############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SRAdb.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings SRAdb_1.54.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/SRAdb.Rcheck' * using R version 4.1.1 (2021-08-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'SRAdb/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'SRAdb' version '1.54.0' * 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 ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section 'Package structure' in the 'Writing R Extensions' manual. * checking for portable file names ... OK * checking whether package 'SRAdb' 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 ... NOTE The following files look like leftovers: 'SRAdb/SRAdb-package.Rd' Please remove them from your package. * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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' call to 'RCurl' which was already attached by Depends. Please remove these calls from your code. Packages in Depends field not imported from: 'RSQLite' 'graph' 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 ... NOTE .socketWrite: no visible global function definition for 'write.socket' .socketWrite: no visible global function definition for 'read.socket' IGVsocket: no visible global function definition for 'make.socket' colDescriptions: no visible global function definition for 'dbGetQuery' entityGraph: no visible global function definition for 'na.omit' entityGraph: no visible global function definition for 'new' entityGraph : : no visible global function definition for 'addEdge' getFASTQfile: no visible global function definition for 'download.file' getFASTQinfo: no visible global function definition for 'dbGetQuery' getSRA: no visible global function definition for 'dbGetQuery' getSRAdbFile: no visible global function definition for 'download.file' getSRAdbFile: no visible global function definition for 'dbConnect' getSRAdbFile: no visible global function definition for 'SQLite' getSRAdbFile: no visible global function definition for 'dbGetQuery' getSRAdbFile: no visible global function definition for 'dbDisconnect' getSRAfile: no visible global function definition for 'download.file' getSRAinfo: no visible global function definition for 'na.omit' sraConvert: no visible global function definition for 'dbGetQuery' startIGV: no visible global function definition for 'browseURL' Undefined global functions or variables: SQLite addEdge browseURL dbConnect dbDisconnect dbGetQuery download.file make.socket na.omit new read.socket write.socket Consider adding importFrom("methods", "new") importFrom("stats", "na.omit") importFrom("utils", "browseURL", "download.file", "make.socket", "read.socket", "write.socket") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * 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 files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... OK * 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: 4 NOTEs See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/SRAdb.Rcheck/00check.log' for details.