Package: SRAdb

Version: 1.2.1

Command: /Library/Frameworks/R.framework/Versions/2.11/Resources/bin/R CMD check --no-vignettes --timings SRAdb_1.2.1.tar.gz

StartedAt: 2010-10-04 18:53:22 -0700 (Mon, 04 Oct 2010)

EndedAt: 2010-10-04 18:54:16 -0700 (Mon, 04 Oct 2010)

EllapsedTime: 54.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: SRAdb.Rcheck

Warnings: 1

* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.6-bioc/meat/SRAdb.Rcheck'
* using R version 2.11.1 Patched (2010-05-31 r52167)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'SRAdb/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SRAdb' version '1.2.1'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'SRAdb' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 ... WARNING
Functions/methods with usage in documentation object 'IGVsnapshotDirectory' but not in code:
  IGVsnapshotDirectory

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
  /Users/biocbuild/bbs-2.6-bioc/meat/SRAdb.Rcheck/00check.log
for details

* install options are ' --no-html'

* installing *source* package ‘SRAdb’ ...
** R
** inst
** preparing package for lazy loading
Loading required package: DBI
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (SRAdb)

name	user	system	elapsed
IGVgenome	0	0	0
IGVgoto	0	0	0
IGVload	0.000	0.000	0.001
IGVsession	0.007	0.003	0.009
IGVsnapshot	0.001	0.000	0.000
IGVsnapshotDirectory	0	0	0
SRAdb-package	0.060	0.002	0.064
colDescriptions	0.002	0.000	0.003
entityGraph	0.005	0.001	0.005
getFastq	0.002	0.000	0.003
getFastqInfo	0.002	0.000	0.002
getSRA	0.013	0.001	0.014
getSRAdbFile	0	0	0
listFastq	0.003	0.001	0.002
sraConvert	0.004	0.001	0.006
sraGraph	0.007	0.000	0.007
startIGV	0.000	0.000	0.001