Package: genomes

Version: 1.7.1

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch genomes_1.7.1.tar.gz

StartedAt: 2011-03-17 16:25:23 -0700 (Thu, 17 Mar 2011)

EndedAt: 2011-03-17 16:26:56 -0700 (Thu, 17 Mar 2011)

EllapsedTime: 92.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: genomes.Rcheck

Warnings: 1

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/genomes.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-03-06 r54683)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'genomes/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'genomes' version '1.7.1'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'genomes' can be installed ... OK
* checking installed package size ... 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 ... WARNING
Undocumented code objects:
  updategold updatehmp
All user-level objects in a package should have documentation entries.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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-2.8-bioc/meat/genomes.Rcheck/00check.log'
for details

* installing *source* package 'genomes' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (genomes)

name	user	system	elapsed
acc2date	0.185	0.006	3.200
doublingTime	0.171	0.003	0.174
genomes-lines	0.207	0.004	0.211
genomes-plot	0.162	0.001	0.163
genomes-print	0.106	0.002	0.108
genomes-subset	0.104	0.001	0.105
genomes-summary	0.024	0.001	0.024
genomes-update	0.002	0.001	0.002
genomes	0.194	0.002	0.196
genus	0.242	0.001	0.244
image2	0.074	0.001	0.075
lenvs	0.026	0.001	0.027
leuks	0.135	0.003	0.138
like	0.136	0.002	0.137
lproks	0.371	0.005	0.377
plotby	0.559	0.003	0.562
pub2date	0.143	0.004	3.080
pubmed	0.112	0.003	0.914
revhist	0.194	0.016	46.620
species	0.376	0.006	0.382
table2	0.018	0.001	0.019
taxid2names	0.010	0.001	0.587
term2neighbor	0.050	0.002	1.161
term2summary	1.597	0.034	6.164
top	0.272	0.002	0.274
virus	0.119	0.004	0.937
year	0.092	0.001	0.092