Package: SRAdb

Version: 1.13.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch SRAdb_1.13.2.tar.gz

StartedAt: 2013-03-25 04:53:10 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 04:54:34 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 83.3 seconds

RetCode: 0

Status:  OK

CheckDir: SRAdb.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/SRAdb.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'SRAdb/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SRAdb' version '1.13.2'
* 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 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 for unstated dependencies in R code ... OK
* 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 examples ... [5s/5s] 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-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
   'SRAdb.Rnw' 
** testing if installed package can be loaded
* DONE (SRAdb)

name	user	system	elapsed
IGVclear	0.019	0.010	0.029
IGVcollapse	0.010	0.008	0.017
IGVgenome	0.011	0.006	0.017
IGVgoto	0.011	0.007	0.018
IGVload	0.013	0.009	0.021
IGVsession	0.028	0.019	0.046
IGVsnapshot	0.010	0.007	0.017
IGVsocket	0.009	0.007	0.016
IGVsort	0.011	0.007	0.019
SRAdb-package	0.157	0.039	0.202
ascpR	0.014	0.013	0.026
ascpSRA	0.016	0.013	0.029
colDescriptions	0.011	0.010	0.021
entityGraph	0.019	0.016	0.036
getFASTQfile	0.014	0.013	0.028
getFASTQinfo	0.008	0.008	0.018
getSRA	0.017	0.015	0.033
getSRAdbFile	0.007	0.007	0.013
getSRAfile	0.015	0.014	0.031
getSRAinfo	0.01	0.01	0.02
listSRAfile	0.014	0.018	0.032
sraConvert	0.010	0.010	0.022
sraGraph	0.019	0.017	0.038
startIGV	0.006	0.006	0.013