############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:protGear.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings protGear_1.11.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/protGear.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 ‘protGear/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘protGear’ version ‘1.11.0’ * 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' INFO Imports includes 28 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 ‘protGear’ 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 ... OK * 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 best_CV_estimation: no visible binding for global variable ‘x’ best_CV_estimation: no visible binding for global variable ‘prop’ best_CV_estimation: no visible binding for global variable ‘val’ best_CV_estimation: no visible binding for global variable ‘meanX1_X2’ best_CV_estimation: no visible binding for global variable ‘meanX2_X3’ best_CV_estimation: no visible binding for global variable ‘xbar’ best_CV_estimation: no visible binding for global variable ‘CVX’ best_CV_estimation: no visible binding for global variable ‘meanX’ best_CV_estimation: no visible binding for global variable ‘selected’ best_CV_estimation: no visible binding for global variable ‘CVX2_X3’ best_CV_estimation: no visible binding for global variable ‘CVX1_X3’ best_CV_estimation: no visible binding for global variable ‘CVX1_X2’ best_CV_estimation: no visible binding for global variable ‘best_CV’ best_CV_estimation: no visible binding for global variable ‘FMedianBG_correct’ bg_correct: no visible binding for global variable ‘sampleID’ bg_correct: no visible binding for global variable ‘Name’ bg_correct: no visible binding for global variable ‘antigen’ bg_correct: no visible binding for global variable ‘sample_array_ID’ bg_correct: no visible binding for global variable ‘Block’ bg_correct: no visible binding for global variable ‘Column’ bg_correct: no visible binding for global variable ‘Row’ bg_correct: no visible binding for global variable ‘FMedian’ bg_correct: no visible binding for global variable ‘FMedianBG_correct’ bg_correct: no visible binding for global variable ‘global_BGMedian’ bg_correct: no visible binding for global variable ‘minimum_BGMedian’ bg_correct: no visible binding for global variable ‘BGMedian’ buffer_spots: no visible binding for global variable ‘sampleID’ buffer_spots: no visible binding for global variable ‘antigen’ buffer_spots: no visible binding for global variable ‘FMedianBG_correct’ buffer_spots: no visible binding for global variable ‘Block’ buffer_spots: no visible binding for global variable ‘Column’ buffer_spots: no visible binding for global variable ‘Row’ cv_by_sample_estimation: no visible binding for global variable ‘variable’ cv_by_sample_estimation: no visible binding for global variable ‘value’ cv_by_sample_estimation: no visible binding for global variable ‘temp’ cv_estimation: no visible binding for global variable ‘FMedianBG_correct’ cv_estimation: no visible binding for global variable ‘sdX’ cv_estimation: no visible binding for global variable ‘meanX’ cv_estimation: no visible binding for global variable ‘sdX2_X3’ cv_estimation: no visible binding for global variable ‘meanX2_X3’ cv_estimation: no visible binding for global variable ‘sdX1_X3’ cv_estimation: no visible binding for global variable ‘meanX1_X3’ cv_estimation: no visible binding for global variable ‘sdX1_X2’ cv_estimation: no visible binding for global variable ‘meanX1_X2’ cv_estimation: no visible binding for global variable ‘CVX’ cv_estimation: no visible binding for global variable ‘CVX2_X3’ cv_estimation: no visible binding for global variable ‘CVX1_X3’ cv_estimation: no visible binding for global variable ‘CVX1_X2’ cv_estimation: no visible binding for global variable ‘antigen’ cv_estimation: no visible binding for global variable ‘sampleID’ cv_estimation: no visible binding for global variable ‘sample_array_ID’ extract_bg: no visible binding for global variable ‘v1’ extract_bg: no visible binding for global variable ‘v2’ extract_bg: no visible binding for global variable ‘index’ extract_bg: no visible binding for global variable ‘Name’ extract_bg: no visible binding for global variable ‘Block’ extract_bg: no visible binding for global variable ‘antigen’ matrix_normalise: no visible binding for global variable ‘day_batches’ matrix_normalise: no visible binding for global variable ‘machines’ matrix_normalise: no visible binding for global variable ‘variable’ matrix_normalise: no