* using log directory ‘/srv/hornik/tmp/CRAN_pretest/MetAlyzer.Rcheck’ * using R Under development (unstable) (2024-10-31 r87278) * 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 ‘MetAlyzer/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MetAlyzer’ version ‘1.1.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [5s/8s] NOTE Maintainer: ‘Nils Mechtel ’ Found the following (possibly) invalid URLs: URL: https://cran.r-project.org/web/packages/MetAlyzer/vignettes/MetAlyzer_User_Guide.html From: README.md Status: 200 Message: OK CRAN URL not in canonical form The canonical URL of the CRAN page for a package is https://CRAN.R-project.org/package=pkgname * 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 whether package ‘MetAlyzer’ can be installed ... [16s/16s] OK * checking package directory ... OK * checking for future file timestamps ... 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 ... [5s/5s] OK * checking whether the package can be loaded with stated dependencies ... [4s/4s] OK * checking whether the package can be unloaded cleanly ... [4s/4s] OK * checking whether the namespace can be loaded with stated dependencies ... [5s/5s] OK * checking whether the namespace can be unloaded cleanly ... [5s/5s] OK * checking loading without being on the library search path ... [5s/5s] OK * checking use of S3 registration ... 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 ... [22s/22s] OK * checking Rd files ... [0s/0s] OK * checking Rd metadata ... OK * checking Rd line widths ... NOTE Rd file 'summarizeConcValues.Rd': \examples lines wider than 100 characters: metalyzer_se <- MetAlyzer_dataset(file_path = "/Users/larrylusi/Downloads/2024-09-10_DISC_THRX_Tissue+TRP.xlsx") These lines will be truncated in the PDF manual. * 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 installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [40s/40s] ERROR Running examples in ‘MetAlyzer-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: summarizeConcValues > ### Title: Summarize concentration values > ### Aliases: summarizeConcValues > > ### ** Examples > > metalyzer_se <- MetAlyzer_dataset(file_path = example_extraction_data()) _____ ______ _______ _________ ________ ___ ___ ___ ________ _______ ________ |\ _ \ _ \|\ ___ \|\___ ___\\ __ \|\ \ |\ \ / /|\_____ \|\ ___ \ |\ __ \ \ \ \\\__\ \ \ \ __/\|___ \ \_\ \ \|\ \ \ \ \ \ \/ / /\|___/ /\ \ __/|\ \ \|\ \ \ \ \\|__| \ \ \ \_|/__ \ \ \ \ \ __ \ \ \ \ \ / / / / /\ \ \_|/_\ \ _ _\ \ \ \ \ \ \ \ \_|\ \ \ \ \ \ \ \ \ \ \ \____ \/ / / / /_/__\ \ \_|\ \ \ \\ \| \ \__\ \ \__\ \_______\ \ \__\ \ \__\ \__\ \_______\__/ / / |\________\ \_______\ \__\\ _\ \|__| \|__|\|_______| \|__| \|__|\|__|\|_______|\____/ / \|_______|\|_______|\|__|\|__| \|____|/ Info: Reading color code "FFFFCCCC" as "#FFCCCC" Info: Reading color code "FF00CD66" as "#00CD66" Info: Reading color code "FF6A5ACD" as "#6A5ACD" Info: Reading color code "FF87CEEB" as "#87CEEB" Info: Reading color code "FFFFFFCC" as "#FFFFCC" Measured concentration values: ------------------------------ 0% 25% 50% 75% 100% 0.000 0.017 1.760 21.200 288149.000 NAs: 5348 (8.38%) Note: 'Metabolism Indicators' are frequently NA! Measured quantification status: ------------------------------- Valid: 24095 (37.77%) LOQ: 5799 (9.09%) LOD: 21789 (34.16%) Invalid: 12105 (18.98%) NAs: 0 (0%) > metalyzer_se <- MetAlyzer_dataset(file_path = "/Users/larrylusi/Downloads/2024-09-10_DISC_THRX_Tissue+TRP.xlsx") _____ ______ _______ _________ ________ ___ ___ ___ ________ _______ ________ |\ _ \ _ \|\ ___ \|\___ ___\\ __ \|\ \ |\ \ / /|\_____ \|\ ___ \ |\ __ \ \ \ \\\__\ \ \ \ __/\|___ \ \_\ \ \|\ \ \ \ \ \ \/ / /\|___/ /\ \ __/|\ \ \|\ \ \ \ \\|__| \ \ \ \_|/__ \ \ \ \ \ __ \ \ \ \ \ / / / / /\ \ \_|/_\ \ _ _\ \ \ \ \ \ \ \ \_|\ \ \ \ \ \ \ \ \ \ \ \____ \/ / / / /_/__\ \ \_|\ \ \ \\ \| \ \__\ \ \__\ \_______\ \ \__\ \ \__\ \__\ \_______\__/ / / |\________\ \_______\ \__\\ _\ \|__| \|__|\|_______| \|__| \|__|\|__|\|_______|\____/ / \|_______|\|_______|\|__|\|__| \|____|/ Error in read.xlsx.default(starter_list$file_path, sheet = starter_list$sheet, : File does not exist. Calls: MetAlyzer_dataset -> open_file -> -> read.xlsx.default Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [105s/106s] OK * checking PDF version of manual ... [4s/4s] OK * checking HTML version of manual ... [0s/0s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 2 NOTEs