############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ISAnalytics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ISAnalytics_1.4.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/ISAnalytics.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ISAnalytics/DESCRIPTION’ ... OK * this is package ‘ISAnalytics’ version ‘1.4.3’ * package encoding: UTF-8 * 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 hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘ISAnalytics’ 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 R 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 .check_file_system_alignment: no visible binding for global variable ‘Found’ .clean_data: no visible binding for global variable ‘alluvia_id’ .count_group_union: no visible binding for global variable ‘..col_groups’ .count_group_union: no visible binding for global variable ‘group_id’ .find_in_common : : no visible binding for global variable ‘group_id’ .sh_obtain_lookup: no visible global function definition for ‘.’ .sh_row_permut: no visible binding for global variable ‘shared’ .sh_row_permut: no visible binding for global variable ‘is_coord’ .sh_row_permut: no visible global function definition for ‘.’ .sh_truth_tbl_venn : retrieve_is: no visible binding for global variable ‘group_id’ .sh_truth_tbl_venn: no visible binding for global variable ‘observed’ .sh_truth_tbl_venn: no visible binding for global variable ‘group_id’ .sharing_multdf_mult_key: no visible binding for global variable ‘shared’ .sharing_multdf_mult_key : : no visible binding for global variable ‘is’ .sharing_multdf_mult_key: no visible binding for global variable ‘.’ .sharing_multdf_single_key: no visible binding for global variable ‘shared’ .sharing_multdf_single_key : : no visible binding for global variable ‘is’ .sharing_multdf_single_key: no visible binding for global variable ‘.’ .sharing_singledf_mult_key: no visible binding for global variable ‘shared’ .sharing_singledf_mult_key: no visible binding for global variable ‘is’ .sharing_singledf_mult_key: no visible binding for global variable ‘.’ .sharing_singledf_single_key: no visible binding for global variable ‘is’ .sharing_singledf_single_key: no visible binding for global variable ‘shared’ .sharing_singledf_single_key : : no visible binding for global variable ‘shared’ .sharing_singledf_single_key : : no visible binding for global variable ‘is_coord’ .sharing_singledf_single_key : : no visible binding for global variable ‘group_id’ .sharing_singledf_single_key: no visible binding for global variable ‘.’ .sliding_window: no visible binding for global variable ‘..mand_vars’ .sliding_window: no visible binding for global variable ‘chr_before’ .sliding_window: no visible binding for global variable ‘integration_locus_before’ .sliding_window: no visible binding for global variable ‘strand_before’ .sliding_window: no visible binding for global variable ‘..num_cols’ compute_near_integrations: no visible binding for global variable ‘..mand_vars’ compute_near_integrations: no visible binding for global variable ‘chr_before’ compute_near_integrations: no visible binding for global variable ‘integration_locus_before’ compute_near_integrations: no visible binding for global variable ‘strand_before’ cumulative_is: no visible global function definition for ‘.’ cumulative_is : : no visible binding for global variable ‘is’ cumulative_is: no visible binding for global variable ‘is’ sharing_heatmap : plot_rel_heat: no visible binding for global variable ‘..fill..’ Undefined global functions or variables: . ..col_groups ..fill.. ..mand_vars ..num_cols Found alluvia_id chr_before group_id integration_locus_before is is_coord observed shared strand_before Consider adding importFrom("methods", "is") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * 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 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 sharing_venn 43.514 0.328 43.903 integration_alluvial_plot 8.487 1.262 5.791 compute_near_integrations 5.120 4.565 2.676 iss_source 5.564 0.769 4.013 sharing_heatmap 5.053 0.062 5.123 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... 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-3.14-bioc/meat/ISAnalytics.Rcheck/00check.log’ for details.