Package: SRAdb

Version: 1.44.0

Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SRAdb.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings SRAdb_1.44.0.tar.gz

StartedAt: 2019-04-13 05:43:41 -0400 (Sat, 13 Apr 2019)

EndedAt: 2019-04-13 05:45:44 -0400 (Sat, 13 Apr 2019)

EllapsedTime: 122.8 seconds

RetCode: 0

Status:  OK

CheckDir: SRAdb.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SRAdb.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings SRAdb_1.44.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/SRAdb.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.44.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 : <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 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-3.8-bioc/meat/SRAdb.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/SRAdb_1.44.0.tar.gz && rm -rf SRAdb.buildbin-libdir && mkdir SRAdb.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SRAdb.buildbin-libdir SRAdb_1.44.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL SRAdb_1.44.0.zip && rm SRAdb_1.44.0.tar.gz SRAdb_1.44.0.zip
###
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install for i386

* installing *source* package 'SRAdb' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'SRAdb'
    finding HTML links ... done
    IGVclear                                html  
    IGVcollapse                             html  
    IGVgenome                               html  
    IGVgoto                                 html  
    IGVload                                 html  
    IGVsession                              html  
    IGVsnapshot                             html  
    IGVsocket                               html  
    IGVsort                                 html  
    SRAdb-package                           html  
    ascpR                                   html  
    ascpSRA                                 html  
    colDescriptions                         html  
    entityGraph                             html  
    getFASTQfile                            html  
    getFASTQinfo                            html  
    getSRA                                  html  
    getSRAdbFile                            html  
    getSRAfile                              html  
    getSRAinfo                              html  
    listSRAfile                             html  
    sraConvert                              html  
    sraGraph                                html  
    startIGV                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'SRAdb' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SRAdb' as SRAdb_1.44.0.zip
* DONE (SRAdb)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'SRAdb' successfully unpacked and MD5 sums checked
In R CMD INSTALL