############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:knowYourCG.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings knowYourCG_1.3.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/knowYourCG.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘knowYourCG/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘knowYourCG’ version ‘1.3.0’ * 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 ‘knowYourCG’ can be installed ... WARNING Found the following significant warnings: Note: possible error in 'dbStats(betas, dbs, long = TRUE)': unused argument (long = TRUE) See ‘/home/biocbuild/bbs-3.21-bioc/meat/knowYourCG.Rcheck/00install.out’ for details. Information on the location(s) of code generating the ‘Note’s can be obtained by re-running with environment variable R_KEEP_PKG_SOURCE set to ‘yes’. * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * 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 loading without being on the library search path ... OK * checking dependencies in R code ... WARNING '::' or ':::' import not declared from: ‘ggrepel’ 'loadNamespace' or 'requireNamespace' call not declared from: ‘ggrepel’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE KYCG_plotBar: no visible global function definition for ‘ggplot’ KYCG_plotBar: no visible global function definition for ‘aes_string’ KYCG_plotBar: no visible global function definition for ‘geom_bar’ KYCG_plotBar: no visible global function definition for ‘coord_flip’ KYCG_plotBar: no visible global function definition for ‘ylab’ KYCG_plotBar: no visible global function definition for ‘xlab’ KYCG_plotBar: no visible global function definition for ‘geom_label’ KYCG_plotDot: no visible global function definition for ‘ggplot’ KYCG_plotDot: no visible global function definition for ‘geom_point’ KYCG_plotDot: no visible global function definition for ‘aes’ KYCG_plotDot: no visible global function definition for ‘coord_flip’ KYCG_plotDot: no visible global function definition for ‘ggtitle’ KYCG_plotDot: no visible global function definition for ‘scale_color_gradient’ KYCG_plotDot: no visible global function definition for ‘ylab’ KYCG_plotDot: no visible global function definition for ‘xlab’ KYCG_plotEnrichAll: no visible global function definition for ‘rownames_to_column’ KYCG_plotEnrichAll: no visible global function definition for ‘ggplot’ KYCG_plotEnrichAll: no visible global function definition for ‘aes’ KYCG_plotEnrichAll: no visible global function definition for ‘geom_point’ KYCG_plotEnrichAll: no visible global function definition for ‘head’ KYCG_plotEnrichAll: no visible global function definition for ‘annotate’ KYCG_plotEnrichAll: no visible global function definition for ‘geom_hline’ KYCG_plotEnrichAll: no visible global function definition for ‘geom_segment’ KYCG_plotEnrichAll: no visible global function definition for ‘geom_text’ KYCG_plotEnrichAll: no visible global function definition for ‘scale_color_discrete’ KYCG_plotEnrichAll: no visible global function definition for ‘ylim’ KYCG_plotEnrichAll: no visible global function definition for ‘xlab’ KYCG_plotEnrichAll: no visible global function definition for ‘scale_size_continuous’ KYCG_plotEnrichAll: no visible global function definition for ‘guide_legend’ KYCG_plotEnrichAll: no visible global function definition for ‘coord_cartesian’ KYCG_plotEnrichAll: no visible global function definition for ‘theme_minimal’ KYCG_plotEnrichAll: no visible global function definition for ‘theme’ KYCG_plotEnrichAll: no visible global function definition for ‘element_blank’ KYCG_plotLollipop: no visible global function definition for ‘head’ KYCG_plotLollipop: no visible global function definition for ‘ggplot’ KYCG_plotLollipop: no visible global function definition for ‘aes_string’ KYCG_plotLollipop: no visible global function definition for ‘geom_hline’ KYCG_plotLollipop: no visible global function definition for ‘geom_segment’ KYCG_plotLollipop: no visible global function definition for ‘aes’ KYCG_plotLollipop: no visible global function definition for ‘geom_point’ KYCG_plotLollipop: no visible global function definition for ‘scale_fill_gradientn’ KYCG_plotLollipop: no visible global function definition for ‘geom_text’ KYCG_plotLollipop: no visible global function definition for ‘ylab’ KYCG_plotLollipop: no visible global function definition for ‘ylim’ KYCG_plotLollipop: no visible global function definition for ‘theme_minimal’ KYCG_plotLollipop: no visible global function definition for ‘theme’ KYCG_plotLollipop: no visible global function definition for ‘element_blank’ KYCG_plotManhattan: no visible global function definition for ‘seqnames’ KYCG_plotManhattan: no visible global function definition for ‘as_tibble’ KYCG_plotManhattan: no visible global function definition for ‘ggplot’ KYCG_plotManhattan: no visible global function definition for ‘aes_string’ KYCG_plotManhattan: no visible global function definition for ‘geom_point’ KYCG_plotManhattan: no visible global function definition for ‘scale_color_manual’ KYCG_plotManhattan: no visible global function definition for ‘scale_x_continuous’ KYCG_plotManhattan: no visible global function definition for ‘scale_y_continuous’ KYCG_plotManhattan: no visible global function definition for ‘theme_bw’ KYCG_plotManhattan: no visible global function definition for ‘theme’ KYCG_plotManhattan: no visible global function definition for ‘element_blank’ KYCG_plotManhattan: no visible global function definition for ‘labs’ KYCG_plotManhattan: no visible global function definition for ‘xlab’ KYCG_plotManhattan: no visible global function definition for ‘ylab’ KYCG_plotMeta: no visible global function definition for ‘KYCG_getDBs’ KYCG_plotMeta: possible error in dbStats(betas, dbs, long = TRUE): unused argument (long = TRUE) KYCG_plotMeta: no visible global function definition for ‘ggplot’ KYCG_plotMeta: no visible global function definition for ‘annotate’ KYCG_plotMeta: no visible global function definition for ‘geom_line’ KYCG_plotMeta: no visible global function definition for ‘aes_string’ KYCG_plotMeta: no visible global function definition for ‘scale_x_continuous’ KYCG_plotMeta: no visible global function definition for ‘ylab’ KYCG_plotMeta: no visible global function definition for ‘xlab’ KYCG_plotMeta: no visible global function definition for ‘theme’ KYCG_plotMeta: no visible global function definition for ‘element_text’ KYCG_plotMetaEnrichment: no visible global function definition for ‘ggplot’ KYCG_plotMetaEnrichment: no visible global function definition for ‘annotate’ KYCG_plotMetaEnrichment: no visible global function definition for ‘geom_line’ KYCG_plotMetaEnrichment: no visible global function definition for ‘aes_string’ KYCG_plotMetaEnrichment: no visible global function definition for ‘scale_x_continuous’ KYCG_plotMetaEnrichment: no visible global function definition for ‘geom_hline’ KYCG_plotMetaEnrichment: no visible global function definition for ‘ylab’ KYCG_plotMetaEnrichment: no visible global function definition for ‘xlab’ KYCG_plotMetaEnrichment: no visible global function definition for ‘theme’ KYCG_plotMetaEnrichment: no visible global function definition for ‘element_text’ KYCG_plotPointRange: no visible global function definition for ‘summarize’ KYCG_plotPointRange: no visible global function definition for ‘ggplot’ KYCG_plotPointRange: no visible global function definition for ‘geom_pointrange’ KYCG_plotPointRange: no visible global function definition for ‘aes_string’ KYCG_plotPointRange: no visible global function definition for ‘geom_hline’ KYCG_plotPointRange: no visible global function definition for ‘ylab’ KYCG_plotPointRange: no visible global function definition for ‘xlab’ KYCG_plotPointRange: no visible global function definition for ‘scale_y_continuous’ KYCG_plotPointRange: no visible global function definition for ‘annotate’ KYCG_plotPointRange: no visible global function definition for ‘coord_flip’ KYCG_plotSetEnrichment: no visible global function definition for ‘WGG’ KYCG_plotSetEnrichment: no visible global function definition for ‘ggplot’ KYCG_plotSetEnrichment: no visible global function definition for ‘geom_segment’ KYCG_plotSetEnrichment: no visible global function definition for ‘aes_string’ KYCG_plotSetEnrichment: no visible global function definition for ‘geom_line’ KYCG_plotSetEnrichment: no visible global function definition for ‘xlab’ KYCG_plotSetEnrichment: no visible global function definition for ‘ylab’ KYCG_plotSetEnrichment: no visible global function definition for ‘geom_area’ KYCG_plotSetEnrichment: no visible global function definition for ‘Beneath’ KYCG_plotVolcano: no visible global function definition for ‘ggplot’ KYCG_plotVolcano: no visible global function definition for ‘aes_string’ KYCG_plotVolcano: no visible global function definition for ‘geom_point’ KYCG_plotVolcano: no visible global function definition for ‘xlab’ KYCG_plotVolcano: no visible global function definition for ‘ylab’ KYCG_plotVolcano: no visible global function definition for ‘scale_colour_manual’ KYCG_plotVolcano: no visible global function definition for ‘unit’ KYCG_plotWaterfall: no visible global function definition for ‘ggplot’ KYCG_plotWaterfall: no visible global function definition for ‘aes’ KYCG_plotWaterfall: no visible global function definition for ‘geom_point’ KYCG_plotWaterfall: no visible global function definition for ‘geom_hline’ KYCG_plotWaterfall: no visible global function definition for ‘theme_minimal’ KYCG_plotWaterfall: no visible global function definition for ‘ylab’ KYCG_plotWaterfall: no visible global function definition for ‘xlab’ KYCG_plotWaterfall: no visible global function definition for ‘head’ KYCG_plotWaterfall: no visible global function definition for ‘aes_string’ preparePlotDF: no visible global function definition for ‘str_split’ preparePlotDF: no visible global function definition for ‘%>%’ preparePlotDF: no visible global function definition for ‘slice_min’ preparePlotDF: no visible global function definition for ‘ungroup’ preparePlotDF: no visible global function definition for ‘head’ Undefined global functions or variables: %>% Beneath KYCG_getDBs WGG aes aes_string annotate as_tibble coord_cartesian coord_flip element_blank element_text geom_area geom_bar geom_hline geom_label geom_line geom_point geom_pointrange geom_segment geom_text ggplot ggtitle guide_legend head labs rownames_to_column scale_color_discrete scale_color_gradient scale_color_manual scale_colour_manual scale_fill_gradientn scale_size_continuous scale_x_continuous scale_y_continuous seqnames slice_min str_split summarize theme theme_bw theme_minimal ungroup unit xlab ylab ylim Consider adding importFrom("utils", "head") 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 files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘knowYourCG-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: KYCG_plotBar > ### Title: Bar plot to show most enriched CG groups from testEnrichment > ### Aliases: KYCG_plotBar > > ### ** Examples > > KYCG_plotBar(data.frame( + estimate=runif(10,0,10), FDR=runif(10,0,1), nD=10, + overlap=as.integer(runif(10,0,30)), group="g", dbname=seq_len(10))) Error in KYCG_plotBar(data.frame(estimate = runif(10, 0, 10), FDR = runif(10, : could not find function "KYCG_plotBar" Execution halted * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 2 WARNINGs, 2 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/knowYourCG.Rcheck/00check.log’ for details.