############################################################################## ############################################################################## ### ### Running command: ### ### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:exomePeak2.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings exomePeak2_1.7.1.tar.gz ### ############################################################################## ############################################################################## * using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/exomePeak2.Rcheck' * using R Under development (unstable) (2021-11-21 r81221) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'exomePeak2/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'exomePeak2' version '1.7.1' * 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 whether package 'exomePeak2' 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 Results,SummarizedExomePeak: no visible global function definition for 'glm_M' exomePeakCalling,MeripBamFileList: no visible global function definition for 'metadata' exomePeakCalling,MeripBamFileList: no visible global function definition for '%over%' plotLfcGC,SummarizedExomePeak: no visible binding for global variable 'GC_idx' plotLfcGC,SummarizedExomePeak: no visible binding for global variable 'Log2FC' plotLfcGC,SummarizedExomePeak: no visible binding for global variable 'Label' plotReadsGC,SummarizedExomePeak: no visible binding for global variable 'GC_cont' plotReadsGC,SummarizedExomePeak: no visible binding for global variable 'value' plotSizeFactors,SummarizedExomePeak: no visible binding for global variable 'samples' plotSizeFactors,SummarizedExomePeak: no visible binding for global variable 'size_factors' plotSizeFactors,SummarizedExomePeak: no visible binding for global variable 'Estimation_Methods' Undefined global functions or variables: %over% Estimation_Methods GC_cont GC_idx Label Log2FC glm_M metadata samples size_factors value * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... WARNING Codoc mismatches from documentation object 'exomePeak2': exomePeak2 Code: function(bam_ip = NULL, bam_input = NULL, bam_treated_ip = NULL, bam_treated_input = NULL, txdb = NULL, bsgenome = NULL, genome = NA, gff_dir = NULL, mod_annot = NULL, paired_end = FALSE, library_type = c("unstranded", "1st_strand", "2nd_strand"), fragment_length = 100, binding_length = 25, step_length = binding_length, min_peak_width = fragment_length/2, max_peak_width = fragment_length * 100, pc_count_cutoff = 5, bg_count_cutoff = 50, p_cutoff = 1e-05, p_adj_cutoff = NULL, log2FC_cutoff = 0, parallel = 1, background_method = c("all", "Gaussian_mixture", "m6Aseq_prior", "manual"), manual_background = NULL, correct_GC_bg = TRUE, qtnorm = FALSE, glm_type = c("DESeq2", "Poisson", "NB"), LFC_shrinkage = c("apeglm", "ashr", "Gaussian", "none"), export_results = TRUE, export_format = c("CSV", "BED", "RDS"), table_style = c("bed", "granges"), save_plot_GC = TRUE, save_plot_analysis = FALSE, save_plot_name = "", save_dir = "exomePeak2_output", peak_calling_mode = c("exon", "full_tx", "whole_genome")) Docs: function(bam_ip = NULL, bam_input = NULL, bam_treated_ip = NULL, bam_treated_input = NULL, txdb = NULL, bsgenome = NULL, genome = NA, gff_dir = NULL, mod_annot = NULL, paired_end = FALSE, library_type = c("unstranded", "1st_strand", "2nd_strand"), fragment_length = 100, binding_length = 25, step_length = binding_length, min_peak_width = fragment_length/2, max_peak_width = fragment_length * 10, pc_count_cutoff = 5, bg_count_cutoff = 50, p_cutoff = 1e-05, p_adj_cutoff = NULL, log2FC_cutoff = 0, parallel = 1, background_method = c("all", "Gaussian_mixture", "m6Aseq_prior", "manual"), manual_background = NULL, correct_GC_bg = TRUE, qtnorm = FALSE, glm_type = c("DESeq2", "Poisson", "NB"), LFC_shrinkage = c("apeglm", "ashr", "Gaussian", "none"), export_results = TRUE, export_format = c("CSV", "BED", "RDS"), table_style = c("bed", "granges"), save_plot_GC = TRUE, save_plot_analysis = FALSE, save_plot_name = "", save_dir = "exomePeak2_output", peak_calling_mode = c("exon", "full_tx", "whole_genome")) Mismatches in argument default values: