Multiple platform build/check report for BioC 3.12 - CHECK report for metaseqR2 on tokay1

Package: metaseqR2

Version: 1.2.0

Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:metaseqR2.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings metaseqR2_1.2.0.tar.gz

StartedAt: 2021-05-06 04:27:11 -0400 (Thu, 06 May 2021)

EndedAt: 2021-05-06 04:41:34 -0400 (Thu, 06 May 2021)

EllapsedTime: 862.7 seconds

RetCode: 0

Status: OK

CheckDir: metaseqR2.Rcheck

Warnings: 0

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:metaseqR2.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings metaseqR2_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/metaseqR2.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'metaseqR2/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'metaseqR2' version '1.2.0'
* 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 whether package 'metaseqR2' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/metaseqR2/libs/i386/metaseqR2.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/metaseqR2/libs/x64/metaseqR2.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
metaseqr2     9.64   2.50   17.13
statNoiseq    7.52   0.00    7.51
getAnnotation 3.72   0.05    7.50
read2count    2.82   0.01    6.31
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
metaseqr2     8.33   1.49   12.71
statNoiseq    8.58   0.00    8.58
getAnnotation 2.64   0.06    6.37
read2count    2.00   0.00    5.33
* 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/metaseqR2.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/metaseqR2_1.2.0.tar.gz && rm -rf metaseqR2.buildbin-libdir && mkdir metaseqR2.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=metaseqR2.buildbin-libdir metaseqR2_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL metaseqR2_1.2.0.zip && rm metaseqR2_1.2.0.tar.gz metaseqR2_1.2.0.zip
###
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100 1977k  100 1977k    0     0  11.7M      0 --:--:-- --:--:-- --:--:-- 11.8M

install for i386

* installing *source* package 'metaseqR2' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c pval.c -o pval.o
pval.c: In function 'add_from_both_sides':
pval.c:26:11: warning: unused variable 'esttotalperlength' [-Wunused-variable]
    double esttotalperlength = total/2;
           ^~~~~~~~~~~~~~~~~
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o metaseqR2.dll tmp.def pval.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/metaseqR2.buildbin-libdir/00LOCK-metaseqR2/00new/metaseqR2/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'metaseqR2'
    finding HTML links ... done
    buildAnnotationDatabase                 html  
    buildCustomAnnotation                   html  
    combineBonferroni                       html  
    combineHarmonic                         html  
    combineMaxp                             html  
    combineMinp                             html  
    combineSimes                            html  
    combineWeight                           html  
    createSignalTracks                      html  
    diagplotAvgFtd                          html  
    diagplotBoxplot                         html  
    diagplotCor                             html  
    diagplotDeHeatmap                       html  
    diagplotEdaseq                          html  
    diagplotFiltered                        html  
    diagplotFtd                             html  
    diagplotMds                             html  
    diagplotNoiseq                          html  
    diagplotPairs                           html  
    diagplotRoc                             html  
    diagplotVenn                            html  
    diagplotVolcano                         html  
    downsampleCounts                        html  
    estimateAufcWeights                     html  
    estimateSimParams                       html  
    getAnnotation                           html  
    getDefaults                             html  
    getInstalledAnnotations                 html  
    getWeights                              html  
    hg19pvalues                             html  
    importCustomAnnotation                  html  
    libsizeListMm9                          html  
    loadAnnotation                          html  
    makeSimDataSd                           html  
    makeSimDataTcc                          html  
    metaTest                                html  
    metaseqr2                               html  
    finding level-2 HTML links ... done

    metaseqrPlot                            html  
    mm9GeneCounts                           html  
    normalizeAbsseq                         html  
    normalizeDeseq                          html  
    normalizeDeseq2                         html  
    normalizeDss                            html  
    normalizeEdaseq                         html  
    normalizeEdger                          html  
    normalizeNbpseq                         html  
    normalizeNoiseq                         html  
    read2count                              html  
    readTargets                             html  
    sampleListMm9                           html  
    statAbsseq                              html  
    statBayseq                              html  
    statDeseq                               html  
    statDeseq2                              html  
    statDss                                 html  
    statEdger                               html  
    statLimma                               html  
    statNbpseq                              html  
    statNoiseq                              html  
** 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

