Charlotte Soneson
| Snapshot Date: 2024-11-24 13:40 -0500 (Sun, 24 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/compcodeR |
| git_branch: devel |
| git_last_commit: fdc74f1 |
| git_last_commit_date: 2024-11-02 11:39:26 -0500 (Sat, 02 Nov 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-11-25 11:39 -0500 (Mon, 25 Nov 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" | 4748 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4459 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4349 |
| 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 409/2272 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| compcodeR 1.43.0 (landing page) Charlotte Soneson
| 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 | | ||||||||
|
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. |
| Package: compcodeR |
| Version: 1.43.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:compcodeR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings compcodeR_1.43.0.tar.gz |
| StartedAt: 2024-11-24 20:43:58 -0500 (Sun, 24 Nov 2024) |
| EndedAt: 2024-11-24 20:53:58 -0500 (Sun, 24 Nov 2024) |
| EllapsedTime: 600.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: compcodeR.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:compcodeR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings compcodeR_1.43.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/compcodeR.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* 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 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘compcodeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘compcodeR’ version ‘1.43.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
INFO
Package which this enhances but not available for checking: ‘rpanel’
Imports includes 21 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 ‘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 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 ... 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 ... NOTE
Documented arguments not in \usage in Rd file 'generateLengthsPhylo.Rd':
‘lengths.lambda’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 18.625 1.101 19.854
DESeq2.createRmd 10.487 0.384 10.924
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.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: 1 NOTE
See
‘/Users/biocbuild/bbs-3.21-bioc/meat/compcodeR.Rcheck/00check.log’
for details.
compcodeR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL compcodeR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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
R Under development (unstable) (2024-11-20 r87352) -- "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.
> if (requireNamespace("testthat", quietly = TRUE)) {
+
+ library(testthat)
+ library(compcodeR)
+
+ test_check("compcodeR")
+
+ }
Loading required package: sm
Package 'sm', version 2.2-6.0: type help(sm) for summary information
2024-11-24 20:49:50.150 R[13534:480842176] XType: com.apple.fonts is not accessible.
2024-11-24 20:49:50.151 R[13534:480842176] XType: XTFontStaticRegistry is enabled.
[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.4.5.0.exact.TMM.movingave.tagwise on Sun Nov 24 20:50:12 2024 .
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.4.5.0.exact.TMM.movingave.tagwise on Sun Nov 24 20:50:12 2024 .
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.3.63.2.limma.TMM.lengthNorm.RPKM.dataTrans.log2.no_trend on Sun Nov 24 20:50:30 2024 .
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.3.63.2.limma.TMM.lengthNorm.RPKM.dataTrans.log2.no_trend on Sun Nov 24 20:50:30 2024 .
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
An object of class phyloCompData
Dataset name: B_625_625
Number of samples: 8
Number of variables: 489
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.3.63.2.limma.TMM.lengthNorm.TPM.dataTrans.log2.no_trend on Sun Nov 24 20:50:52 2024 .
count.matrix:
A1 A2 A3 B1 C1 C2
g1 2 2 3 5 16 5
g2 2 4 4 1 3 4
g3 8 17 18 43 128 97
g4 112 144 180 147 693 519
g5 42 50 36 39 318 236
g6 2144 2813 2980 244 407 301
+ 483 rows and 2 cols...
sample.annotations:
condition depth.factor id.species id.condition
A1 1 0.9345425 1 1
A2 1 1.1908725 1 1
A3 1 1.2883744 1 1
B1 1 1.3178424 2 1
C1 2 1.2366125 3 2
C2 2 0.9254193 3 2
+ 2 rows...
