BioC 3.4: CHECK report for metaseqR on zin1

Package: metaseqR

Version: 1.13.2

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings metaseqR_1.13.2.tar.gz

StartedAt: 2016-09-20 09:09:15 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 09:14:04 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 289.1 seconds

RetCode: 0

Status:  OK

CheckDir: metaseqR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings metaseqR_1.13.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/metaseqR.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘metaseqR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘metaseqR’ version ‘1.13.2’
* package encoding: UTF-8
* 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 ‘metaseqR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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 ... NOTE
'library' or 'require' calls in package code:
  ‘BSgenome’ ‘BiocInstaller’ ‘GenomicRanges’ ‘RMySQL’ ‘RSQLite’
  ‘Rsamtools’ ‘TCC’ ‘VennDiagram’ ‘parallel’ ‘rtracklayer’ ‘survcomp’
  ‘zoo’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
biasPlotToJSON: no visible binding for global variable ‘nams’
cddat: no visible global function definition for ‘assayData’
cddat: no visible global function definition for ‘ks.test’
cddat: no visible global function definition for ‘p.adjust’
cdplot: no visible global function definition for ‘plot’
cdplot: no visible global function definition for ‘lines’
countsBioToJSON: no visible binding for global variable ‘nams’
diagplot.avg.ftd : <anonymous>: no visible binding for global variable
  ‘sd’
diagplot.avg.ftd: no visible global function definition for ‘par’
diagplot.avg.ftd: no visible global function definition for ‘plot.new’
diagplot.avg.ftd: no visible global function definition for
  ‘plot.window’
diagplot.avg.ftd: no visible global function definition for ‘axis’
diagplot.avg.ftd: no visible global function definition for ‘lines’
diagplot.avg.ftd: no visible global function definition for ‘grid’
diagplot.avg.ftd: no visible global function definition for ‘title’
diagplot.cor: no visible global function definition for ‘cor’
diagplot.cor: no visible global function definition for
  ‘colorRampPalette’
diagplot.edaseq: no visible global function definition for
  ‘AnnotatedDataFrame’
diagplot.edaseq: no visible global function definition for ‘grid’
diagplot.filtered: no visible global function definition for ‘par’
diagplot.filtered: no visible global function definition for ‘plot.new’
diagplot.filtered: no visible global function definition for
  ‘plot.window’
diagplot.filtered: no visible global function definition for ‘axis’
diagplot.filtered: no visible global function definition for ‘text’
diagplot.filtered: no visible global function definition for ‘title’
diagplot.filtered: no visible global function definition for ‘mtext’
diagplot.filtered: no visible global function definition for ‘grid’
diagplot.ftd: no visible global function definition for ‘par’
diagplot.ftd: no visible global function definition for ‘plot.new’
diagplot.ftd: no visible global function definition for ‘plot.window’
diagplot.ftd: no visible global function definition for ‘axis’
diagplot.ftd: no visible global function definition for ‘lines’
diagplot.ftd: no visible global function definition for ‘grid’
diagplot.ftd: no visible global function definition for ‘title’
diagplot.mds: no visible global function definition for ‘as.dist’
diagplot.mds: no visible global function definition for ‘cor’
diagplot.mds: no visible global function definition for ‘cmdscale’
diagplot.mds: no visible global function definition for ‘plot’
diagplot.mds: no visible global function definition for ‘text’
diagplot.mds: no visible global function definition for ‘grid’
diagplot.noiseq: no visible global function definition for ‘grid’
diagplot.noiseq: no visible global function definition for ‘new’