install for x64

* installing *source* package 'metaseqR2' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c pval.c -o pval.o
pval.c: In function 'add_from_both_sides':
pval.c:26:11: warning: unused variable 'esttotalperlength' [-Wunused-variable]
    double esttotalperlength = total/2;
           ^~~~~~~~~~~~~~~~~
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o metaseqR2.dll tmp.def pval.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/metaseqR2.buildbin-libdir/metaseqR2/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'metaseqR2' as metaseqR2_1.2.0.zip
* DONE (metaseqR2)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'metaseqR2' successfully unpacked and MD5 sums checked


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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("metaseqR2")

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.max, which.min


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: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Welcome to Bioconductor

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


Attaching package: 'Biobase'

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

    rowMedians

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

    anyMissing, rowMedians


Attaching package: 'limma'

The following object is masked from 'package:DESeq2':

    plotMA

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

    plotMA

locfit 1.5-9.4 	 2020-03-24

Attaching package: 'metaseqR2'

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

    readTargets


Downsampling counts...
Estimating initial dispersion population...
Estimating dispersions using log-likelihood...

Running simulations... This procedure requires time... Please wait...Using Ensembl host https://may2012.archive.ensembl.org

2021-05-06 04:40:20: 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(s): 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-3.12-bioc\tmpdir\RtmpyyBQWy
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
Loading gene annotation...
Saving gene model to C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\RtmpyyBQWy/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...

2021-05-06 04:40:21: Data processing finished!


Total processing time: 00 seconds


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

Retrieving edger
Retrieving limma

2021-05-06 04:40:22: 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: adult_8_weeks_vs_e14.5
Library sizes: 
  e14.5_1: 3102907
  e14.5_2: 2067905
  a8w_1: 3742059
  a8w_2: 4403954
Annotation: embedded
Organism: mm9
Reference source: ensembl
Count type: gene
Analysis preset: medium_basic
Transcriptional level: gene
Exon filters: minActiveExons
  minActiveExons: 
    exonsPerGene: 5
    minExons: 2
    frac: 0.2
Gene filters: length, avgReads, expression, biotype
  length: 
    length: 500
  avgReads: 
    averagePerBp: 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(s): 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-3.12-bioc\tmpdir\RtmpyyBQWy
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
Loading gene annotation...
Saving gene model to C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\RtmpyyBQWy/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 avgReads...
  Threshold below which ignored: 0.0659629215631332
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: adult_8_weeks_vs_e14.5
  Contrast adult_8_weeks_vs_e14.5: found 906 genes
Running statistical tests with: limma
  Contrast: adult_8_weeks_vs_e14.5
  Contrast adult_8_weeks_vs_e14.5: found 911 genes
Performing meta-analysis with simes
Building output files...
  Contrast: adult_8_weeks_vs_e14.5
    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...
    Adding report data...
      binding annotation...
      binding meta p-values...
      binding adjusted meta p-values...
      binding log2 normalized fold changes...
      binding normalized mean counts...
      binding normalized mean counts...
Creating quality control graphs...
Plotting in png format...
  Plotting mds...
  Importing mds...
Writing plot database in C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\RtmpyyBQWy/data/reportdb.js
Creating HTML report...
Compressing figures...  adding: Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpyyBQWy/plots/qc/mds.png (deflated 62%)

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processing file: metaseqr2_report.Rmd
   inline R code fragments

label: knitr_init (with options) 
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label: report_init

Attaching package: 'gplots'

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    space

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    space

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    lowess

Loading required package: plotly
Loading required package: ggplot2

Attaching package: 'plotly'

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    last_plot

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    slice

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    rename

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    filter

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    layout

Loading required package: viridis
Loading required package: viridisLite

======================
Welcome to heatmaply version 1.2.1

Type citation('heatmaply') for how to cite the package.
Type ?heatmaply for the main documentation.

