Panagiotis Moulos
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/metaseqR |
| Branch: RELEASE_3_8 |
| Last Commit: a9560c7 |
| Last Changed Date: 2019-01-04 13:38:41 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:23:38 -0400 (Sat, 13 Apr 2019).
| Package 927/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| metaseqR 1.22.1 Panagiotis Moulos
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: metaseqR |
| Version: 1.22.1 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:metaseqR.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings metaseqR_1.22.1.tar.gz |
| StartedAt: 2019-04-13 03:40:41 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 03:49:52 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 550.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: metaseqR.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:metaseqR.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings metaseqR_1.22.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/metaseqR.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'metaseqR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'metaseqR' version '1.22.1'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
diagplot.de.heatmap 7.81 0.25 8.07
diagplot.volcano 5.11 0.04 5.16
diagplot.filtered 1.08 0.11 5.23
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
diagplot.de.heatmap 8.84 0.12 8.97
diagplot.volcano 5.67 0.02 5.70
diagplot.filtered 3.38 0.07 7.55
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
OK
** running tests for arch 'x64' ...
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
'C:/Users/biocbuild/bbs-3.8-bioc/meat/metaseqR.Rcheck/00check.log'
for details.
metaseqR.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/metaseqR_1.22.1.tar.gz && rm -rf metaseqR.buildbin-libdir && mkdir metaseqR.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=metaseqR.buildbin-libdir metaseqR_1.22.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL metaseqR_1.22.1.zip && rm metaseqR_1.22.1.tar.gz metaseqR_1.22.1.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
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install for i386
* installing *source* package 'metaseqR' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'metaseqR'
finding HTML links ... done
as.class.vector html
build.export html
calc.f1score html
calc.otr html
cddat html
cdplot html
check.contrast.format html
check.file.args html
check.graphics.file html
check.graphics.type html
check.libsize html
check.main.args html
check.num.args html
check.packages html
check.parallel html
check.text.args html
combine.bonferroni html
combine.maxp html
combine.minp html
combine.simes html
combine.weight html
construct.gene.model html
construct.utr.model html
diagplot.avg.ftd html
diagplot.boxplot html
diagplot.cor html
diagplot.de.heatmap html
diagplot.edaseq html
diagplot.filtered html
diagplot.ftd html
diagplot.mds html
diagplot.metaseqr html
diagplot.noiseq html
diagplot.noiseq.saturation html
diagplot.pairs html
diagplot.roc html
diagplot.venn html
diagplot.volcano html
disp html
downsample.counts html
estimate.aufc.weights html
estimate.sim.params html
filter.exons html
filter.genes html
filter.high html
filter.low html
fisher.method html
fisher.method.perm html
fisher.sum html
get.annotation html
get.arg html
get.biotypes html
get.bs.organism html
get.dataset html
get.defaults html
get.ensembl.annotation html
get.exon.attributes html
get.gc.content html
get.gene.attributes html
get.host html
get.preset.opts html
get.strict.biofilter html
get.transcript.utr.attributes html
get.ucsc.annotation html
get.ucsc.credentials html
get.ucsc.dbl html
get.ucsc.organism html
get.ucsc.query html
get.ucsc.tabledef html
get.ucsc.tbl.tpl html
get.valid.chrs html
get.weights html
graphics.close html
graphics.open html
hg19.exon.counts html
libsize.list.hg19 html
libsize.list.mm9 html
load.bs.genome html
log2disp html
make.avg.expression html
make.contrast.list html
make.export.list html
make.fold.change html
make.grid html
make.highcharts.points html
make.html.body html
make.html.cells html
make.html.header html
make.html.rows html
make.html.table html
make.matrix html
make.path.struct html
make.permutation html
make.project.path html
make.report.messages html
make.sample.list html
make.sim.data.sd html
make.sim.data.tcc html
make.stat html
make.transformation html
make.venn.areas html
make.venn.colorscheme html
make.venn.counts html
make.venn.pairs html
meta.perm html
meta.test html
meta.worker html
metaseqR-package html
metaseqr html
mlfo html
mm9.gene.counts html
nat2log html
normalize.deseq html
normalize.edaseq html
normalize.edger html
normalize.nbpseq html
normalize.noiseq html
read.targets html
read2count html
reduce.exons html
reduce.gene.data html
sample.list.hg19 html
sample.list.mm9 html
set.arg html
stat.bayseq html
stat.deseq html
stat.edger html
stat.limma html
stat.nbpseq html
stat.noiseq html
validate.alg.args html
validate.list.args html
wapply html
wp.adjust html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'metaseqR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'metaseqR' as metaseqR_1.22.1.zip
* DONE (metaseqR)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'metaseqR' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
metaseqR.Rcheck/tests_i386/runTests.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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, lengths, 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: 'IRanges'
The following object is masked from 'package:grDevices':
windows
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
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
2019-04-13 03:49:05: 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: C:\Users\biocbuild\bbs-3.8-bioc\tmpdir\RtmpGAYTF9
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 C:\Users\biocbuild\bbs-3.8-bioc\tmpdir\RtmpGAYTF9/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...
2019-04-13 03:49:05: Data processing finished!
Total processing time: 00 seconds
Estimating AUFC weights... Please wait...
Processing edger
Processing limma
Retrieving edger
Retrieving limma
2019-04-13 03:49:06: 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: C:\Users\biocbuild\bbs-3.8-bioc\tmpdir\RtmpGAYTF9
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 C:\Users\biocbuild\bbs-3.8-bioc\tmpdir\RtmpGAYTF9/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: Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGAYTF9/plots/qc/mds.png (deflated 62%)
2019-04-13 03:49:13: Data processing finished!
Total processing time: 06 seconds
RUNIT TEST PROTOCOL -- Sat Apr 13 03:49:13 2019
***********************************************
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
There were 50 or more warnings (use warnings() to see the first 50)
>
> proc.time()
user system elapsed
21.56 1.87 31.40
|
metaseqR.Rcheck/tests_x64/runTests.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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, lengths, 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: 'IRanges'
The following object is masked from 'package:grDevices':
windows
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
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
2019-04-13 03:49:32: 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: C:\Users\biocbuild\bbs-3.8-bioc\tmpdir\Rtmpiihshu
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 C:\Users\biocbuild\bbs-3.8-bioc\tmpdir\Rtmpiihshu/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...
2019-04-13 03:49:32: Data processing finished!
Total processing time: 00 seconds
Estimating AUFC weights... Please wait...
Processing edger
Processing limma
Retrieving edger
Retrieving limma
2019-04-13 03:49:33: 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: C:\Users\biocbuild\bbs-3.8-bioc\tmpdir\Rtmpiihshu
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 C:\Users\biocbuild\bbs-3.8-bioc\tmpdir\Rtmpiihshu/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: Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpiihshu/plots/qc/mds.png (deflated 62%)
2019-04-13 03:49:40: Data processing finished!
Total processing time: 07 seconds
RUNIT TEST PROTOCOL -- Sat Apr 13 03:49:41 2019
***********************************************
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
There were 50 or more warnings (use warnings() to see the first 50)
>
> proc.time()
user system elapsed
19.87 0.56 27.93
|
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metaseqR.Rcheck/examples_i386/metaseqR-Ex.timings
|
metaseqR.Rcheck/examples_x64/metaseqR-Ex.timings
|