molecule’ plot_skyline_output: no visible binding for global variable ‘C_number’ plot_skyline_output: no visible binding for global variable ‘Cl_number’ Undefined global functions or variables: 12C 13C 16O 17O 18O 1H 2H 32S 33S 34S 35Cl 36S 37Cl 79Br 81Br Adduct Adduct_Annotation Adduct_Formula Adduct_Isotopologue Analyte Concentration Analyte_Concentration Area AverageBlank Batch Name Batch_Name Br C C_homologue C_max C_min C_number C_range Charge Chromatogram Precursor M/Z Chromatogram_Precursor_MZ Cl Cl_homologue Cl_number Compound_Class Concentration Count Explicit Retention Time Explicit Retention Time Window H Halo_perc Halogen IS Isotope Label Type Isotope_Formula Isotope_Label_Type Isotopologue Label Type MW MW_atoms Mass Error PPM Mass_Error_PPM Molecule Molecule List Molecule List Name Molecule Name Molecule_Formula Molecule_Halo_perc Molecule_List Note O PCA Precursor Charge QuanMZ QuanQualMZ QuanQualRatio Quan_Area Quantification_Group RF RS RatioSample RatioStd Recovery RecoveryPercentage Rel_ab Relative_Area Replicate Name Replicate_Name S Sample Type Sample_Type Sum_RF_group abundance coef data deconv_coef deconv_resolved deconv_rsquared difflag difflead intercept isotopes m/z models resolved_distribution result rsquared sd sum_Area sum_deconv_RF Consider adding importFrom("stats", "C", "coef", "sd") importFrom("utils", "data") to your NAMESPACE file. * 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 ... WARNING Undocumented data sets: ‘isotopes’ All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... NOTE Argument items with no description in Rd file 'CPions.Rd': ‘...’ Argument items with no description in Rd file 'CPquant.Rd': ‘...’ * checking for unstated dependencies in examples ... OK * checking examples ... NONE * checking PDF version of manual ... [2s/2s] 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: 4 WARNINGs, 5 NOTEs