Panagiotis Moulos
| Snapshot Date: 2024-12-08 13:40 -0500 (Sun, 08 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/metaseqR2 |
| git_branch: devel |
| git_last_commit: 22e1b29 |
| git_last_commit_date: 2024-10-29 10:46:48 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-12-09 11:46 -0500 (Mon, 09 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4749 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4461 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4411 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4366 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4241 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1207/2272 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| metaseqR2 1.19.0 (landing page) Panagiotis Moulos
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the metaseqR2 package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: metaseqR2 |
| Version: 1.19.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:metaseqR2.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings metaseqR2_1.19.0.tar.gz |
| StartedAt: 2024-12-09 07:22:53 -0000 (Mon, 09 Dec 2024) |
| EndedAt: 2024-12-09 07:34:15 -0000 (Mon, 09 Dec 2024) |
| EllapsedTime: 682.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: metaseqR2.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:metaseqR2.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings metaseqR2_1.19.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/metaseqR2.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (conda-forge gcc 14.2.0-1) 14.2.0
GNU Fortran (conda-forge gcc 14.2.0-1) 14.2.0
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘metaseqR2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘metaseqR2’ version ‘1.19.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 45 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* 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
* used C compiler: ‘gcc (conda-forge gcc 14.2.0-1) 14.2.0’
* 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 code 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 loading without being on the library search path ... 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 ... NOTE
getUcscUtr: no visible binding for global variable ‘customDir’
Undefined global functions or variables:
customDir
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
metaseqr2.Rd: render
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 12.716 2.418 20.569
statNoiseq 11.411 0.376 11.810
metaseqr2 6.528 0.841 18.648
buildCustomAnnotation 5.473 0.499 5.987
getAnnotation 2.733 0.216 7.373
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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
‘/home/biocbuild/bbs-3.21-bioc/meat/metaseqR2.Rcheck/00check.log’
for details.
metaseqR2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL metaseqR2 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’ * installing *source* package ‘metaseqR2’ ... ** using staged installation ** libs using C compiler: ‘gcc (conda-forge gcc 14.2.0-1) 14.2.0’ gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c pval.c -o pval.o gcc -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o metaseqR2.so pval.o -L/home/biocbuild/R/R/lib -lR installing to /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-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)
metaseqR2.Rcheck/tests/runTests.Rout
R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
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: 'generics'
The following objects are masked from 'package:base':
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
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, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
unsplit, which.max, which.min
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
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 1.5-9.10 2024-06-24
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://jan2024.archive.ensembl.org
2024-12-09 07:33:55: 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: /home/biocbuild/tmp/RtmpvVgKNQ
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 /home/biocbuild/tmp/RtmpvVgKNQ/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...
2024-12-09 07:33:56: Data processing finished!
Total processing time: 00 seconds
Estimating AUFC weights... Please wait...
Processing edger
Processing limma
Retrieving edger
Retrieving limma
2024-12-09 07:33:56: 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: /home/biocbuild/tmp/RtmpvVgKNQ
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 /home/biocbuild/tmp/RtmpvVgKNQ/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 /home/biocbuild/tmp/RtmpvVgKNQ/data/reportdb.js
Creating HTML report...
Compressing figures... adding: home/biocbuild/tmp/RtmpvVgKNQ/plots/qc/mds.png (deflated 47%)
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 268 KB
trying URL 'https://code.highcharts.com/highcharts-more.js'
downloaded 92 KB
trying URL 'https://code.highcharts.com/modules/exporting.js'
downloaded 19 KB
trying URL 'https://code.highcharts.com/modules/offline-exporting.js'
downloaded 26 KB
trying URL 'https://code.highcharts.com/modules/export-data.js'
downloaded 12 KB
trying URL 'http://jvenn.toulouse.inrae.fr/app/js/canvas2svg.js'
Content type 'application/javascript' length 35122 bytes (34 KB)
==================================================
downloaded 34 KB
trying URL 'http://jvenn.toulouse.inrae.fr/app/js/jvenn.min.js'
Content type 'application/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
output file: metaseqr2_report.knit.md
/home/biocbuild/bin/pandoc +RTS -K512m -RTS metaseqr2_report.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /home/biocbuild/tmp/RtmpvVgKNQ/index.html --lua-filter /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-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/R/R-4.5.0-devel_2024-11-24/site-library/rmdformats/templates/material/material.html --highlight-style kate --variable theme=bootstrap --include-in-header /home/biocbuild/tmp/RtmpvVgKNQ/rmarkdown-str1fd766d8a4082.html
Output created: /home/biocbuild/tmp/RtmpvVgKNQ/index.html
2024-12-09 07:34:10: Data processing finished!
