BioC 3.1: CHECK report for metaseqR on zin2

Package: metaseqR

Version: 1.8.1

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings metaseqR_1.8.1.tar.gz

StartedAt: 2015-10-09 03:22:37 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 03:27:05 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 268.1 seconds

RetCode: 0

Status:  OK

CheckDir: metaseqR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings metaseqR_1.8.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/metaseqR.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.8.1’
* 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 ... [23s/23s] 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
cddat: no visible global function definition for ‘assayData’
diagplot.edaseq: no visible global function definition for
  ‘AnnotatedDataFrame’
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’
estimate.aufc.weights : <anonymous>: no visible global function
  definition for ‘rollmean’
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 ‘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’
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.sample.list: no visible binding for global variable ‘file.type’
meta.perm: no visible global function definition for ‘mclapply’
meta.test : <anonymous>: no visible binding for global variable
  ‘combine.test’
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 ‘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
  ‘BamFile’
read2count : <anonymous>: no visible global function definition for
  ‘countBam’
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: possible error in glmLRT(fit, contrast = co, test =
  stat.args$test): unused argument (test = stat.args$test)
stat.edger: possible error in glmLRT(fit, coef = 2:ncol(fit$design),
  test = stat.args$test): unused argument (test = stat.args$test)
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’
* 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 ... [14s/14s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [18s/29s]
 [18s/29s] 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-3.1-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
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (metaseqR)

name	user	system	elapsed
as.class.vector	0.001	0.000	0.001
build.export	0.001	0.000	0.000
calc.f1score	0.006	0.000	0.006
calc.otr	0.003	0.000	0.002
check.contrast.format	0.000	0.000	0.001
check.file.args	0.001	0.000	0.001
check.libsize	0.001	0.000	0.001
check.num.args	0.001	0.000	0.000
check.packages	0.000	0.000	0.001
check.parallel	0.003	0.013	0.015
check.text.args	0.001	0.000	0.000
combine.bonferroni	0.000	0.000	0.001
combine.maxp	0.001	0.000	0.001
combine.minp	0	0	0
combine.simes	0.001	0.000	0.001
combine.weight	0.000	0.004	0.000
construct.gene.model	0.000	0.000	0.001
diagplot.avg.ftd	0.063	0.016	0.080
diagplot.boxplot	1.705	0.044	1.782
diagplot.cor	1.093	0.020	1.120
diagplot.de.heatmap	0.000	0.000	0.001
diagplot.edaseq	0	0	0
diagplot.filtered	0.000	0.000	0.001
diagplot.ftd	0.020	0.000	0.019
diagplot.mds	1.068	0.000	1.091
diagplot.metaseqr	0.001	0.000	0.000
diagplot.noiseq	0.001	0.000	0.001
diagplot.pairs	0.000	0.004	0.000
diagplot.roc	0.031	0.000	0.034
diagplot.venn	0.001	0.000	0.000
diagplot.volcano	0.000	0.000	0.001
disp	0	0	0
downsample.counts	0.000	0.000	0.001
estimate.aufc.weights	0	0	0
estimate.sim.params	0.001	0.000	0.000
filter.exons	0.000	0.000	0.001
filter.genes	0	0	0
filter.high	0.017	0.004	0.025
filter.low	0.008	0.000	0.008
fisher.method	0.010	0.004	0.014
fisher.method.perm	0.047	0.000	0.047
fisher.sum	0.003	0.000	0.003
get.annotation	0.000	0.000	0.001
get.arg	0	0	0
get.biotypes	0.000	0.000	0.001
get.bs.organism	0	0	0
get.dataset	0	0	0
get.defaults	0.001	0.000	0.001
get.ensembl.annotation	0	0	0
get.exon.attributes	0	0	0
get.gc.content	0.001	0.000	0.001
get.gene.attributes	0.001	0.000	0.001
get.host	0	0	0
get.preset.opts	0.001	0.000	0.001
get.strict.biofilter	0.001	0.000	0.001
get.ucsc.annotation	0	0	0
get.ucsc.credentials	0	0	0
get.ucsc.dbl	0.001	0.000	0.001
get.ucsc.organism	0	0	0
get.ucsc.query	0.001	0.000	0.001
get.ucsc.tabledef	0	0	0
get.ucsc.tbl.tpl	0	0	0
get.valid.chrs	0.001	0.000	0.001
get.weights	0.001	0.000	0.000
graphics.close	0	0	0
graphics.open	0	0	0
load.bs.genome	0.001	0.000	0.001
make.contrast.list	0.001	0.000	0.001
make.fold.change	0	0	0
make.grid	0	0	0
make.html.body	0.000	0.000	0.001
make.html.cells	0	0	0
make.html.header	0.001	0.000	0.001
make.html.rows	0	0	0
make.html.table	0	0	0
make.matrix	0.001	0.000	0.001
make.permutation	0	0	0
make.sample.list	0	0	0
make.sim.data.sd	0.001	0.000	0.001
make.sim.data.tcc	0	0	0
make.stat	0.001	0.000	0.000
make.transformation	0.000	0.000	0.001
make.venn.areas	0.000	0.004	0.000
make.venn.colorscheme	0.000	0.000	0.001
make.venn.counts	0	0	0
make.venn.pairs	0	0	0
meta.perm	0.001	0.000	0.001
meta.test	0	0	0
meta.worker	0	0	0
metaseqr	0.001	0.000	0.001
mlfo	0	0	0
normalize.deseq	0.001	0.000	0.000
normalize.edaseq	0	0	0
normalize.edger	0	0	0
normalize.nbpseq	0.001	0.000	0.001
normalize.noiseq	0	0	0
read.targets	0	0	0
read2count	0.001	0.000	0.001
reduce.exons	0	0	0
reduce.gene.data	0.001	0.000	0.001
set.arg	0	0	0
stat.bayseq	0	0	0
stat.deseq	0.001	0.000	0.001
stat.edger	0	0	0
stat.limma	0.001	0.000	0.001
stat.nbpseq	0	0	0
stat.noiseq	0	0	0
validate.alg.args	0.001	0.000	0.001
validate.list.args	0	0	0
wapply	0	0	0