diagplot.noiseq : <anonymous>: no visible global function definition
  for ‘quantile’
diagplot.noiseq.saturation: no visible global function definition for
  ‘par’
diagplot.noiseq.saturation: no visible global function definition for
  ‘plot.new’
diagplot.noiseq.saturation: no visible global function definition for
  ‘plot.window’
diagplot.noiseq.saturation: no visible global function definition for
  ‘axis’
diagplot.noiseq.saturation: no visible global function definition for
  ‘title’
diagplot.noiseq.saturation: no visible global function definition for
  ‘lines’
diagplot.noiseq.saturation: no visible global function definition for
  ‘points’
diagplot.noiseq.saturation: no visible global function definition for
  ‘grid’
diagplot.noiseq.saturation: no visible global function definition for
  ‘mtext’
diagplot.pairs: no visible global function definition for ‘par’
diagplot.pairs: no visible global function definition for ‘plot’
diagplot.pairs: no visible global function definition for ‘text’
diagplot.pairs: no visible global function definition for ‘arrows’
diagplot.pairs: no visible global function definition for ‘lines’
diagplot.pairs: no visible global function definition for ‘cor’
diagplot.roc: no visible global function definition for ‘par’
diagplot.roc: no visible global function definition for ‘plot.new’
diagplot.roc: no visible global function definition for ‘plot.window’
diagplot.roc: no visible global function definition for ‘axis’
diagplot.roc: no visible global function definition for ‘lines’
diagplot.roc: no visible global function definition for ‘grid’
diagplot.roc: no visible global function definition for ‘title’
diagplot.venn: no visible global function definition for ‘runif’
diagplot.venn: no visible global function definition for
  ‘draw.pairwise.venn’
diagplot.venn: no visible global function definition for
  ‘draw.triple.venn’
diagplot.venn: no visible global function definition for
  ‘draw.quad.venn’
diagplot.venn: no visible global function definition for
  ‘draw.quintuple.venn’
diagplot.volcano: no visible global function definition for ‘runif’
diagplot.volcano: no visible global function definition for ‘par’
diagplot.volcano: no visible global function definition for ‘plot.new’
diagplot.volcano: no visible global function definition for
  ‘plot.window’
diagplot.volcano: no visible global function definition for ‘axis’
diagplot.volcano: no visible global function definition for ‘title’
diagplot.volcano: no visible global function definition for ‘points’
diagplot.volcano: no visible global function definition for ‘abline’
diagplot.volcano: no visible global function definition for ‘grid’
estimate.aufc.weights: no visible global function definition for
  ‘runif’
estimate.aufc.weights : <anonymous>: no visible global function
  definition for ‘rollmean’
estimate.sim.params : <anonymous>: no visible global function
  definition for ‘var’
estimate.sim.params : <anonymous>: no visible global function
  definition for ‘optimize’
estimate.sim.params: no visible global function definition for
  ‘dev.new’
estimate.sim.params: no visible global function definition for ‘plot’
estimate.sim.params: no visible global function definition for ‘title’
estimate.sim.params: no visible global function definition for ‘grid’
filter.genes: no visible binding for global variable ‘quantile’
filter.genes: no visible global function definition for ‘median’
filter.genes: no visible global function definition for ‘quantile’
fisher.method: no visible global function definition for ‘pchisq’
fisher.method: no visible global function definition for ‘p.adjust’
fisher.method.perm : <anonymous> : <anonymous> : <anonymous>: no
  visible global function definition for ‘na.exclude’
fisher.method.perm: no visible global function definition for
  ‘p.adjust’
