Package: genomes

Version: 2.2.0

Command: /home/hpages/test-puck5/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings genomes_2.2.0.tar.gz

StartedAt: 2012-04-01 01:12:37 -0700 (Sun, 01 Apr 2012)

EndedAt: 2012-04-01 01:13:58 -0700 (Sun, 01 Apr 2012)

EllapsedTime: 81.8 seconds

RetCode: 0

Status:  OK

CheckDir: genomes.Rcheck

Warnings: 0

* using log directory '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/genomes.Rcheck'
* using R version 2.15.0 RC (2012-03-22 r58802)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'genomes/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'genomes' version '2.2.0'
* 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 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
complete	0.052	0.000	0.057
doublingTime	0.192	0.016	0.214
efetch	0.020	0.000	1.553
einfo	0.064	0.008	0.800
elink	0.068	0.000	2.430
enaExperiment	1.908	0.004	6.905
enaFiles	0.008	0.004	0.757
enaProject	0.080	0.000	0.756
enaSRA	1.212	0.000	3.057
enaStudy	1.484	0.000	5.195
enaSubmission	0.008	0.000	0.390
enaTaxonomy	0.016	0.000	1.414
esearch	0.020	0.004	1.190
esummary	0.140	0.000	1.668
genomes-lines	0.244	0.000	0.255
genomes-plot	0.172	0.000	0.179
genomes-print	0.088	0.000	0.094
genomes-subset	0.096	0.000	0.099
genomes-summary	0.020	0.000	0.023
genomes-update	0.000	0.000	0.005
genomes	0.168	0.008	0.179
genus	0.124	0.000	0.131
image2	0.240	0.000	0.244
lenvs	0.020	0.000	0.023
leuks	0.032	0.004	0.045
like	0.156	0.000	0.160
lproks	0.252	0.008	0.268
ncbiGenome	0.080	0.000	2.631
ncbiNucleotide	0.396	0.000	4.194
ncbiProject	0.776	0.000	2.364
ncbiPubmed	0.156	0.000	1.240
ncbiRelease	0.008	0.000	2.264
ncbiSubmit	0.100	0.004	3.467
ncbiTaxonomy	0.104	0.000	2.475
plotby	0.340	0.020	0.363
pub	0.064	0.000	0.073
species	0.160	0.000	0.165
sra	0.464	0.004	0.471
table2	0.008	0.004	0.019
virus	0.064	0.004	0.070
year	0.100	0.000	0.104