Package: genomes

Version: 2.4.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch genomes_2.4.0.tar.gz

StartedAt: 2013-03-24 23:42:01 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 23:45:05 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 183.3 seconds

RetCode: 0

Status:  OK

CheckDir: genomes.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/genomes.Rcheck'
* using R version 2.15.3 (2013-03-01)
* 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 '2.4.0'
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
read.prodigal 4.66  5.021  10.462
* 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	0.753	0.036	0.794
efetch	0	0	0
einfo	0.075	0.007	0.660
elink	0.000	0.000	0.001
enaExperiment	0.030	0.006	0.552
enaFiles	0.009	0.002	0.881
enaProject	0.000	0.000	0.001
enaSRA	0.000	0.001	0.000
enaStudy	0.018	0.001	0.348
enaSubmission	0.008	0.001	0.339
enaTaxonomy	0.001	0.000	0.000
esearch	0.000	0.000	0.001
esummary	0.000	0.000	0.001
euks	0.090	0.006	0.096
ftpList	0	0	0
genomes-lines	0.539	0.028	0.569
genomes-plot	0.311	0.035	0.359
genomes-print	0.188	0.020	0.220
genomes-summary	0.036	0.002	0.039
genomes-update	0.002	0.002	0.004
genomes	0.505	0.036	0.545
genus	0.331	0.017	0.349
image2	0.437	0.026	0.463
like	0.311	0.031	0.344
ncbiGenome	0.000	0.000	0.001
ncbiNucleotide	0.024	0.002	0.467
ncbiProject	1.403	0.029	2.278
ncbiPubmed	0.034	0.002	0.477
ncbiRelease	0.012	0.002	0.882
ncbiSubmit	0.015	0.001	1.628
ncbiTaxonomy	0.030	0.002	0.990
plotby	0.640	0.048	0.699
proks	0.765	0.068	0.841
read.genemark	0.150	0.008	1.300
read.gff	0.119	0.033	0.853
read.glimmer	0.114	0.008	1.199
read.ncbi.ftp	0	0	0
read.prodigal	4.660	5.021	10.462
read.ptt	1.967	1.794	4.674
species	0.684	0.026	0.729
table2	0.033	0.005	0.042
virus	0.135	0.009	0.146
year	0.188	0.016	0.212