Package: genomes

Version: 2.5.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch genomes_2.5.1.tar.gz

StartedAt: 2013-03-24 05:37:28 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 05:41:14 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 226.5 seconds

RetCode: 0

Status:  OK

CheckDir: genomes.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/genomes.Rcheck'
* using R version 3.0.0 beta (2013-03-21 r62346)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'genomes/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'genomes' version '2.5.1'
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'genomes' can be installed ... [19s/19s] 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 ... 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 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [34s/40s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
read.prodigal 3.205  4.255   8.187
* 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

* installing *source* package 'genomes' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'genome-tables.Rnw' 
** testing if installed package can be loaded
* DONE (genomes)

name	user	system	elapsed
doublingTime	1.179	0.042	1.238
efetch	0.028	0.004	0.031
einfo	0.017	0.002	0.018
elink	0.033	0.002	0.035
ena	0.026	0.002	0.028
enaParse	0.034	0.001	0.035
esearch	0.019	0.002	0.021
esummary	0.029	0.001	0.031
euks	0.197	0.016	0.215
ftpList	0.277	0.007	0.288
genomes-lines	0.874	0.041	0.998
genomes-plot	0.830	0.033	0.939
genomes-print	0.305	0.029	0.360
genomes-summary	0.083	0.007	0.092
genomes-update	0.033	0.004	0.037
genomes	0.850	0.042	0.899
genus	0.563	0.029	0.595
image2	1.074	0.045	1.282
like	0.810	0.034	0.846
ncbiGenome	0.024	0.004	0.028
ncbiNucleotide	0.070	0.005	0.491
ncbiProject	0.028	0.003	0.033
ncbiPubmed	0.026	0.002	0.028
ncbiRelease	0.043	0.004	1.152
ncbiSubmit	0.030	0.006	0.035
ncbiTaxonomy	0.028	0.005	0.032
plotby	1.325	0.042	1.385
proks	1.219	0.044	1.267
read.genemark	0.180	0.014	1.366
read.gff	0.103	0.032	0.894
read.glimmer	0.119	0.011	1.246
read.ncbi.ftp	0.028	0.006	0.033
read.prodigal	3.205	4.255	8.187
read.ptt	2.765	1.506	4.977
species	0.659	0.030	0.691
table2	0.144	0.011	0.157
virus	0.230	0.014	0.246
year	0.360	0.029	0.391