BioC 2.12: CHECK report for genomes on petty

Package: genomes

Version: 2.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch genomes_2.6.0.tar.gz

StartedAt: 2013-10-08 22:32:29 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 22:36:41 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 252.0 seconds

RetCode: 0

Status:  OK

CheckDir: genomes.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/genomes.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'genomes/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'genomes' version '2.6.0'
* 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/22s] 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [37s/44s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
read.prodigal 3.223  4.447   8.723
read.ptt      3.044  1.487   5.514
* 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	1.299	0.039	1.341
efetch	0.028	0.002	0.029
einfo	0.024	0.001	0.025
elink	0.024	0.001	0.026
ena	0.025	0.002	0.028
enaParse	0.025	0.001	0.026
esearch	0.026	0.000	0.026
esummary	0.025	0.000	0.025
euks	0.242	0.020	0.270
ftpList	0.009	0.008	0.017
genomes-lines	1.005	0.042	1.062
genomes-plot	0.917	0.038	0.958
genomes-print	0.354	0.030	0.412
genomes-summary	0.097	0.008	0.104
genomes-update	0.025	0.002	0.027
genomes	0.615	0.043	0.670
genus	0.699	0.032	0.733
image2	1.206	0.043	1.260
like	0.883	0.029	0.917
ncbiGenome	0.014	0.002	0.016
ncbiNucleotide	0.074	0.004	0.503
ncbiProject	0.050	0.002	0.053
ncbiPubmed	0.028	0.001	0.029
ncbiRelease	0.047	0.006	1.229
ncbiSubmit	0.015	0.004	0.019
ncbiTaxonomy	0.015	0.004	0.019
plotby	1.490	0.040	1.541
proks	1.319	0.054	1.382
read.genemark	0.238	0.014	1.372
read.gff	0.149	0.033	0.868
read.glimmer	0.253	0.012	1.299
read.ncbi.ftp	0.024	0.004	0.029
read.prodigal	3.223	4.447	8.723
read.ptt	3.044	1.487	5.514
species	0.810	0.034	0.845
table2	0.101	0.014	0.116
virus	0.274	0.015	0.290
year	0.413	0.025	0.439