| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-11-02 11:40:33 -0400 (Thu, 02 Nov 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4729 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4463 |
| lconway | macOS 12.6.5 Monterey | x86_64 | 4.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" | 4478 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4464 |
| 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 413/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| compcodeR 1.38.0 (landing page) Charlotte Soneson
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.6.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
|
To the developers/maintainers of the compcodeR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/compcodeR.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: compcodeR |
| Version: 1.38.0 |
| Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:compcodeR.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings compcodeR_1.38.0.tar.gz |
| StartedAt: 2023-11-02 09:30:09 -0000 (Thu, 02 Nov 2023) |
| EndedAt: 2023-11-02 09:35:49 -0000 (Thu, 02 Nov 2023) |
| EllapsedTime: 340.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: compcodeR.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:compcodeR.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings compcodeR_1.38.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/compcodeR.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘compcodeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘compcodeR’ version ‘1.38.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘rpanel’
* 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 ‘compcodeR’ 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 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
NBPSeq.createRmd 40.744 0.690 41.567
DESeq2.createRmd 17.936 4.569 25.554
show-compData-method 5.719 1.034 7.863
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’/home/biocbuild/R/R-4.3.1/bin/BATCH: line 60: 830059 Killed ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
g4 0.4357368637 0.92126849 0.4587872 0.5642631
g5 0.0055826869 0.13179123 0.8217073 0.9944173
g6 0.0003053375 0.03570528 1.7396031 0.9996947
+ 492 rows...
Without phylogenetic tree.
length.matrix:
sample1 sample2 sample3 sample4 sample5 sample6
g1 709 7 1472 475 10112 8029
g2 1533 53870 72873 4209 1085 22717
g3 3749 14799 7828 6446 14243 4638
g4 890 4717 14938 37345 8403 9837
g5 10753 940 13697 6162 13863 1721
g6 6679 15130 9003 9066 9614 9614
* 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 ERROR, 1 NOTE
See
‘/home/biocbuild/bbs-3.18-bioc/meat/compcodeR.Rcheck/00check.log’
for details.
compcodeR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL compcodeR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’ * installing *source* package ‘compcodeR’ ... ** using staged installation ** R ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (compcodeR)
compcodeR.Rcheck/tests/testthat.Rout.fail
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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.
> if (requireNamespace("testthat", quietly = TRUE)) {
+
+ library(testthat)
+ library(compcodeR)
+
+ test_check("compcodeR")
+
+ }
Loading required package: sm
Package 'sm', version 2.2-5.7: type help(sm) for summary information
[1] "DESeq2.createRmd" "DESeq2.length.createRmd"
[3] "DSS.createRmd" "EBSeq.createRmd"
[5] "NBPSeq.createRmd" "NOISeq.prenorm.createRmd"
[7] "TCC.createRmd" "edgeR.GLM.createRmd"
[9] "edgeR.exact.createRmd" "lengthNorm.limma.createRmd"
[11] "lengthNorm.sva.limma.createRmd" "logcpm.limma.createRmd"
[13] "phylolm.createRmd" "sqrtcpm.limma.createRmd"
[15] "ttest.createRmd" "voom.limma.createRmd"
[17] "voom.ttest.createRmd"
An object of class compData
Dataset name: B_625_625
Number of samples: 10
Number of variables: 500
Number of random outliers: 0
Number of single outliers: 0
Number of known truly differentially expressed genes: 50
Differential expression analysis was performed by the method edgeR.4.0.1.exact.TMM.movingave.tagwise on Thu Nov 2 09:34:43 2023 .
count.matrix:
sample1 sample2 sample3 sample4 sample5 sample6
g1 4 8 5 2 8 8
g2 314 419 186 172 294 133
g3 1030 1583 1011 1033 747 1291
g4 0 1 1 0 2 2
g5 48 122 215 62 106 90
g6 27 16 18 44 29 74
+ 494 rows and 4 cols...
sample.annotations:
condition depth.factor
sample1 1 1.1049378
sample2 1 1.2875127
sample3 1 1.1581115
sample4 1 1.3611698
sample5 1 1.0581603
sample6 2 0.7594447
+ 4 rows...
