Package: metaseqR

Version: 1.26.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:metaseqR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings metaseqR_1.26.0.tar.gz

StartedAt: 2020-04-15 03:42:40 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 03:49:46 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 425.3 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 --install=check:metaseqR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings metaseqR_1.26.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/metaseqR.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.26.0’
* 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 ... 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 dependencies in R code ... NOTE
'library' or 'require' calls in package code:
  ‘BSgenome’ ‘BiocManager’ ‘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’
correct.transcripts: no visible global function definition for
  ‘makeGRangesFromDataFrame’
correct.transcripts: no visible global function definition for ‘flank’
correct.transcripts: no visible global function definition for ‘resize’
correct.transcripts: no visible global function definition for ‘start’
correct.transcripts: no visible global function definition for ‘end’
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’
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: no visible global function definition for ‘promoters’
read2count: no visible global function definition for ‘resize’
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<-’
reduce.transcripts.utr : <anonymous>: no visible global function
  definition for ‘reduce’
reduce.transcripts.utr : <anonymous>: no visible global function
  definition for ‘DataFrame’
reduce.transcripts.utr : <anonymous>: no visible global function
  definition for ‘mcols<-’
reduce.transcripts.utr.transcript : <anonymous>: no visible global
  function definition for ‘reduce’
reduce.transcripts.utr.transcript : <anonymous>: no visible global
  function definition for ‘DataFrame’
reduce.transcripts.utr.transcript : <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.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 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 flank 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 promoters quantile readGAlignments
  reduce resize 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
diagplot.de.heatmap 9.124  0.200   9.432
diagplot.volcano    6.480  0.143   6.695
diagplot.filtered   1.883  0.094   5.486
* 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-3.10-bioc/meat/metaseqR.Rcheck/00check.log’
for details.

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL metaseqR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘metaseqR’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (metaseqR)

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("metaseqR")

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid


Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit


Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians


Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply, rowsum

locfit 1.5-9.4 	 2020-03-24

Attaching package: 'locfit'

The following objects are masked from 'package:ShortRead':

    left, right

    Welcome to 'DESeq'. For improved performance, usability and
    functionality, please consider migrating to 'DESeq2'.

Attaching package: 'limma'

The following object is masked from 'package:DESeq':

    plotMA

The following object is masked from 'package:BiocGenerics':

    plotMA

Loading required package: zoo

Attaching package: 'zoo'

The following objects are masked from 'package:Rsamtools':

    index, index<-

The following objects are masked from 'package:base':

    as.Date, as.Date.numeric

Cache found

2020-04-15 03:49:26: Data processing started...

Read counts file: imported custom data frame
Conditions: G1, G2
Samples to include: G1_rep1, G1_rep2, G1_rep3, G2_rep1, G2_rep2, G2_rep3
Samples to exclude: none
Requested contrasts: G1_vs_G2
Annotation: embedded
Organism: mm9
Reference source: ensembl
Count type: gene
Analysis preset: all.basic
Transcriptional level: gene
Exon filters: none applied
Gene filters: none applied
Filter application: postnorm
Normalization algorithm: edaseq
Normalization arguments: 
  within.which: loess
  between.which: full
Statistical algorithm: edger, limma
Statistical arguments: 
  edger: classic, 5, 10, movingave, NULL, grid, 11, c(-6, 6), NULL, CoxReid, 10000, NULL, auto, NULL, NULL, NULL, NULL, 0.125, NULL, auto, chisq, TRUE, FALSE, c(0.05, 0.1)
  limma: none
Meta-analysis method: simes
Multiple testing correction: BH
Logarithmic transformation offset: 1
Analysis preset: all.basic
Quality control plots: 
Figure format: png
Output directory: /tmp/Rtmpjd07R4
Output data: annotation, p.value, adj.p.value, meta.p.value, adj.meta.p.value, fold.change
Output scale(s): natural, log2
Output values: normalized
Saving gene model to /tmp/Rtmpjd07R4/data/gene_model.RData
Removing genes with zero counts in all samples...
Normalizing with: edaseq
Running statistical tests with: edger
  Contrast: G1_vs_G2
Running statistical tests with: limma
  Contrast: G1_vs_G2
Performing meta-analysis with simes
Building output files...
  Contrast: G1_vs_G2
    Adding non-filtered data...
      binding annotation...
      binding p-values...
      binding FDRs...
      binding meta p-values...
      binding adjusted meta p-values...
      binding natural normalized fold changes...
      binding log2 normalized fold changes...
    Writing output...

