Back to Multiple platform build/check report for BioC 3.14
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2021-12-06 13:05:03 -0500 (Mon, 06 Dec 2021).

CHECK results for metaseqR2 on nebbiolo2

To the developers/maintainers of the metaseqR2 package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/metaseqR2.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1106/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
metaseqR2 1.6.1  (landing page)
Panagiotis Moulos
Snapshot Date: 2021-12-05 01:55:05 -0500 (Sun, 05 Dec 2021)
git_url: https://git.bioconductor.org/packages/metaseqR2
git_branch: RELEASE_3_14
git_last_commit: a87443a
git_last_commit_date: 2021-11-26 09:16:15 -0500 (Fri, 26 Nov 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: metaseqR2
Version: 1.6.1
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:metaseqR2.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings metaseqR2_1.6.1.tar.gz
StartedAt: 2021-12-05 08:36:54 -0500 (Sun, 05 Dec 2021)
EndedAt: 2021-12-05 08:44:31 -0500 (Sun, 05 Dec 2021)
EllapsedTime: 457.0 seconds
RetCode: 0
Status:   OK  
CheckDir: metaseqR2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:metaseqR2.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings metaseqR2_1.6.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/metaseqR2.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘metaseqR2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘metaseqR2’ version ‘1.6.1’
* 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 ‘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
* 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
read2count    9.976  0.960  14.533
statDeseq2    6.877  0.124   7.039
statNoiseq    6.587  0.048   6.635
metaseqr2     4.783  0.178   9.069
getAnnotation 2.215  0.072   9.132
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/metaseqR2.Rcheck/00check.log’
for details.



Installation output

metaseqR2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL metaseqR2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘metaseqR2’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c pval.c -o pval.o
pval.c: In function ‘add_from_both_sides’:
pval.c:26:11: warning: unused variable ‘esttotalperlength’ [-Wunused-variable]
   26 |    double esttotalperlength = total/2;
      |           ^~~~~~~~~~~~~~~~~
gcc -shared -L/home/biocbuild/bbs-3.14-bioc/R/lib -L/usr/local/lib -o metaseqR2.so pval.o -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-bioc/R/library/00LOCK-metaseqR2/00new/metaseqR2/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (metaseqR2)

Tests output

metaseqR2.Rcheck/tests/runTests.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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'

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 objects are masked from 'package:base':

    I, expand.grid, unname


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://nov2020.archive.ensembl.org

2021-12-05 08:44:19: 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: mm10
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: /tmp/RtmplGtvfU
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 /tmp/RtmplGtvfU/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...

2021-12-05 08:44:19: Data processing finished!


Total processing time: 00 seconds


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

Retrieving edger
Retrieving limma

2021-12-05 08:44:20: 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: /tmp/RtmplGtvfU
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 /tmp/RtmplGtvfU/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 /tmp/RtmplGtvfU/data/reportdb.js
Creating HTML report...
Compressing figures...  adding: tmp/RtmplGtvfU/plots/qc/mds.png (deflated 52%)

Downloading required JavaScript libraries...trying URL 'https://raw.github.com/HubSpot/pace/v1.0.0/pace.min.js'
Content type 'text/plain; charset=utf-8' length 12363 bytes (12 KB)
==================================================
downloaded 12 KB

trying URL 'https://code.highcharts.com/highcharts.js'
downloaded 293 KB

trying URL 'https://code.highcharts.com/highcharts-more.js'
downloaded 96 KB

trying URL 'https://code.highcharts.com/modules/exporting.js'
downloaded 18 KB

trying URL 'https://code.highcharts.com/modules/offline-exporting.js'
downloaded 8675 bytes

trying URL 'https://code.highcharts.com/modules/export-data.js'
downloaded 10 KB

trying URL 'http://jvenn.toulouse.inra.fr/app/js/canvas2svg.js'
Content type 'text/javascript' length 35122 bytes (34 KB)
==================================================
downloaded 34 KB

trying URL 'http://jvenn.toulouse.inra.fr/app/js/jvenn.min.js'
Content type 'text/javascript' length 100524 bytes (98 KB)
==================================================
downloaded 98 KB

trying URL 'https://unpkg.com/dexie@2.0.4/dist/dexie.min.js'
downloaded 55 KB



processing file: metaseqr2_report.Rmd
   inline R code fragments

label: knitr_init (with options) 
List of 2
 $ echo : logi FALSE
 $ cache: logi FALSE

  ordinary text without R code

label: load_js
  ordinary text without R code

label: pace_opts (with options) 
List of 1
 $ engine: chr "js"

  ordinary text without R code

label: decide_dexie
  ordinary text without R code

label: define_getplot_funs (with options) 
List of 1
 $ engine: chr "js"

  ordinary text without R code

label: report_init

Attaching package: 'gplots'

