Package: genomes

Version: 2.5.1

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings genomes_2.5.1.tar.gz

StartedAt: 2013-03-25 01:54:22 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 01:58:41 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 258.2 seconds

RetCode: 0

Status:  OK

CheckDir: genomes.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/genomes.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 ... [22s/22s] 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 ... [31s/38s] 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

* 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	1.632	0.024	1.657
efetch	0.064	0.000	0.061
einfo	0.040	0.000	0.039
elink	0.084	0.004	0.085
ena	0.056	0.000	0.055
enaParse	0.060	0.000	0.061
esearch	0.040	0.000	0.037
esummary	0.056	0.000	0.057
euks	0.256	0.004	0.258
ftpList	0.552	0.004	0.553
genomes-lines	0.952	0.012	0.970
genomes-plot	0.852	0.016	0.926
genomes-print	0.249	0.032	0.524
genomes-summary	0.092	0.008	0.203
genomes-update	0.044	0.008	0.101
genomes	0.888	0.148	1.130
genus	0.588	0.084	0.886
image2	1.308	0.064	1.507
like	0.984	0.028	1.011
ncbiGenome	0.048	0.000	0.047
ncbiNucleotide	0.104	0.004	0.532
ncbiProject	0.044	0.000	0.046
ncbiPubmed	0.044	0.000	0.044
ncbiRelease	0.064	0.000	0.868
ncbiSubmit	0.048	0.000	0.048
ncbiTaxonomy	0.044	0.000	0.043
plotby	1.292	0.028	1.322
proks	1.308	0.004	1.310
read.genemark	0.200	0.016	1.326
read.gff	0.108	0.012	0.810
read.glimmer	0.136	0.004	1.180
read.ncbi.ftp	0.044	0.000	0.043
read.prodigal	1.448	1.260	3.602
read.ptt	1.276	0.448	2.701
species	0.684	0.016	0.871
table2	0.212	0.004	0.279
virus	0.220	0.004	0.237
year	0.324	0.004	0.328