Package: genomes

Version: 2.4.0

Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings genomes_2.4.0.tar.gz

StartedAt: 2013-03-25 01:28:29 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 01:31:31 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 182.2 seconds

RetCode: 0

Status:  OK

CheckDir: genomes.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/genomes.Rcheck’
* using R version 2.15.3 (2013-03-01)
* 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 ‘2.4.0’
* 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 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 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 ... 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	0.836	0.040	0.883
efetch	0	0	0
einfo	0.064	0.008	0.719
elink	0	0	0
enaExperiment	0.024	0.004	0.527
enaFiles	0.008	0.004	0.897
enaProject	0	0	0
enaSRA	0	0	0
enaStudy	0.032	0.004	0.366
enaSubmission	0.012	0.000	0.352
enaTaxonomy	0	0	0
esearch	0	0	0
esummary	0.000	0.000	0.001
euks	0.076	0.004	0.114
ftpList	0	0	0
genomes-lines	0.568	0.008	0.590
genomes-plot	0.516	0.008	0.635
genomes-print	0.132	0.008	0.263
genomes-summary	0.032	0.000	0.033
genomes-update	0.004	0.000	0.003
genomes	0.520	0.004	0.534
genus	0.300	0.004	0.328
image2	0.424	0.012	0.437
like	0.244	0.004	0.253
ncbiGenome	0	0	0
ncbiNucleotide	0.028	0.000	0.468
ncbiProject	1.272	0.028	2.178
ncbiPubmed	0.036	0.000	0.463
ncbiRelease	0.008	0.004	0.926
ncbiSubmit	0.012	0.004	1.970
ncbiTaxonomy	0.028	0.000	0.889
plotby	0.800	0.004	0.801
proks	0.332	0.004	0.368
read.genemark	0.144	0.004	1.357
read.gff	0.100	0.008	0.815
read.glimmer	0.108	0.000	1.561
read.ncbi.ftp	0	0	0
read.prodigal	1.372	0.952	3.170
read.ptt	0.488	0.352	1.792
species	0.737	0.004	0.835
table2	0.024	0.000	0.026
virus	0.084	0.008	0.095
year	0.128	0.004	0.132