* using log directory 'd:/RCompile/CRANincoming/R-devel/SNPtools.Rcheck' * using R Under development (unstable) (2025-07-13 r88407 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'SNPtools/DESCRIPTION' ... OK * this is package 'SNPtools' version '0.1.0' * package encoding: UTF-8 * checking CRAN incoming feasibility ... WARNING Maintainer: 'Vinícius Junqueira ' New submission Package was archived on CRAN Insufficient package version (submitted: 0.1.0, existing: 1.1) Possibly misspelled words in DESCRIPTION: FImpute (8:312) PLINK (8:324) SNPtools (8:14) anticlustering (8:542) scalable (8:805) Unknown, possibly misspelled, fields in DESCRIPTION: 'Logo' CRAN repository db overrides: X-CRAN-Comment: Archived on 2018-07-03 as check problems were not corrected despite reminders. Found the following (possibly) invalid URLs: URL: https://viniciusjunqueira.github.io/SNPtools (moved to https://viniciusjunqueira.github.io/SNPtools/) From: DESCRIPTION Status: 301 Message: Moved Permanently For content that is 'Moved Permanently', please change http to https, add trailing slashes, or replace the old by the new URL. The Description field should not start with the package name, 'This package' or similar. * 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 'SNPtools' can be installed ... OK * used C++ compiler: 'g++.exe (GCC) 14.2.0' * checking installed package size ... OK * checking package directory ... OK * checking for future file timestamps ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file. Non-standard files/directories found at top level: 'SNPtools-package.R' 'SNPtools_0.1.0.pdf' * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... WARNING Found the following files with non-ASCII characters: R/fimpute_runner.R R/import_batch.R R/qcSNPs.R R/qcSamples.R R/readFimpute.R R/save_fimpute.R R/save_plink.R R/utils_anticlustering.R R/utils_display.R R/utils_geno.R Portable packages must use only ASCII characters in their R code and NAMESPACE directives, except perhaps in comments. Use \uxxxx escapes for other characters. Function 'tools::showNonASCIIfile' can help in finding non-ASCII characters in files. * 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 use of S3 registration ... OK * checking dependencies in R code ... NOTE Packages in Depends field not imported from: 'dplyr' 'tidyverse' These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [18s] NOTE FImputeRunner: no visible global function definition for 'new' check.identical.samples: no visible global function definition for 'dist' check.identical.samples: no visible global function definition for 'as' check.sample.heterozygosity: no visible global function definition for 'sd' combinarSNPData : : no visible global function definition for 'new' combinarSNPData: no visible global function definition for 'new' doPCA: no visible global function definition for 'xxt' doPCA: no visible global function definition for 'snp.pre.multiply' doPCA: no visible global function definition for 'snp.post.multiply' exploratory.plots: no visible global function definition for 'jpeg' exploratory.plots: no visible global function definition for 'par' exploratory.plots: no visible global function definition for 'hist' exploratory.plots: no visible global function definition for 'dev.off' exploratory.plots: no visible global function definition for 'text' exploratory.plots: no visible global function definition for 'isoMDS' exploratory.plots: no visible global function definition for 'hclust' genoToDF: no visible global function definition for 'col.summary' genoToDF: no visible global function definition for 'as' get.hwe.chi2: no visible global function definition for 'pchisq' ibs.pair: no visible global function definition for 'sd' plotPCAgroups: no visible global function definition for 'ggplot' plotPCAgroups: no visible global function definition for 'aes' plotPCAgroups: no visible binding for global variable 'PC1' plotPCAgroups: no visible binding for global variable 'PC2' plotPCAgroups: no visible binding for global variable 'Group' plotPCAgroups: no visible global function definition for 'geom_point' plotPCAgroups: no visible global function definition for 'labs' plotPCAgroups: no visible global function definition for 'theme_minimal' plotPCAgroups: no visible global function definition for 'theme' plotPCAgroups: no visible