BioC 3.2: CHECK report for genomes on linux1.bioconductor.org

Package: genomes

Version: 2.16.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings genomes_2.16.0.tar.gz

StartedAt: 2015-10-27 03:54:35 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 03:56:24 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 108.9 seconds

RetCode: 0

Status:  OK

CheckDir: genomes.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings genomes_2.16.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/genomes.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-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 ‘2.16.0’
* 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 ... [9s/9s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [17s/19s] 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
  ‘/home/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	1.670	0.032	1.706
efetch	0.001	0.000	0.001
einfo	0.001	0.000	0.001
elink	0.001	0.000	0.001
esearch	0.001	0.000	0.000
esummary	0.001	0.000	0.001
euks	0.091	0.000	0.091
ftpList	0.001	0.000	0.001
genomes-lines	0.920	0.011	0.937
genomes-plot	0.553	0.004	0.561
genomes-print	0.299	0.008	0.306
genomes-summary	0.025	0.000	0.025
genomes-update	0.001	0.000	0.001
genomes	0.596	0.004	0.599
genus	0.744	0.000	0.745
image2	0.592	0.008	0.600
like	0.465	0.004	0.469
ncbiGenome	0.000	0.000	0.001
ncbiNucleotide	0	0	0
ncbiProject	0.001	0.000	0.000
ncbiPubmed	0.001	0.000	0.000
ncbiRelease	0.010	0.001	1.159
ncbiSubmit	0	0	0
ncbiTaxonomy	0.000	0.000	0.001
plotby	1.155	0.000	1.155
proks	1.104	0.004	1.108
read.genemark	0.072	0.000	0.206
read.gff	0.025	0.012	0.132
read.glimmer	0.093	0.007	0.389
read.ncbi.ftp	0.001	0.000	0.001
read.prodigal	0.790	1.236	2.143
read.ptt	0.155	0.288	0.536
species	0.803	0.000	0.802
table2	0.015	0.008	0.024
virus	0.064	0.000	0.064
year	0.327	0.004	0.331