############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TSAR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TSAR_1.5.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/TSAR.Rcheck’ * using R Under development (unstable) (2024-11-20 r87352) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘TSAR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘TSAR’ version ‘1.5.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘TSAR’ can be installed ... OK * 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 ... NOTE Found the following CITATION file in a non-standard place: CITATION Most likely ‘inst/CITATION’ should be used instead. * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... 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 ... NOTE TSA_Tms : : no visible binding for global variable ‘well_ID’ TSA_Tms : : no visible binding for global variable ‘Tm’ TSA_Tms : : no visible global function definition for ‘sd’ TSA_Tms: no visible binding for global variable ‘well_ID’ TSA_Tms: no visible binding for global variable ‘Tm’ TSA_Tms: no visible binding for global variable ‘condition_ID’ TSA_Tms: no visible binding for global variable ‘Protein’ TSA_Tms: no visible binding for global variable ‘Ligand’ TSA_average: no visible binding for global variable ‘Temperature’ TSA_average: no visible binding for global variable ‘Fluorescence’ TSA_average: no visible global function definition for ‘sd’ TSA_average: no visible binding for global variable ‘Normalized’ TSA_average: no visible global function definition for ‘predict’ TSA_boxplot: no visible binding for global variable ‘condition_ID’ TSA_boxplot: no visible binding for global variable ‘Tm’ TSA_boxplot: no visible binding for global variable ‘Ligand’ TSA_boxplot: no visible binding for global variable ‘well_ID’ TSA_boxplot: no visible binding for global variable ‘Protein’ TSA_compare_plot: no visible binding for global variable ‘Temperature’ TSA_compare_plot: no visible binding for global variable ‘avg_smooth’ TSA_compare_plot: no visible binding for global variable ‘sd_min_smooth’ TSA_compare_plot: no visible binding for global variable ‘sd_max_smooth’ TSA_compare_plot: no visible global function definition for ‘colorRampPalette’ TSA_wells_plot: no visible binding for global variable ‘Temperature’ TSA_wells_plot: no visible binding for global variable ‘Fluorescence’ TSA_wells_plot: no visible binding for global variable ‘Normalized’ TSA_wells_plot: no visible binding for global variable ‘well_ID’ TSA_wells_plot: no visible binding for global variable ‘sd_min_smooth’ TSA_wells_plot: no visible binding for global variable ‘sd_max_smooth’ TSA_wells_plot: no visible binding for global variable ‘avg_smooth’ TSA_wells_plot: no visible binding for global variable ‘sd_min’ TSA_wells_plot: no visible binding for global variable ‘sd_max’ TSA_wells_plot: no visible binding for global variable ‘average’ build_curves: no visible binding for global variable ‘condition_ID’ build_table: no visible global function definition for ‘head’ build_well: no visible global function definition for ‘head’ dummy_plot: no visible binding for global variable ‘x’ dummy_plot: no visible binding for global variable ‘y’ gam_analysis : process_well: no visible binding for global variable ‘Well.Position’ gam_analysis : process_well: no visible global function definition for ‘all_of’ join_well_info: no visible binding for global variable ‘Col’ join_well_info: no visible binding for global variable ‘pos’ join_well_info: no visible binding for global variable ‘Well’ join_well_info: no visible binding for global variable ‘Protein’ join_well_info: no visible binding for global variable ‘Ligand’ join_well_info: no visible global function definition for ‘na.omit’ merge_norm : : no visible global function definition for ‘read.csv’ merge_norm : : no visible binding for global variable ‘Well.Position’ merge_norm : : no visible binding for global variable ‘Protein’ merge_norm : : no visible binding for global variable ‘Ligand’ merge_norm: no visible binding for global variable ‘tm’ merge_norm: no visible binding for global variable ‘Well.Position’ merge_update: no visible global function definition for ‘na.omit’ model_boltzmann: no visible binding for global variable ‘Temperature’ normalize: no visible global function definition for ‘all_of’ preview_condition: no visible global function definition for ‘head’ preview_model: no visible binding for global variable ‘Well.Position’ read_analysis: no visible global function definition for ‘read.delim’ read_analysis: no visible global function definition for ‘read.csv’ read_raw_data: no visible global function definition for ‘read.delim’ read_raw_data: no visible global function definition for ‘read.csv’ remove_raw: no visible binding for global variable ‘Well.Position’ remove_raw: no visible binding for global variable ‘Well’ remove_selected_graph: no visible binding for global variable ‘condition_ID’ remove_selected_graph: no visible binding for global variable ‘well_ID’ screen: no visible binding for global variable ‘Well.Position’ screen: no visible binding for global variable ‘Well’ screen : normalize_by_well: no visible binding for global variable ‘Well.Position’ screen: no visible binding for global variable ‘Temperature’ screen: no visible binding for global variable ‘Fluorescence’ view_deriv: no visible binding for global variable ‘Temperature’ view_deriv: no visible binding for global variable ‘norm_deriv’ view_deriv: no visible binding for global variable ‘well_ID’ view_deriv: no visible binding for global variable ‘Tm’ view_model: no visible binding for global variable ‘Temperature’ view_model: no visible binding for global variable ‘Normalized’ view_model: no visible binding for global variable ‘fitted’ view_model: no visible global function definition for ‘na.omit’ view_model: no visible binding for global variable ‘norm_deriv’ view_model: no visible binding for global variable ‘Well.Position’ Undefined global functions or variables: Col Fluorescence Ligand Normalized Protein Temperature Tm Well Well.Position all_of average avg_smooth colorRampPalette condition_ID fitted head na.omit norm_deriv pos predict read.csv read.delim sd sd_max sd_max_smooth sd_min sd_min_smooth tm well_ID x y Consider adding importFrom("grDevices", "colorRampPalette") importFrom("stats", "fitted", "na.omit", "predict", "sd") importFrom("utils", "head", "read.csv", "read.delim") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: model_gam.Rd: gam Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed TSA_wells_plot 14.667 0.171 14.860 gam_analysis 7.502 0.554 8.072 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/Users/biocbuild/bbs-3.21-bioc/meat/TSAR.Rcheck/00check.log’ for details.