Name: 'max_peak_width' Code: fragment_length * 100 Docs: fragment_length * 10 Codoc mismatches from documentation object 'exomePeakCalling-methods': exomePeakCalling Code: function(merip_bams = NULL, txdb = NULL, bsgenome = NULL, genome = NA, mod_annot = NULL, glm_type = c("DESeq2", "NB", "Poisson"), background_method = c("Gaussian_mixture", "m6Aseq_prior", "manual", "all"), manual_background = NULL, correct_GC_bg = TRUE, qtnorm = FALSE, gff_dir = NULL, fragment_length = 100, binding_length = 25, step_length = binding_length, min_peak_width = fragment_length/2, max_peak_width = fragment_length * 100, pc_count_cutoff = 5, bg_count_cutoff = 50, p_cutoff = 1e-05, p_adj_cutoff = NULL, log2FC_cutoff = 0, parallel = 3, bp_param = NULL) Docs: function(merip_bams = NULL, txdb = NULL, bsgenome = NULL, genome = NA, mod_annot = NULL, glm_type = c("DESeq2", "NB", "Poisson"), background_method = c("Gaussian_mixture", "m6Aseq_prior", "manual", "all"), manual_background = NULL, correct_GC_bg = TRUE, qtnorm = FALSE, gff_dir = NULL, fragment_length = 100, binding_length = 25, step_length = binding_length, min_peak_width = fragment_length/2, max_peak_width = fragment_length * 10, pc_count_cutoff = 5, bg_count_cutoff = 50, p_cutoff = 1e-05, p_adj_cutoff = NULL, log2FC_cutoff = 0, parallel = 3, bp_param = NULL) Mismatches in argument default values: Name: 'max_peak_width' Code: fragment_length * 100 Docs: fragment_length * 10 \S4method{exomePeakCalling}{MeripBamFileList} Code: function(merip_bams = NULL, txdb = NULL, bsgenome = NULL, genome = NA, mod_annot = NULL, glm_type = c("DESeq2", "NB", "Poisson"), background_method = c("all", "Gaussian_mixture", "m6Aseq_prior", "manual"), manual_background = NULL, correct_GC_bg = TRUE, qtnorm = FALSE, gff_dir = NULL, fragment_length = 100, binding_length = 25, step_length = binding_length, min_peak_width = fragment_length/2, max_peak_width = fragment_length * 100, pc_count_cutoff = 5, bg_count_cutoff = 50, p_cutoff = 1e-05, p_adj_cutoff = NULL, log2FC_cutoff = 0, parallel = 1, bp_param = NULL) Docs: function(merip_bams = NULL, txdb = NULL, bsgenome = NULL, genome = NA, mod_annot = NULL, glm_type = c("DESeq2", "NB", "Poisson"), background_method = c("all", "Gaussian_mixture", "m6Aseq_prior", "manual"), manual_background = NULL, correct_GC_bg = TRUE, qtnorm = FALSE, gff_dir = NULL, fragment_length = 100, binding_length = 25, step_length = binding_length, min_peak_width = fragment_length/2, max_peak_width = fragment_length * 10, pc_count_cutoff = 5, bg_count_cutoff = 50, p_cutoff = 1e-05, p_adj_cutoff = NULL, log2FC_cutoff = 0, parallel = 1, bp_param = NULL) Mismatches in argument default values: Name: 'max_peak_width' Code: fragment_length * 100 Docs: fragment_length * 10 Codoc mismatches from documentation object 'glmM-methods': glmM Code: function(sep, glm_type = c("DESeq2", "NB", "Poisson"), LFC_shrinkage = c("apeglm", "Gaussian", "ashr", "none"), ...) Docs: function(sep, glm_type = c("DESeq2", "NB", "Poisson"), LFC_shrinkage = c("apeglm", "Gaussian", "ashr"), ...) Mismatches in argument default values: Name: 'LFC_shrinkage' Code: c("apeglm", "Gaussian", "ashr", "none") Docs: c("apeglm", "Gaussian", "ashr") \S4method{glmM}{SummarizedExomePeak} Code: function(sep, glm_type = c("DESeq2", "NB", "Poisson"), LFC_shrinkage = c("apeglm", "Gaussian", "ashr", "none"), ...) Docs: function(sep, glm_type = c("DESeq2", "NB", "Poisson"), LFC_shrinkage = c("apeglm", "Gaussian", "ashr"), ...) Mismatches in argument default values: Name: 'LFC_shrinkage' Code: c("apeglm", "Gaussian", "ashr", "none") Docs: c("apeglm", "Gaussian", "ashr") * checking Rd \usage sections ... WARNING Undocumented arguments in documentation object 'exomePeakCalling-methods' 'max_peak_width' Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter 'Writing R documentation files' in the 'Writing R Extensions' manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed exomePeak2 40.85 0.53 41.42 exomePeakCalling-methods 23.89 0.14 24.07 SummarizedExomePeak-class 14.62 1.00 15.66 * 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: 2 WARNINGs, 1 NOTE See 'D:/biocbuild/bbs-3.15-bioc/meat/exomePeak2.Rcheck/00check.log' for details.