BioC 3.3: CHECK report for metaseqR on linux2.bioconductor.org

Package: metaseqR

Version: 1.11.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings metaseqR_1.11.0.tar.gz

StartedAt: 2015-10-27 05:39:31 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 05:44:36 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 305.6 seconds

RetCode: 0

Status:  OK

CheckDir: metaseqR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings metaseqR_1.11.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/metaseqR.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* 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 ‘1.11.0’
* 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 ... [24s/24s] 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’
countsBioToJSON: no visible binding for global variable ‘nams’
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’
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
  ‘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: 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’
Undefined global functions or variables:
  AnnotatedDataFrame BamFile DataFrame GRanges IRanges Rle ScanBamParam
  alphabetFrequency asBam assayData assays biocLite combine.test
  countBam countOverlaps dbConnect dbDisconnect dbDriver dbGetQuery
  dbWriteTable draw.pairwise.venn draw.quad.venn draw.quintuple.venn
  draw.triple.venn getBSgenome getSeq import.bed installed.genomes
  makeGRangesFromDataFrame mclapply mcols<- nams readGAlignments reduce
  rollmean scanBamFlag seqlevels seqnames sizeFactors<- strand strand<-
  summarizeOverlaps
* 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 ... [39s/44s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
diagplot.de.heatmap 10.115  0.056  10.200
diagplot.volcano     5.602  0.020   5.623
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [19s/26s]
 [20s/26s] 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-3.3-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	0	0
calc.f1score	0.008	0.000	0.007
calc.otr	0.003	0.000	0.003
check.contrast.format	0.001	0.000	0.001
check.file.args	0.001	0.000	0.002
check.libsize	0.001	0.000	0.001
check.num.args	0.001	0.000	0.001
check.packages	0.001	0.000	0.001
check.parallel	0.001	0.017	0.020
check.text.args	0.001	0.000	0.001
combine.bonferroni	0.001	0.000	0.001
combine.maxp	0.001	0.000	0.001
combine.minp	0.001	0.000	0.001
combine.simes	0.001	0.000	0.001
combine.weight	0.001	0.000	0.000
construct.gene.model	0	0	0
diagplot.avg.ftd	0.093	0.004	0.098
diagplot.boxplot	2.056	0.061	2.872
diagplot.cor	1.726	0.003	2.477
diagplot.de.heatmap	10.115	0.056	10.200
diagplot.edaseq	1.504	0.032	1.537
diagplot.filtered	0.911	0.013	4.682
diagplot.ftd	0.027	0.000	0.026
diagplot.mds	1.687	0.000	1.689
diagplot.metaseqr	0.955	0.000	0.955
diagplot.noiseq	1.685	0.000	1.685
diagplot.pairs	2.352	0.016	2.368
diagplot.roc	0.042	0.000	0.044
diagplot.venn	0.655	0.000	0.656
diagplot.volcano	5.602	0.020	5.623
disp	0	0	0
downsample.counts	0	0	0
estimate.aufc.weights	0	0	0
estimate.sim.params	0	0	0
filter.exons	0.000	0.000	0.001
filter.genes	0.000	0.000	0.001
filter.high	0.01	0.00	0.01
filter.low	0.006	0.000	0.005
fisher.method	0.008	0.000	0.008
fisher.method.perm	0.028	0.000	0.029
fisher.sum	0.002	0.000	0.001
get.annotation	0.000	0.000	0.001
get.arg	0.000	0.000	0.001
get.biotypes	0.001	0.000	0.000
get.bs.organism	0.001	0.000	0.000
get.dataset	0.001	0.000	0.000
get.defaults	0	0	0
get.ensembl.annotation	0	0	0
get.exon.attributes	0	0	0
get.gc.content	0.000	0.000	0.001
get.gene.attributes	0.001	0.000	0.001
get.host	0.001	0.000	0.000
get.preset.opts	0.001	0.000	0.000
get.strict.biofilter	0.000	0.004	0.001
get.ucsc.annotation	0.000	0.000	0.001
get.ucsc.credentials	0.000	0.000	0.001
get.ucsc.dbl	0	0	0
get.ucsc.organism	0.001	0.000	0.000
get.ucsc.query	0	0	0
get.ucsc.tabledef	0	0	0
get.ucsc.tbl.tpl	0	0	0
get.valid.chrs	0	0	0
get.weights	0.000	0.000	0.001
graphics.close	0.000	0.000	0.001
graphics.open	0.000	0.000	0.001
load.bs.genome	0.001	0.000	0.000
make.avg.expression	0.001	0.000	0.000
make.contrast.list	0.001	0.000	0.000
make.fold.change	0	0	0
make.grid	0	0	0
make.html.body	0.000	0.000	0.001
make.html.cells	0.000	0.000	0.001
make.html.header	0.000	0.000	0.001
make.html.rows	0.000	0.000	0.001
make.html.table	0.001	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	0	0
make.venn.areas	0	0	0
make.venn.colorscheme	0.000	0.000	0.001
make.venn.counts	0.000	0.000	0.001
make.venn.pairs	0.000	0.000	0.001
meta.perm	0.001	0.000	0.000
meta.test	0.001	0.000	0.000
meta.worker	0.001	0.000	0.000
metaseqr	0.001	0.000	0.000
mlfo	0	0	0
normalize.deseq	0	0	0
normalize.edaseq	0	0	0
normalize.edger	0	0	0
normalize.nbpseq	0	0	0
normalize.noiseq	0	0	0
read.targets	0.000	0.000	0.001
read2count	0.001	0.000	0.001
reduce.exons	0.001	0.000	0.000
reduce.gene.data	0.001	0.000	0.000
set.arg	0	0	0
stat.bayseq	0	0	0
stat.deseq	0	0	0
stat.edger	0	0	0
stat.limma	0	0	0
stat.nbpseq	0	0	0
stat.noiseq	0.000	0.000	0.001
validate.alg.args	0.000	0.000	0.001
validate.list.args	0.000	0.000	0.001
wapply	0	0	0