variable.annotations:
truedispersions.S1 truedispersions.S2 truemeans.S1 truemeans.S2
g1 0.11610054 0.11610054 6.878049 16.363472
g2 0.43796296 0.43796296 303.073171 893.165617
g3 0.04321133 0.04321133 1223.414634 2760.990905
g4 0.55624371 0.55624371 0.902439 6.153083
g5 0.15968189 0.15968189 148.146341 316.915193
g6 0.36378999 0.36378999 40.439024 132.785087
n.random.outliers.up.S1 n.random.outliers.up.S2 n.random.outliers.down.S1
g1 0 0 0
g2 0 0 0
g3 0 0 0
g4 0 0 0
g5 0 0 0
g6 0 0 0
n.random.outliers.down.S2 n.single.outliers.up.S1 n.single.outliers.up.S2
g1 0 0 0
g2 0 0 0
g3 0 0 0
g4 0 0 0
g5 0 0 0
g6 0 0 0
n.single.outliers.down.S1 n.single.outliers.down.S2 M.value A.value
g1 0 0 1.158386 2.9291506
g2 0 0 1.349570 8.6365105
g3 0 0 1.050582 10.4859190
g4 0 0 1.432447 0.7393097
g5 0 0 1.185233 7.1150497
g6 0 0 2.176450 5.6916570
truelog2foldchanges upregulation downregulation differential.expression
g1 1.250408 1 0 1
g2 1.559262 1 0 1
g3 1.174273 1 0 1
g4 2.769408 1 0 1
g5 1.097074 1 0 1
g6 1.715273 1 0 1
+ 494 rows...
Differential expression results:
pvalue adjpvalue logFC score dispersion.S1 dispersion.S2
g1 5.804805e-02 5.091934e-01 1.109582 0.9419519 0.2378950 0.2378950
g2 7.039843e-04 2.199951e-02 1.603157 0.9992960 0.2509797 0.2509797
g3 1.014563e-03 2.984008e-02 1.062861 0.9989854 0.1215078 0.1215078
g4 6.539309e-02 5.449424e-01 2.019660 0.9346069 0.5641107 0.5641107
g5 9.940688e-03 1.713912e-01 1.129158 0.9900593 0.2158532 0.2158532
g6 4.983594e-07 8.305991e-05 2.194748 0.9999995 0.1898635 0.1898635
+ 494 rows...
An object of class compData
Dataset name: B_625_625
Number of samples: 4
Number of variables: 500
Number of random outliers: 0
Number of single outliers: 0
Number of known truly differentially expressed genes: 50
Differential expression analysis was performed by the method edgeR.4.0.1.exact.TMM.movingave.tagwise on Thu Nov 2 09:34:43 2023 .
count.matrix:
sample1 sample2 sample3 sample4
g1 4 8 5 2
g2 314 419 186 172
g3 1030 1583 1011 1033
g4 0 1 1 0
g5 48 122 215 62
g6 27 16 18 44
+ 494 rows...
sample.annotations:
condition depth.factor
sample1 1 1.1049378
sample2 1 1.2875127
sample3 1 1.1581115
sample4 1 1.3611698
sample5 1 1.0581603
sample6 2 0.7594447
+ 4 rows...
variable.annotations:
truedispersions.S1 truedispersions.S2 truemeans.S1 truemeans.S2
g1 0.11610054 0.11610054 6.878049 16.363472
g2 0.43796296 0.43796296 303.073171 893.165617
g3 0.04321133 0.04321133 1223.414634 2760.990905
g4 0.55624371 0.55624371 0.902439 6.153083
g5 0.15968189 0.15968189 148.146341 316.915193
g6 0.36378999 0.36378999 40.439024 132.785087
n.random.outliers.up.S1 n.random.outliers.up.S2 n.random.outliers.down.S1
g1 0 0 0
g2 0 0 0
g3 0 0 0
g4 0 0 0
g5 0 0 0
g6 0 0 0
n.random.outliers.down.S2 n.single.outliers.up.S1 n.single.outliers.up.S2
g1 0 0 0
g2 0 0 0
g3 0 0 0
g4 0 0 0
g5 0 0 0
g6 0 0 0
n.single.outliers.down.S1 n.single.outliers.down.S2 M.value A.value
g1 0 0 1.158386 2.9291506
g2 0 0 1.349570 8.6365105
g3 0 0 1.050582 10.4859190
g4 0 0 1.432447 0.7393097
g5 0 0 1.185233 7.1150497
g6 0 0 2.176450 5.6916570
truelog2foldchanges upregulation downregulation differential.expression
g1 1.250408 1 0 1
g2 1.559262 1 0 1
g3 1.174273 1 0 1
g4 2.769408 1 0 1
g5 1.097074 1 0 1
g6 1.715273 1 0 1
+ 494 rows...