variable.annotations:
truedispersions.S1 truedispersions.S2 truemeans.S1 truemeans.S2
g1 0.30951552 0.30951552 9.438596 16.76493
g2 0.10717866 0.10717866 11.087719 17.83999
g3 0.26784154 0.26784154 64.024390 130.13981
g4 0.14093922 0.14093922 380.097561 1569.50731
g5 0.06477025 0.06477025 246.073171 491.17016
g6 0.47668995 0.47668995 306.536585 461.43426
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 1.7048375 2.424683
g2 0 0 0.3415076 1.577042
g3 0 0 2.5311743 5.327476
g4 0 0 2.0962388 8.065006
g5 0 0 2.8226257 6.646218
g6 0 0 -2.3683284 9.160340
truelog2foldchanges upregulation downregulation differential.expression
g1 0.8288024 1 0 1
g2 0.6861520 1 0 1
g3 1.0233688 1 0 1
g4 2.0458701 1 0 1
g5 0.9971356 1 0 1
g6 0.5900659 1 0 1
prop.var.tree lengths.relmeans lengths.dispersions M.value.TPM A.value.TPM
g1 1 6468.643 0.5912307 1.100579 -9.389239
g2 1 2321.214 0.1018562 1.044485 -9.827207
g3 1 7789.857 1.5129387 1.226028 -6.795971
g4 1 3893.429 1.1472771 2.220931 -3.725295
g5 1 3626.786 1.2262940 1.524808 -4.967721
g6 1 9735.071 0.4032376 -1.871160 -4.437845
+ 483 rows...
Differential expression results:
pvalue adjpvalue logFC score
g1 1.358626e-02 0.0671079008 1.074670 0.9864137
g2 7.770022e-02 0.2122648431 1.018576 0.9222998
g3 1.423563e-01 0.3149875048 1.200119 0.8576437
g4 1.801480e-06 0.0004404618 2.195022 0.9999982
g5 2.877064e-04 0.0060718212 1.498899 0.9997123
g6 3.713227e-03 0.0275116347 -1.897069 0.9962868
+ 483 rows...
Phylogenetic tree:
Phylogenetic tree with 8 tips and 6 internal nodes.
Tip labels:
A1, A2, A3, B1, C1, C2, ...
Rooted; includes branch lengths.
length.matrix:
A1 A2 A3 B1 C1 C2
g1 2757 2757 2757 3086 3896 3896
g2 3699 3699 3699 2513 2002 2002
g3 1983 1983 1983 7404 3283 3283
g4 3651 3651 3651 3419 3521 3521
g5 2144 2144 2144 1441 6609 6609
g6 18805 18805 18805 6302 20047 20047
An object of class phyloCompData
Dataset name: B_625_625
Number of samples: 4
Number of variables: 489
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.3.63.2.limma.TMM.lengthNorm.TPM.dataTrans.log2.no_trend on Sun Nov 24 20:50:52 2024 .
count.matrix:
A1 A2 A3 B1
g1 2 2 3 5
g2 2 4 4 1
g3 8 17 18 43
g4 112 144 180 147
g5 42 50 36 39
g6 2144 2813 2980 244
+ 483 rows...
sample.annotations:
condition depth.factor id.species id.condition
A1 1 0.9345425 1 1
A2 1 1.1908725 1 1
A3 1 1.2883744 1 1
B1 1 1.3178424 2 1
C1 2 1.2366125 3 2
C2 2 0.9254193 3 2
+ 2 rows...
variable.annotations:
truedispersions.S1 truedispersions.S2 truemeans.S1 truemeans.S2
g1 0.30951552 0.30951552 9.438596 16.76493
g2 0.10717866 0.10717866 11.087719 17.83999
g3 0.26784154 0.26784154 64.024390 130.13981
g4 0.14093922 0.14093922 380.097561 1569.50731
g5 0.06477025 0.06477025 246.073171 491.17016
g6 0.47668995 0.47668995 306.536585 461.43426
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 1.7048375 2.424683
g2 0 0 0.3415076 1.577042
g3 0 0 2.5311743 5.327476
g4 0 0 2.0962388 8.065006
g5 0 0 2.8226257 6.646218
g6 0 0 -2.3683284 9.160340
truelog2foldchanges upregulation downregulation differential.expression
g1 0.8288024 1 0 1
g2 0.6861520 1 0 1
g3 1.0233688 1 0 1
g4 2.0458701 1 0 1
g5 0.9971356 1 0 1
g6 0.5900659 1 0 1
prop.var.tree lengths.relmeans lengths.dispersions M.value.TPM A.value.TPM
g1 1 6468.643 0.5912307 1.100579 -9.389239
g2 1 2321.214 0.1018562 1.044485 -9.827207
g3 1 7789.857 1.5129387 1.226028 -6.795971
g4 1 3893.429 1.1472771 2.220931 -3.725295
g5 1 3626.786 1.2262940 1.524808 -4.967721
g6 1 9735.071 0.4032376 -1.871160 -4.437845
+ 483 rows...