The github page is: https://github.com/talgalili/heatmaply/
Please submit your suggestions and bug-reports at: https://github.com/talgalili/heatmaply/issues
Or contact: <tal.galili@gmail.com>
======================


Attaching package: 'heatmaply'

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    normalize


Attaching package: 'pander'

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output file: metaseqr2_report.knit.md

"C:/PROGRA~2/Pandoc/pandoc" +RTS -K512m -RTS metaseqr2_report.utf8.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output pandoc19441b362259.html --lua-filter "C:\Users\biocbuild\bbs-3.12-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "C:\Users\biocbuild\bbs-3.12-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" +RTS -K2048m -RTS --variable "material:true" --variable "lightbox:true" --variable "thumbnails:true" --variable "gallery:true" --variable "cards:true" --variable bs3=TRUE --standalone --section-divs --table-of-contents --toc-depth 1 --template "C:\Users\biocbuild\bbs-3.12-bioc\R\library\rmdformats\templates\material\material.html" --highlight-style kate --variable theme=bootstrap --include-in-header "C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\RtmpyyBQWy\rmarkdown-str194423682e00.html" 

Output created: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpyyBQWy/index.html


2021-05-06 04:40:35: Data processing finished!


Total processing time: 13 seconds



RUNIT TEST PROTOCOL -- Thu May 06 04:40:35 2021 
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Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
metaseqR2 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 
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R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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("metaseqR2")

Attaching package: 'BiocGenerics'

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Welcome to Bioconductor

    Vignettes contain introductory material; view with
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locfit 1.5-9.4 	 2020-03-24

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Downsampling counts...
Estimating initial dispersion population...
Estimating dispersions using log-likelihood...

Running simulations... This procedure requires time... Please wait...Using Ensembl host https://may2012.archive.ensembl.org

2021-05-06 04:41:07: 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(s): 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-3.12-bioc\tmpdir\RtmpiyN5tU
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
Loading gene annotation...
Saving gene model to C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\RtmpiyN5tU/data/gene_model.RData
Removing genes with zero counts in all samples...
Normalizing with: edaseq
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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...

2021-05-06 04:41:08: Data processing finished!


Total processing time: 00 seconds


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

Retrieving edger
Retrieving limma

2021-05-06 04:41:10: 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: adult_8_weeks_vs_e14.5
Library sizes: 
  e14.5_1: 3102907
  e14.5_2: 2067905
  a8w_1: 3742059
  a8w_2: 4403954
Annotation: embedded
Organism: mm9
Reference source: ensembl
Count type: gene
Analysis preset: medium_basic
Transcriptional level: gene
Exon filters: minActiveExons
  minActiveExons: 
    exonsPerGene: 5
    minExons: 2
    frac: 0.2
Gene filters: length, avgReads, expression, biotype
  length: 
    length: 500
  avgReads: 
    averagePerBp: 100
    quantile: 0.25
  expression: 
    median: TRUE
    mean: FALSE
    quantile: NA
    known: NA
    custom: NA
  biotype: 
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    snRNA: FALSE
    protein_coding: FALSE
    antisense: FALSE
    miRNA: FALSE
    lincRNA: FALSE
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    processed_transcript: FALSE
    misc_RNA: FALSE
    rRNA: TRUE
    sense_overlapping: FALSE
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    polymorphic_pseudogene: FALSE
    non_coding: FALSE
    three_prime_overlapping_ncrna: FALSE
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Filter application: postnorm
Normalization algorithm: edger
Normalization arguments: 
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  logratioTrim: 0.3
  sumTrim: 0.05
  doWeighting: TRUE
  Acutoff: -1e+10
  p: 0.75
Statistical algorithm(s): 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-3.12-bioc\tmpdir\RtmpiyN5tU
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
Loading gene annotation...
Saving gene model to C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\RtmpiyN5tU/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 avgReads...
  Threshold below which ignored: 0.0659629215631332
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: adult_8_weeks_vs_e14.5
  Contrast adult_8_weeks_vs_e14.5: found 906 genes
Running statistical tests with: limma
  Contrast: adult_8_weeks_vs_e14.5
  Contrast adult_8_weeks_vs_e14.5: found 911 genes
Performing meta-analysis with simes
Building output files...
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    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...
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      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 report data...
      binding annotation...
      binding meta p-values...
      binding adjusted meta p-values...
      binding log2 normalized fold changes...
      binding normalized mean counts...
      binding normalized mean counts...
Creating quality control graphs...
Plotting in png format...
  Plotting mds...
  Importing mds...
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processing file: metaseqr2_report.Rmd
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Loading required package: viridis
Loading required package: viridisLite