get.defaults: no visible binding for global variable ‘median’
get.gc.content: no visible global function definition for ‘GRanges’
get.gc.content: no visible global function definition for ‘Rle’
get.gc.content: no visible global function definition for ‘IRanges’
get.gc.content: no visible global function definition for
  ‘makeGRangesFromDataFrame’
get.gc.content: no visible global function definition for ‘getSeq’
get.gc.content: no visible global function definition for
  ‘alphabetFrequency’
get.ucsc.annotation: no visible global function definition for
  ‘dbDriver’
get.ucsc.annotation: no visible global function definition for
  ‘dbConnect’
get.ucsc.annotation: no visible global function definition for
  ‘dbGetQuery’
get.ucsc.annotation: no visible global function definition for
  ‘dbDisconnect’
get.ucsc.annotation : <anonymous>: no visible global function
  definition for ‘makeGRangesFromDataFrame’
get.ucsc.annotation: no visible global function definition for
  ‘seqnames’
get.ucsc.annotation: no visible global function definition for ‘start’
get.ucsc.annotation: no visible global function definition for ‘end’
get.ucsc.annotation: no visible global function definition for ‘strand’
get.ucsc.dbl: no visible global function definition for ‘dbDriver’
get.ucsc.dbl: no visible global function definition for ‘dbConnect’
get.ucsc.dbl: no visible global function definition for ‘dbWriteTable’
get.ucsc.dbl: no visible global function definition for ‘dbDisconnect’
graphics.close: no visible global function definition for ‘dev.off’
graphics.open: no visible global function definition for ‘dev.new’
graphics.open: no visible global function definition for ‘pdf’
graphics.open: no visible global function definition for ‘postscript’
graphics.open: no visible global function definition for ‘png’
graphics.open: no visible global function definition for ‘jpeg’
graphics.open: no visible global function definition for ‘bmp’
graphics.open: no visible global function definition for ‘tiff’
load.bs.genome: no visible global function definition for
  ‘installed.genomes’
load.bs.genome: no visible global function definition for ‘getBSgenome’
load.bs.genome: no visible global function definition for ‘biocLite’
make.sim.data.sd: no visible global function definition for ‘runif’
make.sim.data.sd: no visible global function definition for ‘rnbinom’
make.sim.data.sd: no visible global function definition for ‘rexp’
make.sim.data.tcc: no visible global function definition for ‘runif’
make.stat : <anonymous>: no visible global function definition for
  ‘median’
make.stat : <anonymous>: no visible global function definition for ‘sd’
make.stat : <anonymous>: no visible global function definition for
  ‘mad’
meta.perm : <anonymous>: no visible global function definition for
  ‘runif’
meta.perm: no visible global function definition for ‘mclapply’
meta.test : <anonymous>: no visible binding for global variable
  ‘combine.test’
metaseqr: no visible binding for global variable ‘p.adjust.methods’
metaseqr : <anonymous>: no visible binding for global variable
  ‘p.adjust’
metaseqr : <anonymous>: no visible global function definition for
  ‘p.adjust’
normalize.edaseq: no visible global function definition for
  ‘AnnotatedDataFrame’
normalize.noiseq: no visible global function definition for ‘assayData’
read2count: no visible global function definition for ‘GRanges’
read2count: no visible global function definition for ‘Rle’
read2count: no visible global function definition for ‘IRanges’
read2count: no visible global function definition for
  ‘makeGRangesFromDataFrame’
read2count: no visible global function definition for ‘seqnames’
read2count: no visible global function definition for ‘start’
read2count: no visible global function definition for ‘end’
read2count: no visible global function definition for ‘strand’
read2count : <anonymous>: no visible global function definition for