Differential expression results:
pvalue adjpvalue logFC score dispersion.S1 dispersion.S2
g1 5.804805e-02 5.091934e-01 1.109582 0.9419519 0.2378950 0.2378950
g2 7.039843e-04 2.199951e-02 1.603157 0.9992960 0.2509797 0.2509797
g3 1.014563e-03 2.984008e-02 1.062861 0.9989854 0.1215078 0.1215078
g4 6.539309e-02 5.449424e-01 2.019660 0.9346069 0.5641107 0.5641107
g5 9.940688e-03 1.713912e-01 1.129158 0.9900593 0.2158532 0.2158532
g6 4.983594e-07 8.305991e-05 2.194748 0.9999995 0.1898635 0.1898635
+ 494 rows...
An object of class phyloCompData
Dataset name: B_625_625
Number of samples: 10
Number of variables: 498
Number of random outliers: 0
Number of single outliers: 0
Number of known truly differentially expressed genes: 49
Differential expression analysis was performed by the method length.3.58.1.limma.TMM.lengthNorm.RPKM.dataTrans.log2.no_trend on Thu Nov 2 09:35:18 2023 .
count.matrix:
sample1 sample2 sample3 sample4 sample5 sample6
g1 2 1 0 0 4 5
g2 18 418 321 25 5 287
g3 2 0 1 4 2 20
g4 8 6 69 126 30 97
g5 2495 148 1736 738 1531 570
g6 18 35 18 9 15 115
+ 492 rows and 4 cols...
sample.annotations:
condition depth.factor
sample1 1 1.1087861
sample2 1 1.2699957
sample3 1 1.1005966
sample4 1 0.8652224
sample5 1 0.7795419
sample6 2 1.2785653
+ 4 rows...
variable.annotations:
truedispersions.S1 truedispersions.S2 truemeans.S1 truemeans.S2
g1 0.63372227 0.63372227 7.736842 20.13148
g2 0.12249434 0.12249434 95.421053 231.21363
g3 0.72255054 0.72255054 3.087719 5.68084
g4 0.32345589 0.32345589 41.634146 96.64933
g5 0.03866619 0.03866619 2015.487805 3792.55744
g6 0.11797778 0.11797778 28.087719 84.52361
n.random.outliers.up.S1 n.random.outliers.up.S2 n.random.outliers.down.S1
g1 0 0 0
g2 0 0 0
g3 0 0 0
g4 0 0 0
g5 0 0 0
g6 0 0 0
n.random.outliers.down.S2 n.single.outliers.up.S1 n.single.outliers.up.S2
g1 0 0 0
g2 0 0 0
g3 0 0 0
g4 0 0 0
g5 0 0 0
g6 0 0 0
n.single.outliers.down.S1 n.single.outliers.down.S2 M.value A.value
g1 0 0 1.5018073 1.152706
g2 0 0 0.2078055 5.766156
g3 0 0 1.0483242 1.390350
g4 0 0 -1.3755162 4.062796
g5 0 0 -0.3685706 9.676270
g6 0 0 1.7362595 5.008725
truelog2foldchanges upregulation downregulation differential.expression
g1 1.3796366 1 0 1
g2 1.2768469 1 0 1
g3 0.8795626 1 0 1
g4 1.2149925 1 0 1
g5 0.9120420 1 0 1
g6 1.5894149 1 0 1
lengths.relmeans lengths.dispersions M.value.TPM A.value.TPM
g1 9917 4.4902541 -0.4669503 -8.754908
g2 9970 2.2026858 1.1693418 -6.592122
g3 10057 0.2040650 0.7688165 -11.695832
g4 9969 1.1343801 0.3068095 -7.838718
g5 9920 0.8830628 0.6697297 -2.400325
g6 9937 0.0484685 1.5876254 -8.210384
+ 492 rows...