======================
Welcome to heatmaply version 1.2.1

Type citation('heatmaply') for how to cite the package.
Type ?heatmaply for the main documentation.

The github page is: https://github.com/talgalili/heatmaply/
Please submit your suggestions and bug-reports at: https://github.com/talgalili/heatmaply/issues
Or contact: <tal.galili@gmail.com>
======================


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output file: metaseqr2_report.knit.md

"C:/PROGRA~2/Pandoc/pandoc" +RTS -K512m -RTS metaseqr2_report.utf8.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output pandoc245c538b4320.html --lua-filter "C:\Users\biocbuild\bbs-3.12-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "C:\Users\biocbuild\bbs-3.12-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" +RTS -K2048m -RTS --variable "material:true" --variable "lightbox:true" --variable "thumbnails:true" --variable "gallery:true" --variable "cards:true" --variable bs3=TRUE --standalone --section-divs --table-of-contents --toc-depth 1 --template "C:\Users\biocbuild\bbs-3.12-bioc\R\library\rmdformats\templates\material\material.html" --highlight-style kate --variable theme=bootstrap --include-in-header "C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\RtmpiyN5tU\rmarkdown-str245c177859f6.html" 

Output created: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpiyN5tU/index.html


2021-05-06 04:41:25: Data processing finished!


Total processing time: 15 seconds



RUNIT TEST PROTOCOL -- Thu May 06 04:41:25 2021 
*********************************************** 
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
metaseqR2 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 
  36.90    2.89   49.45

name	user	system	elapsed
buildAnnotationDatabase	0	0	0
buildCustomAnnotation	0	0	0
combineBonferroni	0	0	0
combineHarmonic	0.00	0.00	0.03
combineMaxp	0	0	0
combineMinp	0	0	0
combineSimes	0	0	0
combineWeight	0	0	0
createSignalTracks	0	0	0
diagplotAvgFtd	0.41	0.00	0.41
diagplotBoxplot	2.84	0.68	3.51
diagplotCor	0.34	0.20	0.54
diagplotDeHeatmap	1.72	0.25	1.97
diagplotEdaseq	0.89	0.11	1.00
diagplotFiltered	0.06	0.03	0.09
diagplotFtd	0.06	0.01	0.08
diagplotMds	0.50	0.02	0.52
diagplotNoiseq	1.05	0.09	1.14
diagplotPairs	1.72	0.02	1.73
diagplotRoc	0.06	0.02	0.08
diagplotVenn	0.25	0.04	0.30
diagplotVolcano	3.30	0.14	3.43
downsampleCounts	0.42	0.00	0.42
estimateAufcWeights	1.81	0.02	1.83
estimateSimParams	1.5	0.0	1.5
getAnnotation	3.72	0.05	7.50
getDefaults	0	0	0
getInstalledAnnotations	0	0	0
getWeights	0	0	0
importCustomAnnotation	1.88	0.04	1.92
loadAnnotation	0	0	0
makeSimDataSd	0.82	0.03	0.86
makeSimDataTcc	3.88	0.86	4.79
metaTest	0.01	0.00	0.01
metaseqr2	9.64	2.50	17.13
metaseqrPlot	0.66	0.07	0.71
normalizeAbsseq	0.89	0.00	0.90
normalizeDeseq	0.22	0.03	0.25
normalizeDeseq2	0.64	0.03	0.67
normalizeDss	0.28	0.04	0.33
normalizeEdaseq	0.41	0.05	0.45
normalizeEdger	0.17	0.02	0.19
normalizeNbpseq	0.16	0.01	0.17
normalizeNoiseq	0.18	0.07	0.25
read2count	2.82	0.01	6.31
readTargets	0.03	0.00	0.03
statAbsseq	1.62	0.00	1.63
statBayseq	0.55	0.00	0.54
statDeseq	2.34	0.02	2.36
statDeseq2	4.53	0.34	4.88
statDss	0.85	0.00	0.84
statEdger	0.95	0.00	0.95
statLimma	0.39	0.00	0.40
statNbpseq	2.28	0.00	2.28
statNoiseq	7.52	0.00	7.51

