##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SRAdb.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SRAdb_1.62.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/SRAdb.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SRAdb/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SRAdb’ version ‘1.62.0’
* 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 for sufficient/correct file permissions ... 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
* 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 : <anonymous>: 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/SRAdb.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SRAdb
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘SRAdb’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SRAdb)