BioC 2.13: CHECK report for SRAdb on perceval

Package: SRAdb

Version: 1.16.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch SRAdb_1.16.0.tar.gz

StartedAt: 2014-04-05 04:36:18 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 04:37:38 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 80.0 seconds

RetCode: 0

Status:  OK

CheckDir: SRAdb.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/SRAdb.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.16.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘SRAdb’ can be installed ... [7s/7s] 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:
  ‘graph’ ‘RSQLite’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of 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 ... OK
* 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘SRAdb.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [4s/4s] 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

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-2.13-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	0.144	0.000	0.147
IGVcollapse	0.009	0.000	0.009
IGVgenome	0.005	0.000	0.006
IGVgoto	0.005	0.000	0.005
IGVload	0.007	0.001	0.007
IGVsession	0.021	0.004	0.025
IGVsnapshot	0.006	0.001	0.005
IGVsocket	0.004	0.000	0.004
IGVsort	0.004	0.000	0.004
SRAdb-package	0.085	0.003	0.088
ascpR	0.010	0.001	0.010
ascpSRA	0.009	0.001	0.010
colDescriptions	0.014	0.001	0.013
entityGraph	0.012	0.001	0.013
getFASTQfile	0.010	0.001	0.011
getFASTQinfo	0.007	0.000	0.008
getSRA	0.021	0.001	0.023
getSRAdbFile	0.010	0.001	0.013
getSRAfile	0.198	0.002	0.203
getSRAinfo	0.011	0.001	0.012
listSRAfile	0.009	0.001	0.010
sraConvert	0.010	0.001	0.010
sraGraph	0.014	0.001	0.014
startIGV	0.004	0.001	0.005