BioC 3.0: CHECK report for metaseqR on perceval

Package: metaseqR

Version: 1.4.13

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch metaseqR_1.4.13.tar.gz

StartedAt: 2015-04-10 03:29:43 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 03:39:12 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 568.7 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 --no-multiarch metaseqR_1.4.13.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/metaseqR.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.4.13’
* 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 ... [48s/52s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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:
  ‘BiocInstaller’ ‘BSgenome’ ‘GenomicRanges’ ‘MADAM’ ‘parallel’
  ‘RMySQL’ ‘Rsamtools’ ‘RSQLite’ ‘rtracklayer’ ‘survcomp’ ‘TCC’
  ‘VennDiagram’ ‘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
File ‘metaseqR/R/zzz.R’:
  .onLoad calls:
    packageStartupMessage("\n\nWelcome to metaseqR 1.4.12. Please do not ",     "include \"bayseq\" in the statistics\nargument in metaseqr calls. ",     "There is an incompatibility with the latest\nversion of baySeq which ",     "we are fixing right now...\n\n")

See section ‘Good practice’ in '?.onAttach'.

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’
meta.perm: no visible global function definition for ‘mclapply’
meta.test : <anonymous>: no visible global function definition for
  ‘fisher.method’
meta.test : <anonymous>: no visible global function definition for
  ‘fisher.method.perm’
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
  ‘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.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 ... [30s/31s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [45s/55s]
 [45s/55s] 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-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	0.009	0.000	0.009
calc.otr	0.005	0.001	0.006
check.contrast.format	0.001	0.000	0.001
check.file.args	0.004	0.001	0.005
check.libsize	0.001	0.001	0.002
check.num.args	0.001	0.000	0.000
check.packages	0.001	0.001	0.001
check.parallel	0.003	0.005	0.007
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	0.002
combine.weight	0.001	0.000	0.001
construct.gene.model	0.000	0.000	0.001
diagplot.avg.ftd	0.119	0.010	0.129
diagplot.boxplot	3.353	0.046	3.399
diagplot.cor	1.824	0.020	1.845
diagplot.de.heatmap	0.001	0.000	0.000
diagplot.edaseq	0.001	0.000	0.001
diagplot.filtered	0.001	0.000	0.001
diagplot.ftd	0.026	0.008	0.035
diagplot.mds	1.941	0.018	1.961
diagplot.metaseqr	0.000	0.000	0.001
diagplot.noiseq	0	0	0
diagplot.pairs	0.001	0.000	0.001
diagplot.roc	0.053	0.011	0.064
diagplot.venn	0.000	0.000	0.001
diagplot.volcano	0.001	0.000	0.001
disp	0.001	0.000	0.002
downsample.counts	0.000	0.000	0.001
estimate.aufc.weights	0.000	0.000	0.001
estimate.sim.params	0.000	0.000	0.001
filter.exons	0.001	0.000	0.001
filter.genes	0.000	0.000	0.001
filter.high	0.042	0.008	0.050
filter.low	0.014	0.003	0.017
get.annotation	0	0	0
get.arg	0.001	0.000	0.001
get.biotypes	0.001	0.000	0.001
get.bs.organism	0.001	0.000	0.000
get.dataset	0.001	0.001	0.001
get.defaults	0.001	0.000	0.001
get.ensembl.annotation	0	0	0
get.exon.attributes	0.001	0.000	0.001
get.gc.content	0.001	0.000	0.000
get.gene.attributes	0.001	0.000	0.002
get.host	0.000	0.000	0.001
get.preset.opts	0.001	0.000	0.002
get.strict.biofilter	0	0	0
get.ucsc.annotation	0.000	0.000	0.001
get.ucsc.credentials	0.000	0.000	0.001
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	0.001	0.000	0.001
get.ucsc.tbl.tpl	0.001	0.000	0.000
get.valid.chrs	0.001	0.000	0.001
get.weights	0.001	0.000	0.001
graphics.close	0.001	0.000	0.000
graphics.open	0	0	0
load.bs.genome	0.000	0.000	0.001
make.contrast.list	0.002	0.000	0.002
make.fold.change	0	0	0
make.grid	0	0	0
make.html.body	0	0	0
make.html.cells	0.001	0.000	0.000
make.html.header	0.000	0.000	0.001
make.html.rows	0.001	0.000	0.001
make.html.table	0	0	0
make.matrix	0.001	0.000	0.001
make.permutation	0.001	0.000	0.000
make.sample.list	0	0	0
make.sim.data.sd	0.000	0.000	0.001
make.sim.data.tcc	0.000	0.000	0.001
make.stat	0	0	0
make.transformation	0.001	0.000	0.001
make.venn.areas	0.001	0.000	0.000
make.venn.colorscheme	0.001	0.000	0.001
make.venn.counts	0	0	0
make.venn.pairs	0.001	0.000	0.000
meta.perm	0.000	0.001	0.001
meta.test	0.000	0.000	0.001
meta.worker	0.001	0.000	0.000
metaseqr	0.000	0.000	0.001
mlfo	0.000	0.001	0.000
normalize.deseq	0.001	0.000	0.001
normalize.edaseq	0.000	0.000	0.001
normalize.edger	0.001	0.000	0.001
normalize.nbpseq	0	0	0
normalize.noiseq	0.001	0.000	0.001
read.targets	0.001	0.000	0.001
read2count	0.001	0.001	0.001
reduce.exons	0.000	0.000	0.001
reduce.gene.data	0.001	0.000	0.001
set.arg	0.001	0.000	0.000
stat.bayseq	0.000	0.000	0.001
stat.deseq	0	0	0
stat.edger	0.001	0.000	0.001
stat.limma	0.001	0.000	0.001
stat.nbpseq	0.000	0.000	0.001
stat.noiseq	0.001	0.000	0.001
validate.alg.args	0.000	0.000	0.001
validate.list.args	0	0	0
wapply	0.000	0.000	0.001