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: 2013-03-25 02:41:20 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 02:44:51 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 210.6 seconds

RetCode: 0

Status:  OK

CheckDir: genomes.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/genomes.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* 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 '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 ... [16s/16s] 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [40s/47s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
read.prodigal 6.975  7.985  15.851
read.ptt      3.475  2.855   7.021
* 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	0.879	0.039	0.920
efetch	0.026	0.010	0.036
einfo	0.026	0.009	0.034
elink	0.027	0.011	0.038
ena	0.023	0.010	0.033
enaParse	0.032	0.011	0.044
esearch	0.024	0.009	0.034
esummary	0.027	0.011	0.037
euks	0.160	0.016	0.176
ftpList	0.024	0.008	0.031
genomes-lines	0.647	0.035	0.683
genomes-plot	0.674	0.041	0.718
genomes-print	0.611	0.029	0.640
genomes-summary	0.092	0.012	0.104
genomes-update	0.014	0.011	0.026
genomes	0.853	0.055	0.911
genus	0.752	0.031	0.784
image2	0.999	0.044	1.045
like	0.403	0.030	0.433
ncbiGenome	0.018	0.006	0.024
ncbiNucleotide	0.054	0.010	0.723
ncbiProject	0.161	0.009	0.170
ncbiPubmed	0.005	0.005	0.011
ncbiRelease	0.019	0.008	1.066
ncbiSubmit	0.006	0.007	0.013
ncbiTaxonomy	0.009	0.009	0.018
plotby	0.816	0.044	0.862
proks	0.729	0.069	0.799
read.genemark	0.159	0.016	1.291
read.gff	0.159	0.059	0.911
read.glimmer	0.161	0.020	1.223
read.ncbi.ftp	0.033	0.011	0.043
read.prodigal	6.975	7.985	15.851
read.ptt	3.475	2.855	7.021
species	0.839	0.049	0.891
table2	0.159	0.018	0.177
virus	0.267	0.025	0.294
year	0.469	0.037	0.507