visible binding for global variable ‘value’ matrix_normalise: no visible binding for global variable ‘antigen’ matrix_normalise: no visible binding for global variable ‘sampleID2’ matrix_normalise: no visible binding for global variable ‘temp’ merge_sampleID: no visible binding for global variable ‘v1’ merge_sampleID: no visible binding for global variable ‘v2’ merge_sampleID: no visible binding for global variable ‘index’ merge_sampleID: no visible binding for global variable ‘Name’ plot_FB: no visible binding for global variable ‘.id’ plot_FB: no visible binding for global variable ‘log_fb’ plot_FB: no visible binding for global variable ‘log_bg’ plot_FB: no visible binding for global variable ‘antigen’ plot_FB: no visible binding for global variable ‘FBG_Median’ plot_FB: no visible binding for global variable ‘BG_Median’ plot_bg: no visible binding for global variable ‘.id’ plot_buffer: no visible binding for global variable ‘buffers’ plot_normalised: no visible binding for global variable ‘mean_all_anti’ plot_normalised: no visible binding for global variable ‘rank_mean_all_anti’ plot_normalised: no visible binding for global variable ‘stdev_all_anti’ plot_normalised_antigen: no visible binding for global variable ‘antigen’ plot_normalised_antigen: no visible binding for global variable ‘MFI’ plot_normalised_antigen: no visible binding for global variable ‘mean_mfi’ plot_normalised_antigen: no visible binding for global variable ‘rank_mean_all_anti’ plot_normalised_antigen: no visible binding for global variable ‘sd_mfi’ read_array_files: no visible binding for global variable ‘Block’ read_array_files: no visible binding for global variable ‘global_BGMedian’ read_array_files: no visible binding for global variable ‘minimum_BGMedian’ rlm_normalise: no visible binding for global variable ‘Description’ rlm_normalise: no visible binding for global variable ‘Array’ rlm_normalise: no visible binding for global variable ‘Block’ rlm_normalise: no visible binding for global variable ‘antigen’ rlm_normalise: no visible binding for global variable ‘MFI_val’ rlm_normalise: no visible binding for global variable ‘antigen_name’ rlm_normalise: no visible binding for global variable ‘meanBest2_RLM’ rlm_normalise: no visible binding for global variable ‘sample_index’ rlm_normalise: no visible binding for global variable ‘slide’ rlm_normalise: no visible binding for global variable ‘sampleID2’ rlm_normalise_matrix: no visible binding for global variable ‘slide’ rlm_normalise_matrix: no visible binding for global variable ‘sample_index’ rlm_normalise_matrix: no visible binding for global variable ‘antigen’ rlm_normalise_matrix: no visible binding for global variable ‘MFI_val’ rlm_normalise_matrix: no visible binding for global variable ‘sample_array_ID’ rlm_normalise_matrix: no visible binding for global variable ‘Block’ tag_subtract: no visible binding for global variable ‘TAG’ tag_subtract: no visible binding for global variable ‘TAG_name’ tag_subtract: no visible binding for global variable ‘TAG_mfi’ visualize_slide: no visible binding for global variable ‘Block’ visualize_slide: no visible binding for global variable ‘X’ visualize_slide: no visible binding for global variable ‘Y’ visualize_slide: no visible binding for global variable ‘meanX’ visualize_slide: no visible binding for global variable ‘meanY’ visualize_slide_2d: no visible binding for global variable ‘Block’ visualize_slide_2d: no visible binding for global variable ‘X’ visualize_slide_2d: no visible binding for global variable ‘Y’ visualize_slide_2d: no visible binding for global variable ‘meanX’ visualize_slide_2d: no visible binding for global variable ‘meanY’ Undefined global functions or variables: .id Array BGMedian BG_Median Block CVX CVX1_X2 CVX1_X3 CVX2_X3 Column Description FBG_Median FMedian FMedianBG_correct MFI MFI_val Name Row TAG TAG_mfi TAG_name X Y antigen antigen_name best_CV buffers day_batches global_BGMedian index log_bg log_fb machines meanBest2_RLM meanX meanX1_X2 meanX1_X3 meanX2_X3 meanY mean_all_anti mean_mfi minimum_BGMedian prop rank_mean_all_anti sampleID sampleID2 sample_array_ID sample_index sdX sdX1_X2 sdX1_X3 sdX2_X3 sd_mfi selected slide stdev_all_anti temp v1 v2 val value variable x xbar * checking Rd files ... OK * checking Rd metadata ... 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 files in ‘vignettes’ ... OK * checking examples ... 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: 1 NOTE See ‘/Users/biocbuild/bbs-3.21-bioc/meat/protGear.Rcheck/00check.log’ for details.