BioC 3.3: CHECK report for metaseqR on oaxaca

Package: metaseqR

Version: 1.12.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings metaseqR_1.12.2.tar.gz

StartedAt: 2016-10-13 03:34:07 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 03:40:42 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 394.8 seconds

RetCode: 0

Status:  OK

CheckDir: metaseqR.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings metaseqR_1.12.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/metaseqR.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.12.2’
* 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 : <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
  ‘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.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.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 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("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.
* 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 10.110  0.152  11.040
diagplot.filtered    1.003  0.060   6.828
* 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
  ‘/Users/biocbuild/bbs-3.3-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	0.001	0.000	0.001
build.export	0.001	0.000	0.001
calc.f1score	0.011	0.000	0.012
calc.otr	0.004	0.000	0.005
check.contrast.format	0.001	0.000	0.001
check.file.args	0.002	0.001	0.001
check.libsize	0.002	0.000	0.002
check.num.args	0.001	0.000	0.002
check.packages	0.001	0.000	0.001
check.parallel	0.004	0.003	0.008
check.text.args	0.001	0.000	0.001
combine.bonferroni	0.001	0.000	0.001
combine.maxp	0.000	0.000	0.001
combine.minp	0.001	0.000	0.000
combine.simes	0.001	0.000	0.001
combine.weight	0.001	0.000	0.001
construct.gene.model	0.000	0.000	0.001
diagplot.avg.ftd	0.093	0.005	0.097
diagplot.boxplot	1.895	0.032	1.926
diagplot.cor	1.357	0.032	1.390
diagplot.de.heatmap	10.110	0.152	11.040
diagplot.edaseq	1.748	0.102	1.885
diagplot.filtered	1.003	0.060	6.828
diagplot.ftd	0.048	0.007	0.055
diagplot.mds	1.477	0.016	1.495
diagplot.metaseqr	1.599	0.050	1.665
diagplot.noiseq	1.605	0.067	1.760
diagplot.pairs	2.740	0.096	3.064
diagplot.roc	0.032	0.005	0.048
diagplot.venn	0.445	0.014	0.580
diagplot.volcano	4.637	0.123	4.776
disp	0	0	0
downsample.counts	0.001	0.000	0.001
estimate.aufc.weights	0.001	0.000	0.001
estimate.sim.params	0	0	0
filter.exons	0.000	0.000	0.001
filter.genes	0	0	0
filter.high	0.012	0.003	0.014
filter.low	0.008	0.001	0.009
fisher.method	0.014	0.001	0.014
fisher.method.perm	0.056	0.000	0.057
fisher.sum	0.004	0.001	0.004
get.annotation	0.000	0.000	0.001
get.arg	0.000	0.000	0.001
get.biotypes	0.001	0.001	0.000
get.bs.organism	0.000	0.000	0.001
get.dataset	0.001	0.000	0.001
get.defaults	0.001	0.000	0.001
get.ensembl.annotation	0	0	0
get.exon.attributes	0.001	0.000	0.000
get.gc.content	0.000	0.000	0.001
get.gene.attributes	0	0	0
get.host	0	0	0
get.preset.opts	0.001	0.000	0.001
get.strict.biofilter	0	0	0
get.ucsc.annotation	0.000	0.000	0.001
get.ucsc.credentials	0	0	0
get.ucsc.dbl	0.001	0.000	0.000
get.ucsc.organism	0	0	0
get.ucsc.query	0.001	0.001	0.000
get.ucsc.tabledef	0.000	0.000	0.001
get.ucsc.tbl.tpl	0.000	0.000	0.001
get.valid.chrs	0	0	0
get.weights	0.000	0.000	0.001
graphics.close	0	0	0
graphics.open	0.001	0.000	0.000
load.bs.genome	0.001	0.000	0.000
make.avg.expression	0.000	0.000	0.001
make.contrast.list	0.001	0.000	0.002
make.fold.change	0.000	0.000	0.001
make.grid	0.000	0.000	0.001
make.html.body	0.000	0.000	0.001
make.html.cells	0	0	0
make.html.header	0.000	0.000	0.001
make.html.rows	0.001	0.000	0.000
make.html.table	0	0	0
make.matrix	0.000	0.000	0.001
make.permutation	0.001	0.000	0.001
make.sample.list	0.001	0.000	0.001
make.sim.data.sd	0.001	0.000	0.000
make.sim.data.tcc	0	0	0
make.stat	0	0	0
make.transformation	0.000	0.001	0.000
make.venn.areas	0.000	0.000	0.001
make.venn.colorscheme	0.001	0.000	0.001
make.venn.counts	0.001	0.000	0.001
make.venn.pairs	0.000	0.001	0.001
meta.perm	0	0	0
meta.test	0	0	0
meta.worker	0.001	0.000	0.000
metaseqr	0.001	0.000	0.000
mlfo	0.001	0.000	0.000
normalize.deseq	0.001	0.000	0.001
normalize.edaseq	0.000	0.000	0.001
normalize.edger	0.000	0.000	0.001
normalize.nbpseq	0.000	0.000	0.001
normalize.noiseq	0	0	0
read.targets	0	0	0
read2count	0.000	0.001	0.001
reduce.exons	0.000	0.000	0.001
reduce.gene.data	0	0	0
set.arg	0	0	0
stat.bayseq	0.001	0.000	0.001
stat.deseq	0.001	0.000	0.001
stat.edger	0	0	0
stat.limma	0.000	0.000	0.001
stat.nbpseq	0	0	0
stat.noiseq	0	0	0
validate.alg.args	0.001	0.000	0.000
validate.list.args	0.001	0.000	0.001
wapply	0.001	0.000	0.000