Differential expression results:
pvalue adjpvalue logFC score
g1 0.8683815621 0.97180678 -0.3149727 0.1316184
g2 0.0368385542 0.41748040 1.3213195 0.9631614
g3 0.4388545775 0.92126849 0.9207942 0.5611454
g4 0.4357368637 0.92126849 0.4587872 0.5642631
g5 0.0055826869 0.13179123 0.8217073 0.9944173
g6 0.0003053375 0.03570528 1.7396031 0.9996947
+ 492 rows...
Without phylogenetic tree.
length.matrix:
sample1 sample2 sample3 sample4 sample5 sample6
g1 709 7 1472 475 10112 8029
g2 1533 53870 72873 4209 1085 22717
g3 3749 14799 7828 6446 14243 4638
g4 890 4717 14938 37345 8403 9837
g5 10753 940 13697 6162 13863 1721
g6 6679 15130 9003 9066 9614 9614
An object of class phyloCompData
Dataset name: B_625_625
Number of samples: 4
Number of variables: 498
Number of random outliers: 0
Number of single outliers: 0
Number of known truly differentially expressed genes: 49
Differential expression analysis was performed by the method length.3.58.1.limma.TMM.lengthNorm.RPKM.dataTrans.log2.no_trend on Thu Nov 2 09:35:18 2023 .
count.matrix:
sample1 sample2 sample3 sample4
g1 2 1 0 0
g2 18 418 321 25
g3 2 0 1 4
g4 8 6 69 126
g5 2495 148 1736 738
g6 18 35 18 9
+ 492 rows...
sample.annotations:
condition depth.factor
sample1 1 1.1087861
sample2 1 1.2699957
sample3 1 1.1005966
sample4 1 0.8652224
sample5 1 0.7795419
sample6 2 1.2785653
+ 4 rows...
variable.annotations:
truedispersions.S1 truedispersions.S2 truemeans.S1 truemeans.S2
g1 0.63372227 0.63372227 7.736842 20.13148
g2 0.12249434 0.12249434 95.421053 231.21363
g3 0.72255054 0.72255054 3.087719 5.68084
g4 0.32345589 0.32345589 41.634146 96.64933
g5 0.03866619 0.03866619 2015.487805 3792.55744
g6 0.11797778 0.11797778 28.087719 84.52361
n.random.outliers.up.S1 n.random.outliers.up.S2 n.random.outliers.down.S1
g1 0 0 0
g2 0 0 0
g3 0 0 0
g4 0 0 0
g5 0 0 0
g6 0 0 0
n.random.outliers.down.S2 n.single.outliers.up.S1 n.single.outliers.up.S2
g1 0 0 0
g2 0 0 0
g3 0 0 0
g4 0 0 0
g5 0 0 0
g6 0 0 0
n.single.outliers.down.S1 n.single.outliers.down.S2 M.value A.value
g1 0 0 1.5018073 1.152706
g2 0 0 0.2078055 5.766156
g3 0 0 1.0483242 1.390350
g4 0 0 -1.3755162 4.062796
g5 0 0 -0.3685706 9.676270
g6 0 0 1.7362595 5.008725
truelog2foldchanges upregulation downregulation differential.expression
g1 1.3796366 1 0 1
g2 1.2768469 1 0 1
g3 0.8795626 1 0 1
g4 1.2149925 1 0 1
g5 0.9120420 1 0 1
g6 1.5894149 1 0 1
lengths.relmeans lengths.dispersions M.value.TPM A.value.TPM
g1 9917 4.4902541 -0.4669503 -8.754908
g2 9970 2.2026858 1.1693418 -6.592122
g3 10057 0.2040650 0.7688165 -11.695832
g4 9969 1.1343801 0.3068095 -7.838718
g5 9920 0.8830628 0.6697297 -2.400325
g6 9937 0.0484685 1.5876254 -8.210384
+ 492 rows...
