BioC 3.3: CHECK report for genomes on linux2.bioconductor.org

Package: genomes

Version: 2.17.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings genomes_2.17.0.tar.gz

StartedAt: 2015-10-27 04:12:15 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 04:13:56 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 101.9 seconds

RetCode: 0

Status:  OK

CheckDir: genomes.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings genomes_2.17.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/genomes.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* 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 ‘2.17.0’
* 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 ... [8s/8s] 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<-’
Undefined global functions or variables:
  isCircular<- metadata metadata<- seqlengths seqlengths<- seqlevels
  seqlevels<-
* 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 ... [15s/18s] 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-3.3-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	1.326	0.028	1.355
efetch	0.001	0.001	0.001
einfo	0.001	0.000	0.000
elink	0	0	0
esearch	0.000	0.000	0.001
esummary	0.001	0.000	0.001
euks	0.224	0.001	0.228
ftpList	0.001	0.000	0.001
genomes-lines	0.446	0.004	0.449
genomes-plot	0.585	0.004	0.589
genomes-print	0.271	0.007	0.279
genomes-summary	0.020	0.004	0.025
genomes-update	0.001	0.000	0.001
genomes	0.631	0.003	0.635
genus	0.692	0.012	0.703
image2	1.062	0.005	1.067
like	0.993	0.000	0.993
ncbiGenome	0.000	0.000	0.001
ncbiNucleotide	0.001	0.000	0.001
ncbiProject	0.001	0.000	0.001
ncbiPubmed	0.001	0.000	0.001
ncbiRelease	0.016	0.000	0.784
ncbiSubmit	0.001	0.000	0.001
ncbiTaxonomy	0.000	0.000	0.001
plotby	1.050	0.008	1.058
proks	0.707	0.016	0.723
read.genemark	0.040	0.004	0.185
read.gff	0.019	0.004	0.394
read.glimmer	0.059	0.004	0.575
read.ncbi.ftp	0.001	0.000	0.001
read.prodigal	0.783	1.112	2.179
read.ptt	0.130	0.308	0.542
species	0.589	0.008	0.597
table2	0.023	0.000	0.024
virus	0.060	0.004	0.065
year	0.341	0.000	0.341