Total processing time: 14 seconds
RUNIT TEST PROTOCOL -- Mon Dec 9 07:34:10 2024
***********************************************
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
36.678 1.977 53.613
metaseqR2.Rcheck/metaseqR2-Ex.timings
| name | user | system | elapsed | |
| buildAnnotationDatabase | 0.001 | 0.000 | 0.000 | |
| buildCustomAnnotation | 5.473 | 0.499 | 5.987 | |
| combineBonferroni | 0.001 | 0.000 | 0.001 | |
| combineHarmonic | 0.001 | 0.000 | 0.002 | |
| combineMaxp | 0.000 | 0.000 | 0.001 | |
| combineMinp | 0.001 | 0.000 | 0.000 | |
| combineSimes | 0.001 | 0.000 | 0.001 | |
| combineWeight | 0.000 | 0.000 | 0.001 | |
| createSignalTracks | 1.670 | 0.067 | 1.740 | |
| diagplotAvgFtd | 0.089 | 0.012 | 0.100 | |
| diagplotBoxplot | 0.914 | 0.044 | 0.961 | |
| diagplotCor | 0.179 | 0.008 | 0.187 | |
| diagplotDeHeatmap | 1.264 | 0.044 | 1.311 | |
| diagplotEdaseq | 0.503 | 0.012 | 0.516 | |
| diagplotFiltered | 0.027 | 0.004 | 0.031 | |
| diagplotFtd | 0.032 | 0.004 | 0.036 | |
| diagplotMds | 0.331 | 0.028 | 0.359 | |
| diagplotNoiseq | 0.636 | 0.020 | 0.656 | |
| diagplotPairs | 0.847 | 0.012 | 0.861 | |
| diagplotRoc | 0.027 | 0.004 | 0.030 | |
| diagplotVenn | 0.228 | 0.024 | 0.254 | |
| diagplotVolcano | 3.549 | 0.275 | 3.831 | |
| downsampleCounts | 0.291 | 0.015 | 0.307 | |
| estimateAufcWeights | 1.427 | 0.093 | 1.510 | |
| estimateSimParams | 1.328 | 0.062 | 1.390 | |
| getAnnotation | 2.733 | 0.216 | 7.373 | |
| getDefaults | 0 | 0 | 0 | |
| getInstalledAnnotations | 0.001 | 0.000 | 0.002 | |
| getWeights | 0.001 | 0.000 | 0.000 | |
| importCustomAnnotation | 1.307 | 0.091 | 1.402 | |
| loadAnnotation | 0.002 | 0.000 | 0.002 | |
| makeSimDataSd | 1.353 | 0.132 | 1.485 | |
| makeSimDataTcc | 0.001 | 0.000 | 0.001 | |
| metaTest | 0.009 | 0.002 | 0.011 | |
| metaseqr2 | 6.528 | 0.841 | 18.648 | |
| metaseqrPlot | 0.776 | 0.027 | 0.806 | |
| normalizeAbsseq | 1.105 | 0.171 | 1.278 | |
| normalizeDeseq | 0.211 | 0.016 | 0.228 | |
| normalizeDeseq2 | 0.788 | 0.036 | 0.826 | |
| normalizeDss | 0.334 | 0.032 | 0.367 | |
| normalizeEdaseq | 0.385 | 0.056 | 0.441 | |
| normalizeEdger | 0.156 | 0.012 | 0.168 | |
| normalizeNbpseq | 0.147 | 0.012 | 0.159 | |
| normalizeNoiseq | 0.213 | 0.012 | 0.225 | |
| read2count | 12.716 | 2.418 | 20.569 | |
| readTargets | 0.028 | 0.004 | 0.032 | |
| statAbsseq | 2.104 | 0.115 | 2.225 | |
| statDeseq | 1.437 | 0.068 | 1.508 | |
| statDeseq2 | 4.610 | 0.164 | 4.785 | |
| statDss | 1.079 | 0.048 | 1.130 | |
| statEdger | 0.886 | 0.030 | 0.918 | |
| statLimma | 0.421 | 0.000 | 0.423 | |
| statNbpseq | 1.687 | 0.043 | 1.734 | |
| statNoiseq | 11.411 | 0.376 | 11.810 | |