name	user	system	elapsed
buildAnnotationDatabase	0	0	0
buildCustomAnnotation	0	0	0
combineBonferroni	0	0	0
combineHarmonic	0.00	0.00	0.03
combineMaxp	0	0	0
combineMinp	0	0	0
combineSimes	0	0	0
combineWeight	0	0	0
createSignalTracks	0	0	0
diagplotAvgFtd	0.11	0.02	0.12
diagplotBoxplot	1.08	0.05	1.13
diagplotCor	0.28	0.03	0.31
diagplotDeHeatmap	2.40	0.00	2.41
diagplotEdaseq	0.57	0.06	0.62
diagplotFiltered	0.03	0.02	0.05
diagplotFtd	0.01	0.03	0.05
diagplotMds	0.25	0.03	0.28
diagplotNoiseq	0.57	0.04	0.61
diagplotPairs	0.88	0.07	0.94
diagplotRoc	0.03	0.01	0.05
diagplotVenn	0.2	0.0	0.2
diagplotVolcano	2.22	0.03	2.25
downsampleCounts	0.25	0.00	0.25
estimateAufcWeights	0.92	0.02	0.94
estimateSimParams	0.8	0.0	0.8
getAnnotation	2.64	0.06	6.37
getDefaults	0	0	0
getInstalledAnnotations	0	0	0
getWeights	0	0	0
importCustomAnnotation	1.38	0.02	1.39
loadAnnotation	0	0	0
makeSimDataSd	0.88	0.00	0.87
makeSimDataTcc	2.15	0.03	2.19
metaTest	0	0	0
metaseqr2	8.33	1.49	12.71
metaseqrPlot	0.70	0.05	0.75
normalizeAbsseq	0.85	0.01	0.86
normalizeDeseq	0.22	0.03	0.25
normalizeDeseq2	0.73	0.05	0.78
normalizeDss	0.33	0.03	0.36
normalizeEdaseq	0.37	0.05	0.43
normalizeEdger	0.19	0.03	0.21
normalizeNbpseq	0.14	0.05	0.19
normalizeNoiseq	0.19	0.03	0.22
read2count	2.00	0.00	5.33
readTargets	0.02	0.00	0.01
statAbsseq	1.67	0.00	1.68
statBayseq	0.53	0.04	0.57
statDeseq	1.83	0.00	1.83
statDeseq2	4.22	0.04	4.25
statDss	0.73	0.00	0.74
statEdger	0.83	0.00	0.83
statLimma	0.34	0.00	0.34
statNbpseq	1.89	0.00	1.89
statNoiseq	8.58	0.00	8.58

CHECK report for metaseqR2 on tokay1

Summary

Command output

Installation output

Tests output

Example timings