2020-04-15 03:49:26: Data processing finished!


Total processing time: 00 seconds


Estimating AUFC weights... Please wait...
Processing edger
Processing limma

Retrieving edger
Retrieving limma

2020-04-15 03:49:27: Data processing started...

Read counts file: imported custom data frame
Conditions: e14.5, adult_8_weeks
Samples to include: e14.5_1, e14.5_2, a8w_1, a8w_2
Samples to exclude: none
Requested contrasts: e14.5_vs_adult_8_weeks
Library sizes: 
  e14.5_1: 3102907
  e14.5_2: 2067905
  a8w_1: 3742059
  a8w_2: 4403954
Annotation: download
Organism: mm9
Reference source: ensembl
Count type: gene
Analysis preset: medium.basic
Transcriptional level: gene
Exon filters: min.active.exons
  min.active.exons: 
    exons.per.gene: 5
    min.exons: 2
    frac: 0.2
Gene filters: length, avg.reads, expression, biotype
  length: 
    length: 500
  avg.reads: 
    average.per.bp: 100
    quantile: 0.25
  expression: 
    median: TRUE
    mean: FALSE
    quantile: NA
    known: NA
    custom: NA
  biotype: 
    pseudogene: FALSE
    snRNA: FALSE
    protein_coding: FALSE
    antisense: FALSE
    miRNA: FALSE
    lincRNA: FALSE
    snoRNA: FALSE
    processed_transcript: FALSE
    misc_RNA: FALSE
    rRNA: TRUE
    sense_overlapping: FALSE
    sense_intronic: FALSE
    polymorphic_pseudogene: FALSE
    non_coding: FALSE
    three_prime_overlapping_ncrna: FALSE
    IG_C_gene: FALSE
    IG_J_gene: FALSE
    IG_D_gene: FALSE
    IG_V_gene: FALSE
    ncrna_host: FALSE
Filter application: postnorm
Normalization algorithm: edger
Normalization arguments: 
  method: TMM
  logratioTrim: 0.3
  sumTrim: 0.05
  doWeighting: TRUE
  Acutoff: -1e+10
  p: 0.75
Statistical algorithm: edger, limma
Statistical arguments: 
  edger: classic, 5, 10, movingave, NULL, grid, 11, c(-6, 6), NULL, CoxReid, 10000, NULL, auto, NULL, NULL, NULL, NULL, 0.125, NULL, auto, chisq, TRUE, FALSE, c(0.05, 0.1)
  limma: none
Meta-analysis method: simes
Multiple testing correction: BH
p-value threshold: 0.05
Logarithmic transformation offset: 1
Analysis preset: medium.basic
Quality control plots: mds
Figure format: png
Output directory: /tmp/Rtmpjd07R4
Output data: annotation, p.value, adj.p.value, meta.p.value, adj.meta.p.value, fold.change
Output scale(s): natural, log2
Output values: normalized
Downloading gene annotation for mm9...Cache found

Saving gene model to /tmp/Rtmpjd07R4/data/gene_model.RData
Removing genes with zero counts in all samples...
Normalizing with: edger
Applying gene filter length...
  Threshold below which ignored: 500
Applying gene filter avg.reads...
  Threshold below which ignored: 0.0659670745106788
Applying gene filter expression...
  Threshold below which ignored: 68
Applying gene filter biotype...
  Biotypes ignored: rRNA
2106 genes filtered out
1681 genes remain after filtering
Running statistical tests with: edger
  Contrast: e14.5_vs_adult_8_weeks
  Contrast e14.5_vs_adult_8_weeks: found 906 genes
Running statistical tests with: limma
  Contrast: e14.5_vs_adult_8_weeks
  Contrast e14.5_vs_adult_8_weeks: found 911 genes
Performing meta-analysis with simes
Building output files...
  Contrast: e14.5_vs_adult_8_weeks
    Adding non-filtered data...
      binding annotation...
      binding p-values...
      binding FDRs...
      binding meta p-values...
      binding adjusted meta p-values...
      binding natural normalized fold changes...
      binding log2 normalized fold changes...
    Writing output...
    Adding filtered data...
      binding annotation...
      binding p-values...
      binding FDRs...
      binding meta p-values...
      binding adjusted meta p-values...
      binding natural normalized fold changes...
      binding log2 normalized fold changes...
    Writing output...
Creating quality control graphs...
Plotting in png format...
  Plotting mds...
Creating HTML report...
Compressing figures...  adding: tmp/Rtmpjd07R4/plots/qc/mds.png (deflated 48%)


2020-04-15 03:49:33: Data processing finished!


