Panagiotis Moulos
| Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/metaseqR2 |
| git_branch: devel |
| git_last_commit: 8378cbf |
| git_last_commit_date: 2024-03-14 07:24:34 -0400 (Thu, 14 Mar 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-28 11:39:33 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
| 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 1209/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| metaseqR2 1.15.2 (landing page) Panagiotis Moulos
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | 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. |
| Package: metaseqR2 |
| Version: 1.15.2 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:metaseqR2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings metaseqR2_1.15.2.tar.gz |
| StartedAt: 2024-03-27 22:16:35 -0400 (Wed, 27 Mar 2024) |
| EndedAt: 2024-03-27 22:29:07 -0400 (Wed, 27 Mar 2024) |
| EllapsedTime: 752.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: metaseqR2.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:metaseqR2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings metaseqR2_1.15.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/metaseqR2.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘metaseqR2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘metaseqR2’ version ‘1.15.2’
* 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
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 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 ... 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 11.918 1.610 35.446
statNoiseq 8.507 0.107 8.697
metaseqr2 5.851 0.714 19.402
buildCustomAnnotation 5.192 0.226 5.466
getAnnotation 2.406 0.138 100.750
* 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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.19-bioc/meat/metaseqR2.Rcheck/00check.log’
for details.
metaseqR2.Rcheck/00install.out
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL metaseqR2
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘metaseqR2’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pval.c -o pval.o
pval.c:26:11: warning: unused variable 'esttotalperlength' [-Wunused-variable]
double esttotalperlength = total/2;
^
1 warning generated.
clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o metaseqR2.so pval.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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) (2024-03-18 r86148) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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, aperm, 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, table, tapply,
union, 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 1.5-9.9 2024-03-01
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 http://www.ensembl.org
2024-03-27 22:28:41: 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/RtmpzWqhMo
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/RtmpzWqhMo/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...
2024-03-27 22:28:41: Data processing finished!
Total processing time: 00 seconds
Estimating AUFC weights... Please wait...
Processing edger
Processing limma
Retrieving edger
Retrieving limma
2024-03-27 22:28:43: 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/RtmpzWqhMo
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/RtmpzWqhMo/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...2024-03-27 22:28:45.222 R[1845:1364388913] XType: com.apple.fonts is not accessible.
2024-03-27 22:28:45.222 R[1845:1364388913] XType: XTFontStaticRegistry is enabled.
Importing mds...
Writing plot database in /tmp/RtmpzWqhMo/data/reportdb.js
Creating HTML report...
Compressing figures... adding: tmp/RtmpzWqhMo/plots/qc/mds.png (deflated 48%)
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 9681 bytes
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 'text/javascript' length 35122 bytes (34 KB)
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downloaded 34 KB
trying URL 'http://jvenn.toulouse.inrae.fr/app/js/jvenn.min.js'
Content type 'text/javascript' length 100524 bytes (98 KB)
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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
/usr/local/bin/pandoc +RTS -K512m -RTS metaseqr2_report.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /private/tmp/RtmpzWqhMo/index.html --lua-filter /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rmdformats/templates/material/material.html --highlight-style kate --variable theme=bootstrap --include-in-header /tmp/RtmpzWqhMo/rmarkdown-str735a67eaf.html
Output created: /private/tmp/RtmpzWqhMo/index.html
2024-03-27 22:28:55: Data processing finished!
Total processing time: 11 seconds
RUNIT TEST PROTOCOL -- Wed Mar 27 22:28:55 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
32.865 2.476 64.905
metaseqR2.Rcheck/metaseqR2-Ex.timings
| name | user | system | elapsed | |
| buildAnnotationDatabase | 0.000 | 0.000 | 0.001 | |
| buildCustomAnnotation | 5.192 | 0.226 | 5.466 | |
| combineBonferroni | 0.001 | 0.001 | 0.001 | |
| combineHarmonic | 0.002 | 0.002 | 0.004 | |
| combineMaxp | 0.000 | 0.001 | 0.000 | |
| combineMinp | 0 | 0 | 0 | |
| combineSimes | 0.001 | 0.000 | 0.002 | |
| combineWeight | 0 | 0 | 0 | |
| createSignalTracks | 1.236 | 0.117 | 1.386 | |
| diagplotAvgFtd | 0.049 | 0.006 | 0.055 | |
| diagplotBoxplot | 0.809 | 0.025 | 0.838 | |
| diagplotCor | 0.133 | 0.023 | 0.156 | |
| diagplotDeHeatmap | 0.902 | 0.046 | 0.952 | |
| diagplotEdaseq | 0.387 | 0.065 | 0.456 | |
| diagplotFiltered | 0.027 | 0.010 | 0.038 | |
| diagplotFtd | 0.020 | 0.010 | 0.031 | |
| diagplotMds | 0.233 | 0.014 | 0.249 | |
| diagplotNoiseq | 0.501 | 0.058 | 0.564 | |
| diagplotPairs | 0.535 | 0.069 | 0.610 | |
| diagplotRoc | 0.021 | 0.012 | 0.034 | |
| diagplotVenn | 0.204 | 0.019 | 0.229 | |
| diagplotVolcano | 1.487 | 0.061 | 1.559 | |
| downsampleCounts | 0.230 | 0.002 | 0.235 | |
| estimateAufcWeights | 2.427 | 0.143 | 2.680 | |
| estimateSimParams | 0.889 | 0.043 | 0.963 | |
| getAnnotation | 2.406 | 0.138 | 100.750 | |
| getDefaults | 0.001 | 0.001 | 0.001 | |
| getInstalledAnnotations | 0.002 | 0.001 | 0.003 | |
| getWeights | 0.000 | 0.001 | 0.001 | |
| importCustomAnnotation | 1.233 | 0.018 | 1.258 | |
| loadAnnotation | 0.001 | 0.000 | 0.002 | |
| makeSimDataSd | 0.980 | 0.033 | 1.052 | |
| makeSimDataTcc | 2.092 | 0.046 | 2.169 | |
| metaTest | 0.009 | 0.009 | 0.031 | |
| metaseqr2 | 5.851 | 0.714 | 19.402 | |
| metaseqrPlot | 0.722 | 0.040 | 0.775 | |
| normalizeAbsseq | 0.771 | 0.063 | 0.841 | |
| normalizeDeseq | 0.155 | 0.021 | 0.178 | |
| normalizeDeseq2 | 0.686 | 0.027 | 0.719 | |
| normalizeDss | 0.309 | 0.026 | 0.340 | |
| normalizeEdaseq | 0.389 | 0.024 | 0.415 | |
| normalizeEdger | 0.123 | 0.022 | 0.146 | |
| normalizeNbpseq | 0.109 | 0.024 | 0.134 | |
| normalizeNoiseq | 0.163 | 0.024 | 0.190 | |
| read2count | 11.918 | 1.610 | 35.446 | |
| readTargets | 0.034 | 0.007 | 0.042 | |
| statAbsseq | 1.585 | 0.087 | 1.691 | |
| statDeseq | 1.09 | 0.04 | 1.14 | |
| statDeseq2 | 4.403 | 0.103 | 4.549 | |
| statDss | 0.892 | 0.032 | 0.932 | |
| statEdger | 0.623 | 0.029 | 0.656 | |
| statLimma | 0.330 | 0.003 | 0.336 | |
| statNbpseq | 1.060 | 0.024 | 1.097 | |
| statNoiseq | 8.507 | 0.107 | 8.697 | |