BioC 3.3: CHECK report for genomes on windows2.bioconductor.org

Package: genomes

Version: 2.17.0

Command: rm -rf genomes.buildbin-libdir genomes.Rcheck && mkdir genomes.buildbin-libdir genomes.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=genomes.buildbin-libdir genomes_2.17.0.tar.gz >genomes.Rcheck\00install.out 2>&1 && cp genomes.Rcheck\00install.out genomes-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=genomes.buildbin-libdir --install="check:genomes-install.out" --force-multiarch --no-vignettes --timings genomes_2.17.0.tar.gz

StartedAt: 2015-10-27 02:41:02 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 02:43:35 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 153.2 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 && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=genomes.buildbin-libdir genomes_2.17.0.tar.gz >genomes.Rcheck\00install.out 2>&1 && cp genomes.Rcheck\00install.out genomes-install.out  && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=genomes.buildbin-libdir --install="check:genomes-install.out" --force-multiarch --no-vignettes --timings genomes_2.17.0.tar.gz
###
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* using log directory 'c:/biocbld/bbs-3.3-bioc/meat/genomes.Rcheck'
* using R Under development (unstable) (2015-09-22 r69418)
* 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 '2.17.0'
* 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 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<-'
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 ...
** running examples for arch 'i386' ... [24s] OK
** running examples for arch 'x64' ... [22s] 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
  'c:/biocbld/bbs-3.3-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_2.17.0.zip
* DONE (genomes)

name	user	system	elapsed
doublingTime	1.25	0.01	1.27
efetch	0	0	0
einfo	0	0	0
elink	0	0	0
esearch	0	0	0
esummary	0	0	0
euks	0.08	0.00	0.08
ftpList	0	0	0
genomes-lines	0.86	0.01	0.88
genomes-plot	0.91	0.00	0.90
genomes-print	0.36	0.00	0.36
genomes-summary	0.03	0.00	0.03
genomes-update	0	0	0
genomes	0.81	0.00	0.81
genus	0.52	0.00	0.52
image2	0.76	0.02	0.78
like	1.07	0.00	1.06
ncbiGenome	0	0	0
ncbiNucleotide	0	0	0
ncbiProject	0	0	0
ncbiPubmed	0	0	0
ncbiRelease	0.25	0.12	2.17
ncbiSubmit	0	0	0
ncbiTaxonomy	0	0	0
plotby	1.2	0.0	1.2
proks	1.04	0.00	1.04
read.genemark	0.06	0.02	0.34
read.gff	0.01	0.03	0.17
read.glimmer	0.08	0.02	0.39
read.ncbi.ftp	0	0	0
read.prodigal	3.06	1.33	4.49
read.ptt	1.44	0.51	2.04
species	0.70	0.03	0.74
table2	0.04	0.02	0.04
virus	0.12	0.00	0.13
year	0.75	0.00	0.75

name	user	system	elapsed
doublingTime	1.39	0.05	1.43
efetch	0	0	0
einfo	0	0	0
elink	0	0	0
esearch	0.01	0.00	0.02
esummary	0	0	0
euks	0.25	0.00	0.25
ftpList	0	0	0
genomes-lines	0.75	0.00	0.75
genomes-plot	0.83	0.01	0.85
genomes-print	0.28	0.00	0.28
genomes-summary	0.03	0.00	0.03
genomes-update	0	0	0
genomes	0.89	0.02	0.91
genus	0.41	0.00	0.40
image2	0.72	0.03	0.75
like	1.04	0.00	1.05
ncbiGenome	0.00	0.01	0.02
ncbiNucleotide	0	0	0
ncbiProject	0	0	0
ncbiPubmed	0	0	0
ncbiRelease	0.27	0.08	0.75
ncbiSubmit	0	0	0
ncbiTaxonomy	0	0	0
plotby	1.31	0.02	1.32
proks	1.28	0.01	1.30
read.genemark	0.11	0.00	0.17
read.gff	0.08	0.02	0.19
read.glimmer	0.09	0.00	0.33
read.ncbi.ftp	0	0	0
read.prodigal	2.92	1.70	4.72
read.ptt	0.80	0.67	1.50
species	0.86	0.02	0.87
table2	0.03	0.00	0.03
virus	0.12	0.02	0.14
year	0.53	0.00	0.53