* using log directory ‘/srv/hornik/tmp/CRAN_pretest/EZTCGA.Rcheck’ * using R Under development (unstable) (2024-11-15 r87338) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.1 (1) Debian flang-new version 19.1.1 (1) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘EZTCGA/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘EZTCGA’ version ‘0.1.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [1s/1s] NOTE Maintainer: ‘Ehsan Keramati ’ New submission Non-FOSS package license (-) Possibly misspelled words in DESCRIPTION: Ehsan (3:19) Keramati (3:25) TCGA (3:13, 7:36) No Authors@R field in DESCRIPTION. Please add one, modifying Authors@R: person(given = "Ehsan", family = "Keramati", role = c("aut", "cre"), email = "ehsan.keramati14@gmail.com") as necessary. * 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 executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking serialization versions ... OK * checking whether package ‘EZTCGA’ can be installed ... [1s/1s] OK * checking package directory ... OK * checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. Non-standard license specification: - Standardizable: FALSE * 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 ... [0s/0s] OK * checking whether the package can be loaded with stated dependencies ... [0s/0s] OK * checking whether the package can be unloaded cleanly ... [0s/0s] OK * checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK * checking whether the namespace can be unloaded cleanly ... [0s/0s] OK * checking loading without being on the library search path ... [0s/0s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... WARNING '::' or ':::' import not declared from: ‘BiocManager’ 'library' or 'require' calls not declared from: ‘BiocManager’ ‘DESeq2’ ‘EnhancedVolcano’ ‘SummarizedExperiment’ ‘TCGAbiolinks’ ‘crayon’ ‘ggplot2’ ‘gplots’ ‘pheatmap’ 'library' or 'require' calls in package code: ‘BiocManager’ ‘DESeq2’ ‘EnhancedVolcano’ ‘SummarizedExperiment’ ‘TCGAbiolinks’ ‘crayon’ ‘ggplot2’ ‘gplots’ ‘pheatmap’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [2s/2s] NOTE eztcga_get_projects: no visible global function definition for ‘red’ eztcga_get_projects: no visible global function definition for ‘getGDCprojects’ eztcga_get_projects: no visible global function definition for ‘blue’ eztcga_just_do_it: no visible global function definition for ‘?’ eztcga_just_do_it: no visible binding for global variable ‘EZTCGA’ eztcga_just_do_it: no visible global function definition for ‘red’ eztcga_just_do_it: no visible global function definition for ‘GDCquery’ eztcga_just_do_it: no visible global function definition for ‘getResults’ eztcga_just_do_it: no visible global function definition for ‘write.table’ eztcga_just_do_it: no visible global function definition for ‘GDCdownload’ eztcga_just_do_it: no visible global function definition for ‘GDCprepare’ eztcga_just_do_it: no visible global function definition for ‘assay’ eztcga_just_do_it: no visible global function definition for ‘prcomp’ eztcga_just_do_it: no visible global function definition for ‘ggplot’ eztcga_just_do_it: no visible global function definition for ‘aes’ eztcga_just_do_it: no visible binding for global variable ‘PC1’ eztcga_just_do_it: no visible binding for global variable ‘PC2’ eztcga_just_do_it: no visible global function definition for ‘geom_point’ eztcga_just_do_it: no visible global function definition for ‘ggsave’ eztcga_just_do_it: no visible global function definition for ‘DESeqDataSetFromMatrix’ eztcga_just_do_it: no visible global function definition for ‘estimateSizeFactors’ eztcga_just_do_it: no visible global function definition for ‘DESeq’ eztcga_just_do_it: no visible global function definition for ‘results’ eztcga_just_do_it: no visible global function definition for ‘mcols’ eztcga_just_do_it: no visible global function definition for ‘read.table’ eztcga_just_do_it: no visible global function definition for ‘EnhancedVolcano’ eztcga_just_do_it: no visible global function definition for ‘png’ eztcga_just_do_it: no visible global function definition for ‘pheatmap’ eztcga_just_do_it: no visible global function definition for ‘greenred’ eztcga_just_do_it: no visible global function definition for ‘dev.off’ eztcga_just_do_it: no visible global function definition for ‘green’ eztcga_prepare_me: no visible global function definition for ‘install.packages’ Undefined global functions or variables: ? DESeq DESeqDataSetFromMatrix EZTCGA EnhancedVolcano GDCdownload GDCprepare GDCquery PC1 PC2 aes assay blue dev.off estimateSizeFactors geom_point getGDCprojects getResults ggplot ggsave green greenred install.packages mcols pheatmap png prcomp read.table red results write.table Consider adding importFrom("grDevices", "dev.off", "png") importFrom("stats", "prcomp") importFrom("utils", "?", "install.packages", "read.table", "write.table") to your NAMESPACE file. * checking Rd files ... [0s/0s] OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented code objects: ‘eztcga_get_projects’ ‘eztcga_just_do_it’ ‘eztcga_prepare_me’ All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking examples ... NONE * checking PDF version of manual ... [2s/2s] OK * checking HTML version of manual ... [0s/0s] OK * checking for code which exercises the package ... WARNING No examples, no tests, no vignettes * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 3 WARNINGs, 3 NOTEs