Differential expression results:
pvalue adjpvalue logFC score
g1 1.358626e-02 0.0671079008 1.074670 0.9864137
g2 7.770022e-02 0.2122648431 1.018576 0.9222998
g3 1.423563e-01 0.3149875048 1.200119 0.8576437
g4 1.801480e-06 0.0004404618 2.195022 0.9999982
g5 2.877064e-04 0.0060718212 1.498899 0.9997123
g6 3.713227e-03 0.0275116347 -1.897069 0.9962868
+ 483 rows...
Phylogenetic tree:
Phylogenetic tree with 8 tips and 6 internal nodes.
Tip labels:
A1, A2, A3, B1, C1, C2, ...
Rooted; includes branch lengths.
length.matrix:
A1 A2 A3 B1 C1 C2
g1 2757 2757 2757 3086 3896 3896
g2 3699 3699 3699 2513 2002 2002
g3 1983 1983 1983 7404 3283 3283
g4 3651 3651 3651 3419 3521 3521
g5 2144 2144 2144 1441 6609 6609
g6 18805 18805 18805 6302 20047 20047
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1413 ]
>
> proc.time()
user system elapsed
230.792 22.248 256.659
compcodeR.Rcheck/compcodeR-Ex.timings
| name | user | system | elapsed | |
| DESeq2.createRmd | 10.487 | 0.384 | 10.924 | |
| DESeq2.length.createRmd | 0.411 | 0.023 | 0.436 | |
| DSS.createRmd | 4.749 | 0.234 | 4.999 | |
| EBSeq.createRmd | 0.924 | 0.083 | 1.012 | |
| NBPSeq.createRmd | 18.625 | 1.101 | 19.854 | |
| NOISeq.prenorm.createRmd | 1.661 | 0.106 | 1.776 | |
| TCC.createRmd | 1.593 | 0.094 | 1.702 | |
| checkDataObject | 0.153 | 0.003 | 0.154 | |
| checkTableConsistency | 0.690 | 0.059 | 0.757 | |
| check_compData | 0.154 | 0.003 | 0.157 | |
| check_compData_results | 0.390 | 0.030 | 0.422 | |
| check_phyloCompData | 0.415 | 0.041 | 0.462 | |
| compData | 0.001 | 0.001 | 0.002 | |
| convertListTocompData | 0.002 | 0.000 | 0.003 | |
| convertListTophyloCompData | 0.007 | 0.001 | 0.009 | |
| convertcompDataToList | 1.972 | 0.094 | 2.074 | |
| convertphyloCompDataToList | 0.147 | 0.001 | 0.149 | |
| edgeR.GLM.createRmd | 0.616 | 0.028 | 0.648 | |
| edgeR.exact.createRmd | 0.475 | 0.034 | 0.512 | |
| generateCodeHTMLs | 0.560 | 0.084 | 0.781 | |
| generateSyntheticData | 0.379 | 0.003 | 0.382 | |
| lengthNorm.limma.createRmd | 0.302 | 0.015 | 0.318 | |
| lengthNorm.sva.limma.createRmd | 1.009 | 0.124 | 1.137 | |
| listcreateRmd | 0.009 | 0.000 | 0.009 | |
| logcpm.limma.createRmd | 0.323 | 0.026 | 0.350 | |
| nEffRatio | 0.224 | 0.002 | 0.226 | |
| phyloCompData | 0.005 | 0.000 | 0.005 | |
| phylolm.createRmd | 0.345 | 0.015 | 0.363 | |
| runComparison | 0.661 | 0.054 | 0.719 | |
| runComparisonGUI | 0.001 | 0.000 | 0.000 | |
| runComparisonShiny | 0.001 | 0.001 | 0.001 | |
| runDiffExp | 0.380 | 0.029 | 0.413 | |
| show-compData-method | 1.969 | 0.038 | 2.010 | |
| show-phyloCompData-method | 0.310 | 0.008 | 0.320 | |
| sqrtcpm.limma.createRmd | 0.314 | 0.029 | 0.344 | |
| summarizeSyntheticDataSet | 0.182 | 0.003 | 0.187 | |
| ttest.createRmd | 0.441 | 0.103 | 0.546 | |
| voom.limma.createRmd | 0.363 | 0.027 | 0.392 | |
| voom.ttest.createRmd | 0.347 | 0.030 | 0.379 | |