BioC 3.2: CHECK report for genomes on oaxaca

Package: genomes

Version: 2.16.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings genomes_2.16.1.tar.gz

StartedAt: 2016-04-23 00:30:21 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 00:32:33 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 131.8 seconds

RetCode: 0

Status:  OK

CheckDir: genomes.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings genomes_2.16.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/genomes.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘2.16.1’
* 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 ... [11s/12s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
read.genemark: no visible global function definition for ‘isCircular<-’
read.genemark: no visible global function definition for ‘seqlengths<-’
read.genemark: no visible global function definition for ‘metadata<-’
read.gff: no visible global function definition for ‘seqlengths<-’
read.gff: no visible global function definition for ‘metadata<-’
read.glimmer: no visible global function definition for ‘isCircular<-’
read.glimmer: no visible global function definition for ‘seqlengths<-’
read.glimmer: no visible global function definition for ‘metadata<-’
read.ncbi.ftp : <anonymous>: no visible global function definition for
  ‘metadata’
read.ncbi.ftp: no visible global function definition for ‘seqlengths’
read.ncbi.ftp: no visible global function definition for ‘seqlevels<-’
read.ncbi.ftp: no visible global function definition for ‘seqlevels’
read.ncbi.ftp: no visible global function definition for ‘metadata<-’
read.prodigal: no visible global function definition for ‘isCircular<-’
read.prodigal: no visible global function definition for ‘seqlengths<-’
read.prodigal: no visible global function definition for ‘metadata<-’
read.ptt: no visible global function definition for ‘isCircular<-’
read.ptt: no visible global function definition for ‘seqlengths<-’
read.ptt: no visible global function definition for ‘metadata<-’
* 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 ... [16s/17s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/genomes.Rcheck/00check.log’
for details.

* 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	1.510	0.040	1.559
efetch	0.000	0.000	0.001
einfo	0.001	0.000	0.000
elink	0.001	0.001	0.001
esearch	0.001	0.000	0.000
esummary	0.001	0.000	0.001
euks	0.117	0.006	0.126
ftpList	0.001	0.000	0.001
genomes-lines	0.703	0.034	0.746
genomes-plot	0.873	0.028	0.904
genomes-print	0.378	0.015	0.393
genomes-summary	0.037	0.007	0.044
genomes-update	0.001	0.000	0.001
genomes	0.639	0.022	0.664
genus	0.973	0.017	0.996
image2	0.925	0.021	0.948
like	0.726	0.024	0.752
ncbiGenome	0.001	0.000	0.000
ncbiNucleotide	0.001	0.000	0.001
ncbiProject	0.001	0.000	0.000
ncbiPubmed	0.000	0.000	0.001
ncbiRelease	0.014	0.001	0.935
ncbiSubmit	0.001	0.000	0.001
ncbiTaxonomy	0.001	0.000	0.001
plotby	1.151	0.035	1.188
proks	0.952	0.037	0.990
read.genemark	0.001	0.000	0.000
read.gff	0.001	0.000	0.001
read.glimmer	0.001	0.000	0.001
read.ncbi.ftp	0.001	0.000	0.001
read.prodigal	0.001	0.000	0.001
read.ptt	0.001	0.000	0.001
species	0.846	0.021	0.869
table2	0.050	0.006	0.056
virus	0.120	0.007	0.126
year	0.494	0.009	0.504