BioC 2.13: CHECK report for genomes on perceval

Package: genomes

Version: 2.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch genomes_2.8.0.tar.gz

StartedAt: 2014-04-05 01:34:03 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 01:37:54 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 230.2 seconds

RetCode: 0

Status:  OK

CheckDir: genomes.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/genomes.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘2.8.0’
* 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 ... [19s/19s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘genome-tables.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [33s/40s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
read.prodigal 2.281  2.959   5.903
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/genomes.Rcheck/00check.log’
for details.

* 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	2.526	0.054	2.605
efetch	0.030	0.004	0.035
einfo	0.026	0.003	0.029
elink	0.047	0.003	0.051
ena	0.043	0.002	0.044
enaParse	0.029	0.004	0.034
esearch	0.031	0.004	0.036
esummary	0.032	0.005	0.037
euks	0.184	0.016	0.203
ftpList	0.044	0.001	0.045
genomes-lines	0.906	0.050	0.979
genomes-plot	1.029	0.039	1.083
genomes-print	0.778	0.037	0.818
genomes-summary	0.084	0.012	0.096
genomes-update	0.018	0.004	0.022
genomes	0.907	0.048	0.961
genus	0.614	0.038	0.656
image2	0.890	0.056	0.959
like	1.030	0.050	1.094
ncbiGenome	0.057	0.004	0.062
ncbiNucleotide	0.083	0.006	0.488
ncbiProject	0.034	0.006	0.040
ncbiPubmed	0.016	0.003	0.019
ncbiRelease	0.059	0.007	0.963
ncbiSubmit	0.045	0.005	0.050
ncbiTaxonomy	0.026	0.006	0.032
plotby	1.352	0.062	1.446
proks	0.858	0.072	0.946
read.genemark	0.207	0.015	1.227
read.gff	0.107	0.030	0.844
read.glimmer	0.180	0.016	1.529
read.ncbi.ftp	0.009	0.008	0.016
read.prodigal	2.281	2.959	5.903
read.ptt	1.721	1.061	3.441
species	1.307	0.046	1.405
table2	0.068	0.018	0.088
virus	0.156	0.022	0.190
year	0.309	0.031	0.347