############################################################################## ############################################################################## ### ### Running command: ### ### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:REMP.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings REMP_1.19.1.tar.gz ### ############################################################################## ############################################################################## * using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/REMP.Rcheck' * using R Under development (unstable) (2021-11-21 r81221) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'REMP/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'REMP' version '1.19.1' * package encoding: UTF-8 * 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 'REMP' can be installed ... OK * checking installed package size ... OK * checking package directory ... 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 R 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 dependencies in R code ... NOTE 'library' or 'require' calls in package code: 'IlluminaHumanMethylation450kanno.ilmn12.hg19' 'IlluminaHumanMethylationEPICanno.ilm10b2.hg19' 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 ... NOTE initREMP: no visible binding for global variable 'IlluminaHumanMethylation450kanno.ilmn12.hg19' initREMP: no visible binding for global variable 'IlluminaHumanMethylationEPICanno.ilm10b2.hg19' remprofile: no visible binding for global variable 'IlluminaHumanMethylation450kanno.ilmn12.hg19' remprofile: no visible binding for global variable 'IlluminaHumanMethylationEPICanno.ilm10b2.hg19' Undefined global functions or variables: IlluminaHumanMethylation450kanno.ilmn12.hg19 IlluminaHumanMethylationEPICanno.ilm10b2.hg19 * 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 contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in 'vignettes' ... OK * checking examples ... ERROR Running examples in 'REMP-Ex.R' failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: fetchRMSK > ### Title: Get RE database from RepeatMasker > ### Aliases: fetchRMSK > > ### ** Examples > > L1 <- fetchRMSK(REtype = "L1", + annotation.source = "AH", + genome = "hg19", + verbose = TRUE) Loading L1 annotation data from RepeatMasker (hg19) database from AnnotationHub: AH5122 Error: Public Resource removed on: 2022-01-30 Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 2 NOTEs See 'D:/biocbuild/bbs-3.15-bioc/meat/REMP.Rcheck/00check.log' for details.