BioC 3.2: CHECK report for genomes on moscato1

Package: genomes

Version: 2.16.1

Command: rm -rf genomes.buildbin-libdir genomes.Rcheck && mkdir genomes.buildbin-libdir genomes.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=genomes.buildbin-libdir genomes_2.16.1.tar.gz >genomes.Rcheck\00install.out 2>&1 && cp genomes.Rcheck\00install.out genomes-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=genomes.buildbin-libdir --install="check:genomes-install.out" --force-multiarch --no-vignettes --timings genomes_2.16.1.tar.gz

StartedAt: 2016-04-23 02:44:47 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 02:48:56 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 248.4 seconds

RetCode: 0

Status:  OK

CheckDir: genomes.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf genomes.buildbin-libdir genomes.Rcheck && mkdir genomes.buildbin-libdir genomes.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=genomes.buildbin-libdir genomes_2.16.1.tar.gz >genomes.Rcheck\00install.out 2>&1 && cp genomes.Rcheck\00install.out genomes-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=genomes.buildbin-libdir --install="check:genomes-install.out" --force-multiarch --no-vignettes --timings genomes_2.16.1.tar.gz
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/genomes.Rcheck'
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'genomes' can be installed ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... [26s] OK
** running examples for arch 'x64' ... [24s] 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
  'D:/biocbld/bbs-3.2-bioc/meat/genomes.Rcheck/00check.log'
for details.

install for i386

* 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

install for x64

* installing *source* package 'genomes' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'genomes' as genomes_2.16.1.zip
* DONE (genomes)

name	user	system	elapsed
doublingTime	1.89	0.04	1.92
efetch	0	0	0
einfo	0	0	0
elink	0	0	0
esearch	0	0	0
esummary	0	0	0
euks	0.13	0.01	0.26
ftpList	0	0	0
genomes-lines	1.57	0.03	2.17
genomes-plot	1.45	0.02	1.47
genomes-print	0.51	0.00	0.52
genomes-summary	0.05	0.00	0.04
genomes-update	0	0	0
genomes	1.31	0.01	1.33
genus	0.84	0.00	0.84
image2	1.42	0.02	1.44
like	1.95	0.00	1.95
ncbiGenome	0.02	0.00	0.01
ncbiNucleotide	0	0	0
ncbiProject	0	0	0
ncbiPubmed	0	0	0
ncbiRelease	0.36	0.16	2.26
ncbiSubmit	0	0	0
ncbiTaxonomy	0	0	0
plotby	1.97	0.00	1.96
proks	1.87	0.01	2.65
read.genemark	0	0	0
read.gff	0	0	0
read.glimmer	0	0	0
read.ncbi.ftp	0	0	0
read.prodigal	0	0	0
read.ptt	0	0	0
species	0.99	0.02	1.00
table2	0.04	0.01	0.06
virus	0.28	0.00	0.28
year	1.07	0.02	1.08

name	user	system	elapsed
doublingTime	2.01	0.00	2.01
efetch	0	0	0
einfo	0	0	0
elink	0	0	0
esearch	0	0	0
esummary	0	0	0
euks	0.13	0.02	0.14
ftpList	0	0	0
genomes-lines	0.89	0.01	0.90
genomes-plot	1.53	0.00	1.64
genomes-print	0.36	0.00	0.36
genomes-summary	0.03	0.00	0.03
genomes-update	0.01	0.00	0.01
genomes	0.91	0.00	0.91
genus	0.67	0.00	0.67
image2	0.92	0.02	0.95
like	1.14	0.00	1.14
ncbiGenome	0	0	0
ncbiNucleotide	0	0	0
ncbiProject	0	0	0
ncbiPubmed	0	0	0
ncbiRelease	0.18	0.37	1.34
ncbiSubmit	0	0	0
ncbiTaxonomy	0	0	0
plotby	1.70	0.02	3.77
proks	1.56	0.03	1.82
read.genemark	0	0	0
read.gff	0	0	0
read.glimmer	0	0	0
read.ncbi.ftp	0	0	0
read.prodigal	0	0	0
read.ptt	0.02	0.00	0.02
species	0.73	0.00	0.73
table2	0.08	0.02	0.10
virus	0.19	0.00	0.18
year	0.74	0.00	0.75