  ‘import.bed’
read2count : <anonymous>: no visible global function definition for
  ‘as’
read2count : <anonymous>: no visible global function definition for
  ‘seqnames’
read2count : <anonymous>: no visible global function definition for
  ‘seqlevels’
read2count : <anonymous>: no visible global function definition for
  ‘countOverlaps’
read2count: no visible global function definition for ‘asBam’
read2count : <anonymous>: no visible global function definition for
  ‘readGAlignments’
read2count : <anonymous>: no visible global function definition for
  ‘BamFile’
read2count : <anonymous>: no visible global function definition for
  ‘countBam’
read2count : <anonymous>: no visible global function definition for
  ‘ScanBamParam’
read2count : <anonymous>: no visible global function definition for
  ‘scanBamFlag’
read2count : <anonymous>: no visible global function definition for
  ‘strand<-’
read2count : <anonymous>: no visible global function definition for
  ‘strand’
read2count : <anonymous>: no visible global function definition for
  ‘summarizeOverlaps’
read2count : <anonymous>: no visible global function definition for
  ‘assays’
reduce.exons : <anonymous>: no visible global function definition for
  ‘reduce’
reduce.exons : <anonymous>: no visible global function definition for
  ‘DataFrame’
reduce.exons : <anonymous>: no visible global function definition for
  ‘mcols<-’
stat.bayseq: no visible global function definition for ‘new’
stat.deseq: no visible global function definition for ‘sizeFactors<-’
stat.edger: no visible global function definition for ‘model.matrix’
stat.edger: possible error in glmLRT(fit, contrast = co, test =
  stat.args$test): unused argument (test = stat.args$test)
stat.limma: no visible global function definition for ‘model.matrix’
stat.nbpseq: no visible global function definition for ‘sizeFactors<-’
stat.noiseq: no visible global function definition for ‘assayData’
stat.noiseq: no visible global function definition for ‘sizeFactors<-’
wapply: no visible global function definition for ‘mclapply’
wp.adjust: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
  AnnotatedDataFrame BamFile DataFrame GRanges IRanges Rle ScanBamParam
  abline alphabetFrequency arrows as as.dist asBam assayData assays
  axis biocLite bmp cmdscale colorRampPalette combine.test cor countBam
  countOverlaps dbConnect dbDisconnect dbDriver dbGetQuery dbWriteTable
  dev.new dev.off draw.pairwise.venn draw.quad.venn draw.quintuple.venn
  draw.triple.venn end getBSgenome getSeq grid import.bed
  installed.genomes jpeg ks.test lines mad makeGRangesFromDataFrame
  mclapply mcols<- median model.matrix mtext na.exclude nams new
  optimize p.adjust p.adjust.methods par pchisq pdf plot plot.new
  plot.window png points postscript quantile readGAlignments reduce
  rexp rnbinom rollmean runif scanBamFlag sd seqlevels seqnames
  sizeFactors<- start strand strand<- summarizeOverlaps text tiff title
  var
Consider adding
  importFrom("grDevices", "bmp", "colorRampPalette", "dev.new",
             "dev.off", "jpeg", "pdf", "png", "postscript", "tiff")
  importFrom("graphics", "abline", "arrows", "axis", "grid", "lines",
             "mtext", "par", "plot", "plot.new", "plot.window", "points",
             "text", "title")
  importFrom("methods", "as", "new")
  importFrom("stats", "as.dist", "cmdscale", "cor", "end", "ks.test",
             "mad", "median", "model.matrix", "na.exclude", "optimize",
             "p.adjust", "p.adjust.methods", "pchisq", "quantile",
             "rexp", "rnbinom", "runif", "sd", "start", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
diagplot.de.heatmap 13.248  0.088  13.339
diagplot.volcano     7.608  0.004   7.612
diagplot.filtered    0.632  0.040   6.027
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/metaseqR.Rcheck/00check.log’
for details.