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

    space

The following object is masked from 'package:S4Vectors':

    space

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

    lowess

Loading required package: plotly
Loading required package: ggplot2

Attaching package: 'plotly'

The following object is masked from 'package:ggplot2':

    last_plot

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

    slice

The following object is masked from 'package:S4Vectors':

    rename

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

    filter

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

    layout

Loading required package: viridis
Loading required package: viridisLite

======================
Welcome to heatmaply version 1.3.0

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
You may ask questions at stackoverflow, use the r and heatmaply tags: 
	 https://stackoverflow.com/questions/tagged/heatmaply
======================


Attaching package: 'heatmaply'

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

    normalize


Attaching package: 'pander'

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

    p

  ordinary text without R code

label: summary_analysis_summary
  ordinary text without R code

label: summary_input_options_1
  ordinary text without R code

label: summary_input_options_2
  ordinary text without R code

label: summary_input_options_3
  ordinary text without R code

label: summary_input_options_4
  ordinary text without R code

label: summary_input_options_5
  ordinary text without R code

label: summary_input_options_6
  ordinary text without R code

label: summary_input_options_7
  ordinary text without R code

label: summary_input_options_8
  ordinary text without R code

label: summary_input_options_9
  ordinary text without R code

label: summary_input_options_10
  ordinary text without R code

label: summary_input_options_11
  ordinary text without R code

label: summary_input_options_12
  ordinary text without R code

label: summary_input_options_13
  ordinary text without R code

label: summary_input_options_14
  ordinary text without R code

label: summary_input_options_15
  ordinary text without R code

label: summary_input_options_16
  ordinary text without R code

label: summary_input_options_17
  ordinary text without R code

label: summary_input_options_18
  ordinary text without R code

label: summary_input_options_19
  ordinary text without R code

label: summary_input_options_20
  ordinary text without R code

label: summary_input_options_21
  ordinary text without R code

label: summary_input_options_22
  ordinary text without R code

label: summary_input_options_23
  ordinary text without R code

label: summary_input_options_24
  ordinary text without R code

label: summary_input_options_25
  ordinary text without R code

label: summary_input_options_26
  ordinary text without R code

label: summary_input_options_27
  ordinary text without R code

label: summary_input_options_28
  ordinary text without R code

label: summary_input_options_29
  ordinary text without R code

label: summary_input_options_30
  ordinary text without R code

label: summary_input_options_31
  ordinary text without R code

label: summary_filtered_what_1
  ordinary text without R code

label: summary_filtered_what_2
label: summary_filtered_howmany_1
  ordinary text without R code

label: summary_filtered_howmany_2
  ordinary text without R code

label: summary_filtered_howmany_3
  ordinary text without R code

label: summary_filtered_howmany_4
  ordinary text without R code

label: summary_filtered_howmany_5
  ordinary text without R code

label: summary_de_what_1
  ordinary text without R code

label: summary_de_what_2
  ordinary text without R code

label: fun_call
  ordinary text without R code

label: display_targets
  ordinary text without R code

label: summary_run_log
   inline R code fragments

label: tracks_1
  ordinary text without R code

label: tracks_2
  ordinary text without R code

label: decide_qc
  ordinary text without R code

label: analysis_figures_mds
  ordinary text without R code

label: analysis_figures_biodetection
  ordinary text without R code

label: analysis_figures_countsbio
  ordinary text without R code

label: analysis_figures_saturation
  ordinary text without R code

label: analysis_figures_readsnoise
  ordinary text without R code

label: analysis_figures_correl
  ordinary text without R code

label: analysis_figures_pairwise
  ordinary text without R code

label: analysis_figures_filtered
  ordinary text without R code

label: decide_norm
  ordinary text without R code

label: analysis_figures_boxplot
  ordinary text without R code

label: analysis_figures_gcbias
  ordinary text without R code

label: analysis_figures_lengthbias
  ordinary text without R code

label: analysis_figures_meandiff
  ordinary text without R code

label: analysis_figures_meanvar
  ordinary text without R code

label: analysis_figures_rnacomp
  ordinary text without R code

label: decide_stat
  ordinary text without R code

label: analysis_figures_volcano
  ordinary text without R code

label: analysis_figures_mastat
  ordinary text without R code

label: analysis_figures_deheatmap
  ordinary text without R code

label: deheatmap_render (with options) 
List of 1
 $ engine: chr "js"

