BioC 3.2: CHECK report for SRAdb on oaxaca

Package: SRAdb

Version: 1.28.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SRAdb_1.28.1.tar.gz

StartedAt: 2016-04-20 05:01:30 -0700 (Wed, 20 Apr 2016)

EndedAt: 2016-04-20 05:02:18 -0700 (Wed, 20 Apr 2016)

EllapsedTime: 47.3 seconds

RetCode: 0

Status:  OK

CheckDir: SRAdb.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SRAdb_1.28.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/SRAdb.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SRAdb/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SRAdb’ version ‘1.28.1’
* 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 ... [4s/4s] 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 loading without being on the library search path ... 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
colDescriptions: no visible global function definition for ‘dbGetQuery’
entityGraph : <anonymous>: no visible global function definition for
  ‘addEdge’
getFASTQinfo: no visible global function definition for ‘dbGetQuery’
getSRA: no visible global function definition for ‘dbGetQuery’
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’
sraConvert: no visible global function definition for ‘dbGetQuery’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [2s/3s] 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-3.2-bioc/meat/SRAdb.Rcheck/00check.log’
for details.

* installing *source* package ‘SRAdb’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (SRAdb)

name	user	system	elapsed
IGVclear	0.001	0.000	0.001
IGVcollapse	0.001	0.000	0.000
IGVgenome	0.001	0.000	0.001
IGVgoto	0.001	0.000	0.001
IGVload	0.000	0.000	0.001
IGVsession	0.002	0.001	0.019
IGVsnapshot	0.001	0.000	0.001
IGVsocket	0.000	0.000	0.001
IGVsort	0	0	0
SRAdb-package	0.034	0.001	0.035
ascpR	0.002	0.000	0.002
ascpSRA	0.001	0.000	0.001
colDescriptions	0.002	0.001	0.002
entityGraph	0.003	0.000	0.003
getFASTQfile	0.002	0.001	0.003
getFASTQinfo	0.001	0.000	0.001
getSRA	0.008	0.000	0.008
getSRAdbFile	0	0	0
getSRAfile	0.004	0.000	0.004
getSRAinfo	0.002	0.001	0.002
listSRAfile	0.001	0.000	0.001
sraConvert	0.001	0.000	0.002
sraGraph	0.004	0.001	0.004
startIGV	0.000	0.000	0.001