BioC 2.12: CHECK report for genomes on george2

Package: genomes

Version: 2.6.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings genomes_2.6.0.tar.gz

StartedAt: 2013-10-09 02:05:00 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 02:09:16 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 256.3 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 3.0.1 (2013-05-16)
* 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 ‘2.6.0’
* 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 ... [21s/21s] 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 ... [32s/39s] 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
** testing if installed package can be loaded
* DONE (genomes)

name	user	system	elapsed
doublingTime	2.004	0.048	2.081
efetch	0.028	0.008	0.035
einfo	0.032	0.000	0.033
elink	0.040	0.012	0.055
ena	0.028	0.012	0.040
enaParse	0.036	0.008	0.043
esearch	0.044	0.000	0.043
esummary	0.048	0.000	0.048
euks	0.216	0.004	0.221
ftpList	0.028	0.004	0.034
genomes-lines	1.068	0.012	1.080
genomes-plot	0.932	0.024	0.959
genomes-print	0.276	0.024	0.301
genomes-summary	0.108	0.004	0.113
genomes-update	0.060	0.000	0.061
genomes	0.993	0.016	1.010
genus	0.600	0.012	0.613
image2	0.676	0.028	0.703
like	0.524	0.016	0.540
ncbiGenome	0.052	0.000	0.053
ncbiNucleotide	0.112	0.004	0.542
ncbiProject	0.072	0.000	0.073
ncbiPubmed	0.056	0.000	0.054
ncbiRelease	0.088	0.004	1.206
ncbiSubmit	0.560	0.000	0.587
ncbiTaxonomy	0.020	0.004	0.026
plotby	0.880	0.020	0.898
proks	1.632	0.016	1.645
read.genemark	0.216	0.012	1.370
read.gff	0.120	0.016	0.838
read.glimmer	0.248	0.004	1.314
read.ncbi.ftp	0.028	0.012	0.040
read.prodigal	2.056	1.332	4.406
read.ptt	0.596	0.420	1.919
species	0.804	0.020	0.903
table2	0.160	0.000	0.159
virus	0.292	0.004	0.296
year	1.024	0.012	1.036