global function definition for 'element_rect' plotPCAgroups: no visible global function definition for 'ggsave' rbindSnpFlexible: no visible global function definition for 'new' read.fimpute: no visible global function definition for 'new' runAnticlusteringPCA: no visible global function definition for 'prcomp' runAnticlusteringPCA: no visible global function definition for 'fast_anticlustering' savePlink: no visible global function definition for 'as' savePlink: no visible global function definition for 'write.table' save_fimpute_raw: no visible global function definition for 'as' save_fimpute_raw: no visible global function definition for 'write.table' getGeno,ANY: no visible global function definition for 'read.table' getGeno,ANY: no visible global function definition for '%>%' getGeno,ANY: no visible binding for global variable 'Name' getGeno,ANY: no visible global function definition for 'new' qcSNPs,SNPDataLong: no visible global function definition for 'col.summary' qcSNPs,SNPDataLong: no visible global function definition for 'new' qcSamples,SNPDataLong: no visible global function definition for 'row.summary' qcSamples,SNPDataLong: no visible global function definition for 'new' Undefined global functions or variables: %>% Group Name PC1 PC2 aes as col.summary dev.off dist element_rect fast_anticlustering geom_point ggplot ggsave hclust hist isoMDS jpeg labs new par pchisq prcomp read.table row.summary sd snp.post.multiply snp.pre.multiply text theme theme_minimal write.table xxt Consider adding importFrom("grDevices", "dev.off", "jpeg") importFrom("graphics", "hist", "par", "text") importFrom("methods", "as", "new") importFrom("stats", "dist", "hclust", "pchisq", "prcomp", "sd") importFrom("utils", "read.table", "write.table") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... NOTE Rd file 'check.snp.same.position.Rd': \examples lines wider than 100 characters: df <- data.frame(Chromosome = c(1, 1, 2), Position = c(100, 100, 200), Name = c("SNP1", "SNP2", "SNP3")) Rd file 'qcSNPs.Rd': \examples lines wider than 100 characters: qcSNPs(x, min_snp_cr = 0.8, min_maf = 0.05, snp_mono = TRUE, no_position = TRUE, snp_position = TRUE, action = "filter") These lines will be truncated in the PDF manual. * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented S4 methods: generic 'Subset' and siglist 'SNPDataLong' generic 'getGeno' and siglist 'ANY' generic 'importAllGenos' and siglist 'SNPImportList' generic 'qcSNPs' and siglist 'SNPDataLong' All user-level objects in a package (including S4 classes and methods) 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 ... WARNING Undocumented arguments in Rd file 'FImputeRunner.Rd' 'object' Documented arguments not in \usage in Rd file 'FImputeRunner.Rd': 'geno' 'map' Undocumented arguments in Rd file 'getGeno.Rd' '...' Documented arguments not in \usage in Rd file 'getGeno.Rd': 'path' 'fields' 'codes' 'threshold' 'sep' 'skip' 'verbose' 'every' Undocumented arguments in Rd file 'qcSNPs.Rd' '...' Documented arguments not in \usage in Rd file 'qcSNPs.Rd': 'missing_ind' 'missing_snp' 'min_snp_cr' 'min_maf' 'hwe' 'snp_position' 'no_position' 'snp_mono' 'remove_chr' 'action' Undocumented arguments in Rd file 'qcSamples.Rd' '...' Undocumented arguments in Rd file 'summary-SNPDataLong-method.Rd' '...' 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 line endings in C/C++/Fortran sources/headers ... OK * checking pragmas in C/C++ headers and code ... OK * checking compilation flags used ... OK * checking compiled code ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... ERROR Running examples in 'SNPtools-Ex.R' failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: check.snp.same.position > ### Title: Check SNPs mapped to the same position > ### Aliases: check.snp.same.position > > ### ** Examples > > df <- data.frame(Chromosome = c(1, 1, 2), Position = c(100, 100, 200), Name = c("SNP1", "SNP2", "SNP3")) > check.snp.same.position(df) [1] "Analyzing chromosome 1" [1] "SNPs in same position: SNP1 - SNP2" [1] "Analyzing chromosome 2" Error in if (sorted.snpmap.chr[j, "Position"] == sorted.snpmap.chr[j1, : missing value where TRUE/FALSE needed Calls: check.snp.same.position Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... [30s] OK * checking HTML version of manual ... OK * DONE Status: 1 ERROR, 4 WARNINGs, 4 NOTEs