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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_1.23.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/metaseqR.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.23.1’
* 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 ... 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 11.369 0.573 12.031
diagplot.volcano 4.776 0.396 5.172
diagplot.filtered 1.398 0.142 6.728
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’
ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
Mean relative difference: 0.076923
Test files with failing tests
test_estimate_aufc_weights.R
test_estimate_aufc_weights
Error in BiocGenerics:::testPackage("metaseqR") :
unit tests failed for package metaseqR
In addition: Warning message:
In regularize.values(x, y, ties, missing(ties)) :
collapsing to unique 'x' values
Execution halted
* 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: 1 ERROR, 3 NOTEs
See
‘/Users/biocbuild/bbs-3.9-bioc/meat/metaseqR.Rcheck/00check.log’
for details.
R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 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, colMeans, colSums, 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, rowMeans, rowSums,
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 object is masked from 'package:Biostrings':
type
The following objects are masked from 'package:base':
aperm, apply, rowsum
locfit 1.5-9.1 2013-03-22
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
2019-04-09 03:32:54: 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/Rtmpia9Q9X
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/Rtmpia9Q9X/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...
2019-04-09 03:32:55: Data processing finished!
Total processing time: 00 seconds
Estimating AUFC weights... Please wait...
Processing edger
Processing limma
Retrieving edger
Retrieving limma
Timing stopped at: 9.223 4.309 12.31
Error in checkEqualsNumeric(weights, c(0.5384615, 0.4615385), tolerance = 1e-05) :
Mean relative difference: 0.076923
In addition: Warning messages:
1: 'exprs' is deprecated.
Use 'counts' instead.
See help("Deprecated")
2: In regularize.values(x, y, ties, missing(ties)) :
collapsing to unique 'x' values
2019-04-09 03:32:57: 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/Rtmpia9Q9X
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...
Saving gene model to /tmp/Rtmpia9Q9X/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/Rtmpia9Q9X/plots/qc/mds.png (deflated 48%)
2019-04-09 03:33:08: Data processing finished!
Total processing time: 10 seconds
RUNIT TEST PROTOCOL -- Tue Apr 9 03:33:08 2019
***********************************************
Number of test functions: 2
Number of errors: 0
Number of failures: 1
1 Test Suite :
metaseqR RUnit Tests - 2 test functions, 0 errors, 1 failure
FAILURE in test_estimate_aufc_weights: Error in checkEqualsNumeric(weights, c(0.5384615, 0.4615385), tolerance = 1e-05) :
Mean relative difference: 0.076923
Test files with failing tests
test_estimate_aufc_weights.R
test_estimate_aufc_weights
Error in BiocGenerics:::testPackage("metaseqR") :
unit tests failed for package metaseqR
In addition: Warning message:
In regularize.values(x, y, ties, missing(ties)) :
collapsing to unique 'x' values
Execution halted