* using log directory ‘/srv/hornik/tmp/CRAN/DisVar.Rcheck’ * using R Under development (unstable) (2023-08-07 r84885) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 16.0.6 (6) GNU Fortran (Debian 13.2.0-1) 13.2.0 * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘DisVar/DESCRIPTION’ ... OK * this is package ‘DisVar’ version ‘1.1.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/4s] NOTE Maintainer: ‘Khunanon Chanasongkhram ’ New submission Possibly misspelled words in DESCRIPTION: VCF (2:31, 7:75, 7:117) The Description field should not start with the package name, 'This package' or similar. Size of tarball: 42183048 bytes * 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 ‘DisVar’ can be installed ... [64s/64s] WARNING Found the following significant warnings: Warning: replacing previous import ‘data.table::between’ by ‘dplyr::between’ when loading ‘DisVar’ Warning: replacing previous import ‘data.table::first’ by ‘dplyr::first’ when loading ‘DisVar’ Warning: replacing previous import ‘data.table::last’ by ‘dplyr::last’ when loading ‘DisVar’ See ‘/srv/hornik/tmp/CRAN/DisVar.Rcheck/00install.out’ for details. * checking package directory ... OK * checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... NOTE Non-standard files/directories found at top level: ‘1000genome_clinvar_testing’ ‘file_name.vcf’ ‘file_name_DisVar.txt’ * 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 ... [1s/1s] OK * checking whether the package can be loaded with stated dependencies ... [1s/1s] OK * checking whether the package can be unloaded cleanly ... [1s/1s] OK * checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK * checking whether the namespace can be unloaded cleanly ... [1s/1s] OK * checking loading without being on the library search path ... [1s/1s] 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 ... [4s/4s] NOTE DisVar: no visible global function definition for ‘install.packages’ DisVar: no visible global function definition for ‘data’ DisVar: no visible binding for global variable ‘GWASdb_GRCh38’ DisVar: no visible binding for global variable ‘GRASP_GRCh38’ DisVar: no visible binding for global variable ‘GWAS_catalog_GRCh38’ DisVar: no visible binding for global variable ‘JnO_GRCh38’ DisVar: no visible global function definition for ‘fread’ DisVar: no visible global function definition for ‘setDT’ DisVar: no visible global function definition for ‘.’ DisVar: no visible binding for global variable ‘V2’ DisVar: no visible binding for global variable ‘V1’ DisVar: no visible binding for global variable ‘P_value’ DisVar: no visible binding for global variable ‘Rsid’ DisVar: no visible binding for global variable ‘Chr’ DisVar: no visible binding for global variable ‘V4’ DisVar: no visible binding for global variable ‘V5’ DisVar: no visible binding for global variable ‘Ref’ DisVar: no visible binding for global variable ‘Alt’ DisVar: no visible binding for global variable ‘Gwas_trait’ DisVar: no visible binding for global variable ‘Gene’ DisVar: no visible binding for global variable ‘Variant_type’ DisVar: no visible binding for global variable ‘V6’ DisVar: no visible binding for global variable ‘V7’ DisVar: no visible binding for global variable ‘V8’ DisVar: no visible global function definition for ‘setNames’ DisVar: no visible global function definition for ‘%>%’ DisVar: no visible global function definition for ‘arrange’ DisVar: no visible binding for global variable ‘Disease’ DisVar: no visible binding for global variable ‘Confident’ DisVar: no visible global function definition for ‘write.table’ Undefined global functions or variables: %>% . Alt Chr Confident Disease GRASP_GRCh38 GWAS_catalog_GRCh38 GWASdb_GRCh38 Gene Gwas_trait JnO_GRCh38 P_value Ref Rsid V1 V2 V4 V5 V6 V7 V8 Variant_type arrange data fread install.packages setDT setNames write.table Consider adding importFrom("stats", "setNames") importFrom("utils", "data", "install.packages", "write.table") to your NAMESPACE file. Found the following calls to data() loading into the global environment: File ‘DisVar/R/DisVar.R’: data(GWASdb_GRCh38) data(GRASP_GRCh38) data(GWAS_catalog_GRCh38) data(GAD_GRCh38) data(JnO_GRCh38) See section ‘Good practice’ in ‘?data’. * 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: ‘GAD_GRCh38’ ‘GRASP_GRCh38’ ‘GWAS_catalog_GRCh38’ ‘GWASdb_GRCh38’ ‘JnO_GRCh38’ Undocumented data sets: ‘GAD_GRCh38’ ‘GRASP_GRCh38’ ‘GWAS_catalog_GRCh38’ ‘GWASdb_GRCh38’ ‘JnO_GRCh38’ 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... [8s/8s] WARNING Warning: found non-ASCII strings 'Fagerstrm_test_for_nicotine_dependence' in object 'GWAS_catalog_GRCh38' 'Minimum_ankle<80><93>brachial_index' in object 'GWAS_catalog_GRCh38' 'C10orf32<80><93>ASMT' in object 'GWAS_catalog_GRCh38' 'CYP11B1<80><93>CYP11B2' in object 'GWAS_catalog_GRCh38' 'FIGN<80><93>GRB14' in object 'GWAS_catalog_GRCh38' 'HLA<80><93>DRB1' in object 'GWAS_catalog_GRCh38' 'HOXA10<80><93>HOXA9' in object 'GWAS_catalog_GRCh38' 'LOC105375794<80><93>LOC100133669' in object 'GWAS_catalog_GRCh38' 'LOC105377992<80><93>LOC105377989' in object 'GWAS_catalog_GRCh38' 'LSP1<80><93>TNNT3' in object 'GWAS_catalog_GRCh38' 'MEF2B,MEF2BNB<80><93>MEF2B' in object 'GWAS_catalog_GRCh38' 'NPR3<80><93>C5orf23' in object 'GWAS_catalog_GRCh38' 'PRDM8<80><93>FGF5' in object 'GWAS_catalog_GRCh38' 'TBX5<80><93>TBX3' in object 'GWAS_catalog_GRCh38' 'UBA52P4<80><93>LOC105377005' in object 'GWAS_catalog_GRCh38' * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking examples ... [1s/1s] ERROR Running examples in ‘DisVar-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: DisVar > ### Title: Find diseases from the VCF file > ### Aliases: DisVar > > ### ** Examples > > DisVar("file_name.vcf") Loading required package: sqldf Loading required package: gsubfn Loading required package: proto Loading required package: RSQLite Loading required package: data.table Loading required package: dplyr Attaching package: ‘dplyr’ The following objects are masked from ‘package:data.table’: between, first, last The following objects are masked from ‘package:stats’: filter, lag The following objects are masked from ‘package:base’: intersect, setdiff, setequal, union Error in DisVar("file_name.vcf") : File does not exist Execution halted * checking PDF version of manual ... [2s/2s] 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, 3 WARNINGs, 3 NOTEs