############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ppcseq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ppcseq_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/ppcseq.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-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 Ventura 13.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ppcseq/DESCRIPTION’ ... OK * this is package ‘ppcseq’ version ‘1.14.0’ * 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 ‘ppcseq’ can be installed ... OK * used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ * used SDK: ‘MacOSX11.3.sdk’ * checking C++ specification ... OK Not all R platforms support C++17 * 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 add_partition: no visible binding for global variable ‘.’ add_scaled_counts_bulk.calcNormFactor: no visible binding for global variable ‘transcript’ add_scaled_counts_bulk.get_low_expressed: no visible binding for global variable ‘transcript’ check_if_within_posterior: no visible binding for global variable ‘.lower’ check_if_within_posterior: no visible binding for global variable ‘.upper’ check_if_within_posterior: no visible binding for global variable ‘ppc’ do_inference: no visible binding for global variable ‘idx_MPI’ do_inference: no visible binding for global variable ‘read_count_MPI_row’ do_inference: no visible binding for global variable ‘.’ do_inference: no visible binding for global variable ‘symbol MPI row’ draws_to_tibble_x: no visible binding for global variable ‘.’ draws_to_tibble_x: no visible binding for global variable ‘dummy’ draws_to_tibble_x: no visible binding for global variable ‘.variable’ draws_to_tibble_x: no visible binding for global variable ‘.chain’ draws_to_tibble_x: no visible binding for global variable ‘.iteration’ draws_to_tibble_x: no visible binding for global variable ‘.draw’ draws_to_tibble_x: no visible binding for global variable ‘.value’ draws_to_tibble_x_y: no visible binding for global variable ‘.’ draws_to_tibble_x_y: no visible binding for global variable ‘dummy’ draws_to_tibble_x_y: no visible binding for global variable ‘.variable’ draws_to_tibble_x_y: no visible binding for global variable ‘.chain’ draws_to_tibble_x_y: no visible binding for global variable ‘.iteration’ draws_to_tibble_x_y: no visible binding for global variable ‘.draw’ draws_to_tibble_x_y: no visible binding for global variable ‘.value’ find_optimal_number_of_chains: no visible binding for global variable ‘tot’ find_optimal_number_of_chains: no visible binding for global variable ‘chains’ fit_to_counts_rng: no visible binding for global variable ‘.variable’ fit_to_counts_rng: no visible binding for global variable ‘S’ fit_to_counts_rng: no visible binding for global variable ‘G’ fit_to_counts_rng: no visible binding for global variable ‘.’ fit_to_counts_rng_approximated: no visible binding for global variable ‘.’ fit_to_counts_rng_approximated: no visible binding for global variable ‘S’ fit_to_counts_rng_approximated: no visible binding for global variable ‘G’ fit_to_counts_rng_approximated: no visible binding for global variable ‘CI’ format_for_MPI: no visible binding for global variable ‘.’ format_for_MPI: no visible binding for global variable ‘G’ format_for_MPI: no visible binding for global variable ‘idx_MPI’ format_input: no visible binding for global variable ‘.’ format_results: no visible binding for global variable ‘sample_wise_data’ get_scaled_counts_bulk: no visible binding for global variable ‘med’ get_scaled_counts_bulk: no visible binding for global variable ‘tot_filt’ get_scaled_counts_bulk: no visible binding for global variable ‘nf’ get_scaled_counts_bulk: no visible binding for global variable ‘.’ get_scaled_counts_bulk: no visible binding for global variable ‘tot’ identify_outliers: no visible binding for global variable ‘.’ identify_outliers: no visible binding for global variable ‘do_check___’ identify_outliers: no visible binding for global variable ‘multiplier’ identify_outliers: no visible binding for global variable ‘exposure_rate’ identify_outliers: no visible binding for global variable ‘write_on_disk’ identify_outliers: no visible binding for global variable ‘.variable’ identify_outliers: no visible binding for global variable ‘S’ identify_outliers: no visible binding for global variable ‘G’ identify_outliers: no visible binding for global variable ‘.lower’ identify_outliers: no visible binding for global variable ‘.upper’ identify_outliers_1_step: no visible binding for global variable ‘.’ identify_outliers_1_step: no visible global function definition for ‘scale_abundance’ identify_outliers_1_step: no visible binding for global variable ‘TMM’ identify_outliers_1_step: no visible binding for global variable ‘multiplier’ identify_outliers_1_step: no visible binding for global variable ‘l’ identify_outliers_1_step: no visible binding for global variable ‘l %>% sd’ identify_outliers_1_step: no visible binding for global variable ‘cc’ identify_outliers_1_step: no visible binding for global variable ‘write_on_disk’ identify_outliers_1_step: no visible binding for global variable ‘.variable’ identify_outliers_1_step: no visible binding for global variable ‘S’ identify_outliers_1_step: no visible binding for global variable ‘G’ identify_outliers_1_step: no visible binding for global variable ‘.lower’ identify_outliers_1_step: no visible binding for global variable ‘.upper’ identify_outliers_1_step: no visible binding for global variable ‘ppc’ identify_outliers_1_step: no visible binding for global variable ‘exposure_rate’ inits_fx: no visible binding for global variable ‘res_discovery’ inits_fx: no visible binding for global variable ‘.variable’ inits_fx: no visible binding for global variable ‘S’ inits_fx: no visible binding for global variable ‘G’ inits_fx: no visible binding for global variable ‘init’ merge_results: no visible binding for global variable ‘.variable’ merge_results: no visible binding for global variable ‘S’ merge_results: no visible binding for global variable ‘G’ merge_results: no visible binding for global variable ‘slope’ merge_results: no visible binding for global variable ‘exposure_rate’ merge_results: no visible binding for global variable ‘multiplier’ merge_results: no visible binding for global variable ‘.lower’ merge_results: no visible binding for global variable ‘.upper’ merge_results: no visible binding for global variable ‘ppc’ plot_credible_intervals: no visible binding for global variable ‘sample_wise_data’ produce_plots: no visible binding for global variable ‘.upper’ select_to_check_and_house_keeping: no visible binding for global variable ‘.’ summary_to_tibble: no visible binding for global variable ‘.’ Undefined global functions or variables: . .chain .draw .iteration .lower .upper .value .variable CI G S TMM cc chains do_check___ dummy exposure_rate idx_MPI init l l %>% sd med multiplier nf ppc read_count_MPI_row res_discovery sample_wise_data scale_abundance slope symbol MPI row tot tot_filt transcript write_on_disk Consider adding importFrom("base", "row") importFrom("stats", "sd") to your NAMESPACE file. * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in shell scripts ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements. * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK * 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-3.20-bioc/meat/ppcseq.Rcheck/00check.log’ for details.