Package: genomes

Version: 2.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch genomes_2.6.0.tar.gz

StartedAt: 2013-05-01 05:57:49 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 06:01:39 -0700 (Wed, 01 May 2013)

EllapsedTime: 229.9 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 Patched (2013-04-08 r62531)
* 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 '2.6.0'
* 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 ... [18s/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 ... [35s/42s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
read.prodigal 3.139  4.321   8.472
read.ptt      2.746  1.532   5.130
* 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
** testing if installed package can be loaded
* DONE (genomes)

name	user	system	elapsed
doublingTime	1.256	0.050	1.337
efetch	0.031	0.004	0.034
einfo	0.027	0.003	0.030
elink	0.032	0.004	0.037
ena	0.033	0.004	0.039
enaParse	0.032	0.003	0.037
esearch	0.026	0.001	0.027
esummary	0.026	0.001	0.028
euks	0.214	0.013	0.235
ftpList	0.008	0.006	0.015
genomes-lines	0.946	0.041	1.006
genomes-plot	0.868	0.031	0.926
genomes-print	0.317	0.033	0.357
genomes-summary	0.092	0.010	0.104
genomes-update	0.022	0.002	0.025
genomes	0.507	0.043	0.553
genus	0.596	0.029	0.637
image2	1.055	0.039	1.103
like	0.844	0.038	0.897
ncbiGenome	0.015	0.003	0.019
ncbiNucleotide	0.062	0.006	0.499
ncbiProject	0.040	0.004	0.047
ncbiPubmed	0.026	0.002	0.029
ncbiRelease	0.042	0.006	0.889
ncbiSubmit	0.016	0.004	0.019
ncbiTaxonomy	0.016	0.004	0.021
plotby	1.327	0.043	1.441
proks	1.169	0.062	1.297
read.genemark	0.183	0.015	1.732
read.gff	0.119	0.036	0.846
read.glimmer	0.214	0.013	1.650
read.ncbi.ftp	0.030	0.006	0.035
read.prodigal	3.139	4.321	8.472
read.ptt	2.746	1.532	5.130
species	0.717	0.042	0.790
table2	0.069	0.016	0.089
virus	0.246	0.016	0.266
year	0.355	0.025	0.389