Total processing time: 05 seconds



RUNIT TEST PROTOCOL -- Wed Apr 15 03:49:33 2020 
*********************************************** 
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
metaseqR RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 
Warning message:
'exprs' is deprecated.
Use 'counts' instead.
See help("Deprecated") 
> 
> proc.time()
   user  system elapsed 
 29.663   3.311  32.165 

name	user	system	elapsed
as.class.vector	0.000	0.000	0.001
build.export	0	0	0
calc.f1score	0.009	0.001	0.010
calc.otr	0.004	0.000	0.005
check.contrast.format	0.001	0.001	0.001
check.file.args	0.001	0.000	0.002
check.libsize	0	0	0
check.num.args	0.001	0.000	0.001
check.packages	0.000	0.000	0.001
check.parallel	0.004	0.005	0.010
check.text.args	0.001	0.000	0.001
combine.bonferroni	0.000	0.000	0.001
combine.maxp	0.001	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	0	0
construct.utr.model	0.000	0.000	0.001
diagplot.avg.ftd	0.119	0.008	0.127
diagplot.boxplot	3.151	0.085	3.271
diagplot.cor	1.373	0.071	1.461
diagplot.de.heatmap	9.124	0.200	9.432
diagplot.edaseq	1.882	0.093	2.005
diagplot.filtered	1.883	0.094	5.486
diagplot.ftd	0.027	0.008	0.034
diagplot.mds	1.342	0.029	1.383
diagplot.metaseqr	1.642	0.050	1.702
diagplot.noiseq	1.886	0.047	1.951
diagplot.pairs	2.587	0.134	2.752
diagplot.roc	0.031	0.009	0.040
diagplot.venn	0.238	0.015	0.257
diagplot.volcano	6.480	0.143	6.695
disp	0.000	0.000	0.001
downsample.counts	0.000	0.000	0.001
estimate.aufc.weights	0.000	0.000	0.001
estimate.sim.params	0.000	0.001	0.001
filter.exons	0	0	0
filter.genes	0	0	0
filter.high	0.011	0.001	0.013
filter.low	0.009	0.001	0.013
fisher.method	0.015	0.000	0.015
fisher.method.perm	0.053	0.000	0.056
fisher.sum	0.004	0.000	0.003
get.annotation	0	0	0
get.arg	0.000	0.001	0.000
get.biotypes	0.001	0.000	0.000
get.bs.organism	0	0	0
get.dataset	0.000	0.001	0.001
get.defaults	0	0	0
get.ensembl.annotation	0	0	0
get.exon.attributes	0.001	0.000	0.000
get.gc.content	0	0	0
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.transcript.utr.attributes	0.001	0.000	0.000
get.ucsc.annotation	0	0	0
get.ucsc.credentials	0	0	0
get.ucsc.dbl	0	0	0
get.ucsc.organism	0	0	0
get.ucsc.query	0.001	0.000	0.000
get.ucsc.tabledef	0.000	0.001	0.000
get.ucsc.tbl.tpl	0.000	0.000	0.001
get.valid.chrs	0.001	0.000	0.000
get.weights	0.001	0.000	0.001
graphics.close	0	0	0
graphics.open	0	0	0
load.bs.genome	0.000	0.001	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	0.001	0.000	0.000
make.html.body	0	0	0
make.html.cells	0	0	0
make.html.header	0	0	0
make.html.rows	0	0	0
make.html.table	0	0	0
make.matrix	0	0	0
make.permutation	0	0	0
make.sample.list	0.000	0.000	0.001
make.sim.data.sd	0	0	0
make.sim.data.tcc	0	0	0
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	0.000
make.venn.counts	0.000	0.001	0.001
make.venn.pairs	0	0	0
meta.perm	0.000	0.000	0.001
meta.test	0	0	0
meta.worker	0.000	0.000	0.001
metaseqr	0.001	0.000	0.000
mlfo	0.000	0.000	0.001
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	0	0
read2count	0	0	0
reduce.exons	0	0	0
reduce.gene.data	0	0	0
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	0.001	0.000	0.001
validate.alg.args	0.000	0.000	0.001
validate.list.args	0.000	0.000	0.001
wapply	0.000	0.000	0.001