* installing *source* package ‘metaseqR’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (metaseqR)

name	user	system	elapsed
as.class.vector	0	0	0
build.export	0.000	0.000	0.001
calc.f1score	0.004	0.000	0.006
calc.otr	0.000	0.000	0.003
check.contrast.format	0	0	0
check.file.args	0.000	0.000	0.001
check.libsize	0.000	0.000	0.001
check.num.args	0.000	0.000	0.001
check.packages	0.004	0.000	0.000
check.parallel	0.000	0.016	0.017
check.text.args	0.000	0.000	0.001
combine.bonferroni	0.000	0.000	0.001
combine.maxp	0	0	0
combine.minp	0.000	0.000	0.001
combine.simes	0	0	0
combine.weight	0.000	0.000	0.001
construct.gene.model	0.000	0.000	0.001
diagplot.avg.ftd	0.128	0.008	0.134
diagplot.boxplot	1.492	0.036	1.530
diagplot.cor	1.012	0.000	1.008
diagplot.de.heatmap	13.248	0.088	13.339
diagplot.edaseq	1.520	0.024	1.543
diagplot.filtered	0.632	0.040	6.027
diagplot.ftd	0.020	0.000	0.019
diagplot.mds	1.008	0.004	1.009
diagplot.metaseqr	1.148	0.004	1.290
diagplot.noiseq	1.260	0.004	1.264
diagplot.pairs	2.820	0.008	2.834
diagplot.roc	0.024	0.000	0.028
diagplot.venn	0.404	0.000	0.416
diagplot.volcano	7.608	0.004	7.612
disp	0	0	0
downsample.counts	0.000	0.000	0.001
estimate.aufc.weights	0	0	0
estimate.sim.params	0	0	0
filter.exons	0	0	0
filter.genes	0.000	0.000	0.001
filter.high	0.012	0.000	0.010
filter.low	0.008	0.000	0.007
fisher.method	0.012	0.000	0.010
fisher.method.perm	0.468	0.000	0.466
fisher.sum	0.004	0.000	0.002
get.annotation	0.000	0.000	0.001
get.arg	0	0	0
get.biotypes	0.004	0.000	0.000
get.bs.organism	0	0	0
get.dataset	0.000	0.000	0.001
get.defaults	0.004	0.000	0.001
get.ensembl.annotation	0	0	0
get.exon.attributes	0	0	0
get.gc.content	0.000	0.000	0.001
get.gene.attributes	0	0	0
get.host	0	0	0
get.preset.opts	0.004	0.000	0.001
get.strict.biofilter	0	0	0
get.ucsc.annotation	0	0	0
get.ucsc.credentials	0.000	0.000	0.001
get.ucsc.dbl	0.000	0.000	0.001
get.ucsc.organism	0	0	0
get.ucsc.query	0	0	0
get.ucsc.tabledef	0	0	0
get.ucsc.tbl.tpl	0.000	0.000	0.001
get.valid.chrs	0.000	0.000	0.001
get.weights	0.004	0.000	0.000
graphics.close	0.000	0.000	0.001
graphics.open	0.000	0.000	0.001
load.bs.genome	0.004	0.000	0.000
make.avg.expression	0	0	0
make.contrast.list	0.000	0.000	0.001
make.fold.change	0.004	0.000	0.000
make.grid	0	0	0
make.html.body	0	0	0
make.html.cells	0.004	0.000	0.000
make.html.header	0	0	0
make.html.rows	0.000	0.000	0.001
make.html.table	0.004	0.000	0.000
make.matrix	0	0	0
make.permutation	0	0	0
make.sample.list	0	0	0
make.sim.data.sd	0	0	0
make.sim.data.tcc	0	0	0
make.stat	0	0	0
make.transformation	0.000	0.000	0.001
make.venn.areas	0.000	0.000	0.001
make.venn.colorscheme	0.004	0.000	0.000
make.venn.counts	0	0	0
make.venn.pairs	0	0	0
meta.perm	0.000	0.000	0.001
meta.test	0.000	0.000	0.001
meta.worker	0	0	0
metaseqr	0	0	0
mlfo	0	0	0
normalize.deseq	0	0	0
normalize.edaseq	0.000	0.000	0.001
normalize.edger	0	0	0
normalize.nbpseq	0	0	0
normalize.noiseq	0	0	0
read.targets	0	0	0
read2count	0.000	0.000	0.001
reduce.exons	0	0	0
reduce.gene.data	0	0	0
set.arg	0	0	0
stat.bayseq	0	0	0
stat.deseq	0.000	0.000	0.001
stat.edger	0	0	0
stat.limma	0	0	0
stat.nbpseq	0	0	0
stat.noiseq	0	0	0
validate.alg.args	0.000	0.000	0.001
validate.list.args	0.000	0.000	0.001
wapply	0	0	0