BioC 2.14: CHECK report for genomes on petty

Package: genomes

Version: 2.10.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch genomes_2.10.0.tar.gz

StartedAt: 2014-10-07 22:11:07 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 22:15:51 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 284.4 seconds

RetCode: 0

Status:  OK

CheckDir: genomes.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch genomes_2.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/genomes.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘2.10.0’
* 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 ... [23s/24s] 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 loading without being on the library search path ... 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 files in ‘vignettes’ ... OK
* checking examples ... [39s/45s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
read.prodigal 3.360  4.463   8.523
read.ptt      2.839  1.631   5.169
* 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

* 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	1.698	0.043	1.757
efetch	0.001	0.000	0.001
einfo	0.001	0.000	0.001
elink	0.002	0.000	0.002
ena	0.002	0.000	0.002
enaParse	0.002	0.001	0.002
esearch	0.001	0.000	0.002
esummary	0.002	0.000	0.001
euks	0.176	0.011	0.188
ftpList	0.001	0.000	0.002
genomes-lines	1.348	0.034	1.383
genomes-plot	1.050	0.031	1.085
genomes-print	0.481	0.025	0.507
genomes-summary	0.352	0.013	0.366
genomes-update	0.005	0.001	0.006
genomes	0.724	0.034	0.760
genus	0.912	0.022	0.937
image2	1.153	0.030	1.195
like	0.754	0.024	0.788
ncbiGenome	0.001	0.000	0.001
ncbiNucleotide	0.002	0.000	0.001
ncbiProject	0.001	0.000	0.002
ncbiPubmed	0.001	0.000	0.001
ncbiRelease	0.025	0.002	1.309
ncbiSubmit	0.001	0.000	0.002
ncbiTaxonomy	0.001	0.001	0.001
plotby	1.753	0.036	1.797
proks	1.430	0.040	1.474
read.genemark	0.270	0.010	1.403
read.gff	0.163	0.046	0.846
read.glimmer	0.356	0.008	1.572
read.ncbi.ftp	0.001	0.001	0.002
read.prodigal	3.360	4.463	8.523
read.ptt	2.839	1.631	5.169
species	1.473	0.034	1.513
table2	0.067	0.015	0.082
virus	0.226	0.017	0.246
year	0.512	0.027	0.541