Differential expression results:
pvalue adjpvalue logFC score
g1 0.8683815621 0.97180678 -0.3149727 0.1316184
g2 0.0368385542 0.41748040 1.3213195 0.9631614
g3 0.4388545775 0.92126849 0.9207942 0.5611454
g4 0.4357368637 0.92126849 0.4587872 0.5642631
g5 0.0055826869 0.13179123 0.8217073 0.9944173
g6 0.0003053375 0.03570528 1.7396031 0.9996947
+ 492 rows...
Without phylogenetic tree.
length.matrix:
sample1 sample2 sample3 sample4 sample5 sample6
g1 709 7 1472 475 10112 8029
g2 1533 53870 72873 4209 1085 22717
g3 3749 14799 7828 6446 14243 4638
g4 890 4717 14938 37345 8403 9837
g5 10753 940 13697 6162 13863 1721
g6 6679 15130 9003 9066 9614 9614
compcodeR.Rcheck/compcodeR-Ex.timings
| name | user | system | elapsed | |
| DESeq2.createRmd | 17.936 | 4.569 | 25.554 | |
| DESeq2.length.createRmd | 0.895 | 0.037 | 0.939 | |
| DSS.createRmd | 0.001 | 0.000 | 0.002 | |
| EBSeq.createRmd | 2.000 | 0.028 | 2.097 | |
| NBPSeq.createRmd | 40.744 | 0.690 | 41.567 | |
| NOISeq.prenorm.createRmd | 4.030 | 0.039 | 4.088 | |
| TCC.createRmd | 2.615 | 0.052 | 2.703 | |
| checkDataObject | 0.382 | 0.000 | 0.384 | |
| checkTableConsistency | 1.254 | 0.044 | 1.303 | |
| check_compData | 0.365 | 0.004 | 0.370 | |
| check_compData_results | 0.718 | 0.008 | 0.729 | |
| check_phyloCompData | 0.918 | 0.008 | 0.943 | |
| compData | 0.002 | 0.000 | 0.002 | |
| convertListTocompData | 0.005 | 0.000 | 0.005 | |
| convertListTophyloCompData | 0.012 | 0.000 | 0.012 | |
| convertcompDataToList | 4.628 | 0.008 | 4.646 | |
| convertphyloCompDataToList | 0.310 | 0.000 | 0.314 | |
| edgeR.GLM.createRmd | 1.181 | 0.026 | 1.300 | |
| edgeR.exact.createRmd | 0.947 | 0.209 | 1.897 | |
| generateCodeHTMLs | 1.067 | 0.972 | 4.752 | |
| generateSyntheticData | 0.931 | 0.000 | 0.940 | |
| lengthNorm.limma.createRmd | 0.651 | 0.016 | 0.668 | |
| lengthNorm.sva.limma.createRmd | 2.618 | 0.167 | 2.860 | |
| listcreateRmd | 0.01 | 0.00 | 0.01 | |
| logcpm.limma.createRmd | 0.617 | 0.004 | 0.623 | |
| nEffRatio | 0.493 | 0.004 | 0.503 | |
| phyloCompData | 0.007 | 0.000 | 0.008 | |
| phylolm.createRmd | 0.759 | 0.008 | 0.771 | |
| runComparison | 1.248 | 0.080 | 1.646 | |
| runComparisonGUI | 0.000 | 0.000 | 0.001 | |
| runComparisonShiny | 0.000 | 0.000 | 0.001 | |
| runDiffExp | 0.752 | 0.012 | 0.771 | |
| show-compData-method | 5.719 | 1.034 | 7.863 | |
| show-phyloCompData-method | 0.729 | 0.020 | 0.753 | |
| sqrtcpm.limma.createRmd | 0.622 | 0.003 | 0.755 | |
| summarizeSyntheticDataSet | 0.391 | 0.000 | 0.392 | |
| ttest.createRmd | 0.600 | 0.000 | 0.606 | |
| voom.limma.createRmd | 0.735 | 0.031 | 0.769 | |
| voom.ttest.createRmd | 0.637 | 0.040 | 0.679 | |