  ordinary text without R code

label: analysis_figures_biodist
  ordinary text without R code

label: analysis_figures_deregulogram
  ordinary text without R code

label: analysis_figures_statvenn
label: analysis_figures_foldvenn
  ordinary text without R code

label: results_tables_header
  ordinary text without R code

label: dt_hack (with options) 
List of 1
 $ include: logi FALSE

  ordinary text without R code

label: results_tables
  ordinary text without R code

label: detable_render (with options) 
List of 1
 $ engine: chr "js"

  ordinary text without R code

label: export_links
  ordinary text without R code

label: references
  ordinary text without R code

label: bind_event_changes (with options) 
List of 1
 $ engine: chr "js"

output file: metaseqr2_report.knit.md

/usr/bin/pandoc +RTS -K512m -RTS metaseqr2_report.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmplGtvfU/index.html --lua-filter /home/biocbuild/bbs-3.14-bioc/R/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.14-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 /home/biocbuild/bbs-3.14-bioc/R/library/rmdformats/templates/material/material.html --highlight-style kate --variable theme=bootstrap --include-in-header /tmp/RtmplGtvfU/rmarkdown-str32ebda107b2d85.html 

Output created: /tmp/RtmplGtvfU/index.html


2021-12-05 08:44:26: Data processing finished!


Total processing time: 06 seconds



RUNIT TEST PROTOCOL -- Sun Dec  5 08:44:26 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 
 24.971   1.168  33.427 

Example timings

metaseqR2.Rcheck/metaseqR2-Ex.timings

nameusersystemelapsed
buildAnnotationDatabase000
buildCustomAnnotation4.6360.1684.805
combineBonferroni0.0010.0000.001
combineHarmonic0.0020.0000.002
combineMaxp000
combineMinp000
combineSimes0.0010.0000.001
combineWeight0.0000.0000.001
createSignalTracks1.0880.0611.147
diagplotAvgFtd0.0420.0000.042
diagplotBoxplot1.0550.0081.063
diagplotCor0.1640.0160.180
diagplotDeHeatmap0.7320.0040.736
diagplotEdaseq0.5000.0160.516
diagplotFiltered0.0250.0000.025
diagplotFtd0.0110.0040.015
diagplotMds0.2300.0160.246
diagplotNoiseq1.6720.0241.696
diagplotPairs0.8440.0040.848
diagplotRoc0.0160.0000.016
diagplotVenn0.1540.0040.159
diagplotVolcano1.2240.0161.239
downsampleCounts0.2130.0000.213
estimateAufcWeights0.7480.0310.769
estimateSimParams0.6310.0140.642
getAnnotation2.2150.0729.132
getDefaults000
getInstalledAnnotations0.0010.0000.001
getWeights0.0010.0000.001
importCustomAnnotation1.0850.0441.129
loadAnnotation000
makeSimDataSd0.6820.0250.705
makeSimDataTcc1.8390.0241.864
metaTest0.0130.0000.011
metaseqr24.7830.1789.069
metaseqrPlot0.9980.0161.013
normalizeAbsseq0.6530.0400.693
normalizeDeseq0.2010.0000.202
normalizeDeseq21.0010.0241.024
normalizeDss0.2620.0000.262
normalizeEdaseq0.3670.0040.371
normalizeEdger0.1110.0000.111
normalizeNbpseq0.1420.0000.142
normalizeNoiseq0.1510.0000.151
read2count 9.976 0.96014.533
readTargets0.0310.0000.031
statAbsseq1.4320.0761.508
statBayseq0.6210.0000.621
statDeseq1.2500.0321.283
statDeseq26.8770.1247.039
statDss0.7280.0080.736
statEdger0.5860.0000.586
statLimma0.2630.0200.283
statNbpseq1.130.001.13
statNoiseq6.5870.0486.635