Package: genomes

Version: 2.0.0

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings genomes_2.0.0.tar.gz

StartedAt: 2012-03-24 00:36:15 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 00:38:03 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 108.2 seconds

RetCode: 0

Status:  OK

CheckDir: genomes.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/genomes.Rcheck’
* using R version 2.14.2 (2012-02-29)
* 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 ‘2.0.0’
* 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 ... NOTE
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
               old_size new_size compress
  complete.rda     56Kb     41Kb       xz
  leuks.rda        49Kb     40Kb       xz
  lproks.rda      307Kb    233Kb       xz
  pub.rda          66Kb     56Kb       xz
  sra.rda         501Kb    324Kb       xz
  virus.rda        83Kb     63Kb       xz
* 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 ...
*** tangling vignette sources ...
   ‘genome-tables.Rnw’ 
** testing if installed package can be loaded

* DONE (genomes)

name	user	system	elapsed
complete	0.052	0.000	0.051
doublingTime	0.292	0.016	0.306
enaExperiment	2.156	0.016	7.207
enaFiles	0.008	0.000	0.843
enaProject	0	0	0
enaSRA	1.224	0.008	3.091
enaStudy	1.660	0.004	4.555
enaSubmission	0.004	0.000	0.407
enaTaxonomy	0.016	0.004	2.340
genomes-lines	0.368	0.008	0.376
genomes-plot	0.264	0.004	0.270
genomes-print	0.220	0.000	0.218
genomes-subset	0.100	0.004	0.103
genomes-summary	0.024	0.000	0.022
genomes-update	0.004	0.000	0.003
genomes	0.260	0.000	0.265
genus	0.280	0.000	0.278
image2	0.256	0.004	0.259
lenvs	0.016	0.004	0.019
leuks	0.120	0.004	0.125
like	0.148	0.000	0.150
lproks	0.368	0.008	0.376
ncbiGenome	0	0	0
ncbiInfo	0.068	0.004	0.755
ncbiNucleotide	0.488	0.012	3.591
ncbiProject	0.76	0.00	1.80
ncbiPubmed	0.148	0.004	1.378
ncbiRelease	0.108	0.000	28.025
ncbiSubmit	0.128	0.000	2.540
ncbiTaxonomy	0.156	0.004	1.232
plotby	0.536	0.016	0.557
pub	0.048	0.008	0.056
species	0.424	0.000	0.425
sra	0.748	0.000	0.749
table2	0.016	0.000	0.016
top	0.336	0.000	0.338
virus	0.132	0.000	0.132
year	0.112	0.000	0.112