BioC 3.2: CHECK report for genomes on perceval

Package: genomes

Version: 2.15.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings genomes_2.15.0.tar.gz

StartedAt: 2015-08-24 01:02:59 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 01:05:55 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 175.9 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 genomes_2.15.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/genomes.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* 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 ‘2.15.0’
* 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 ... [13s/14s] 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 ... [28s/34s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
read.prodigal 2.099  2.961   5.702
* 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	2.648	0.065	2.719
efetch	0.001	0.000	0.001
einfo	0.001	0.000	0.001
elink	0.001	0.001	0.001
esearch	0.001	0.000	0.001
esummary	0.001	0.000	0.001
euks	0.093	0.008	0.101
ftpList	0.001	0.000	0.001
genomes-lines	0.746	0.045	0.791
genomes-plot	1.105	0.047	1.154
genomes-print	0.435	0.027	0.462
genomes-summary	0.039	0.012	0.050
genomes-update	0.002	0.000	0.002
genomes	0.739	0.036	0.777
genus	0.783	0.029	0.813
image2	0.914	0.032	0.946
like	0.745	0.034	0.778
ncbiGenome	0.001	0.000	0.001
ncbiNucleotide	0.001	0.000	0.001
ncbiProject	0.001	0.000	0.001
ncbiPubmed	0.001	0.000	0.000
ncbiRelease	0.016	0.003	1.377
ncbiSubmit	0.001	0.000	0.001
ncbiTaxonomy	0.001	0.000	0.001
plotby	1.702	0.057	1.823
proks	1.309	0.062	1.379
read.genemark	0.073	0.008	1.235
read.gff	0.044	0.021	0.700
read.glimmer	0.086	0.012	1.178
read.ncbi.ftp	0.002	0.000	0.001
read.prodigal	2.099	2.961	5.702
read.ptt	1.595	1.042	3.493
species	0.869	0.037	0.908
table2	0.135	0.017	0.152
virus	0.134	0.010	0.144
year	0.485	0.030	0.514