Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-09 21:30 -0500 (Sat, 09 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4505 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4506 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4538 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4486 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 416/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
compcodeR 1.42.0 (landing page) Charlotte Soneson
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | 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: 1.42.0 |
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_1.42.0.tar.gz |
StartedAt: 2024-11-08 23:26:21 -0500 (Fri, 08 Nov 2024) |
EndedAt: 2024-11-08 23:32:47 -0500 (Fri, 08 Nov 2024) |
EllapsedTime: 386.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: compcodeR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_1.42.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/compcodeR.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-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 Ventura 13.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘compcodeR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘compcodeR’ version ‘1.42.0’ * 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' 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 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 7.843 0.503 8.358 * 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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.20-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/4.4-arm64/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 version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-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 2024-11-08 23:30:55.790 R[8477:4175753] XType: Using static font registry. [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.4.4.0.exact.TMM.movingave.tagwise on Fri Nov 8 23:31:04 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.4.4.0.exact.TMM.movingave.tagwise on Fri Nov 8 23:31:04 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.3.62.1.limma.TMM.lengthNorm.RPKM.dataTrans.log2.no_trend on Fri Nov 8 23:31:12 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.3.62.1.limma.TMM.lengthNorm.RPKM.dataTrans.log2.no_trend on Fri Nov 8 23:31:12 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.3.62.1.limma.TMM.lengthNorm.TPM.dataTrans.log2.no_trend on Fri Nov 8 23:31:22 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.3.62.1.limma.TMM.lengthNorm.TPM.dataTrans.log2.no_trend on Fri Nov 8 23:31:22 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 103.096 12.485 116.145
compcodeR.Rcheck/compcodeR-Ex.timings
name | user | system | elapsed | |
DESeq2.createRmd | 3.941 | 0.108 | 4.052 | |
DESeq2.length.createRmd | 0.148 | 0.005 | 0.154 | |
DSS.createRmd | 2.035 | 0.066 | 2.101 | |
EBSeq.createRmd | 0.389 | 0.031 | 0.421 | |
NBPSeq.createRmd | 7.843 | 0.503 | 8.358 | |
NOISeq.prenorm.createRmd | 0.638 | 0.030 | 0.668 | |
TCC.createRmd | 0.626 | 0.034 | 0.663 | |
checkDataObject | 0.065 | 0.001 | 0.066 | |
checkTableConsistency | 0.299 | 0.017 | 0.316 | |
check_compData | 0.062 | 0.001 | 0.063 | |
check_compData_results | 0.148 | 0.008 | 0.156 | |
check_phyloCompData | 0.177 | 0.012 | 0.190 | |
compData | 0.000 | 0.000 | 0.001 | |
convertListTocompData | 0.001 | 0.001 | 0.001 | |
convertListTophyloCompData | 0.003 | 0.000 | 0.003 | |
convertcompDataToList | 0.895 | 0.020 | 0.916 | |
convertphyloCompDataToList | 0.066 | 0.001 | 0.066 | |
edgeR.GLM.createRmd | 0.233 | 0.011 | 0.244 | |
edgeR.exact.createRmd | 0.230 | 0.011 | 0.241 | |
generateCodeHTMLs | 0.349 | 0.040 | 0.411 | |
generateSyntheticData | 0.163 | 0.004 | 0.168 | |
lengthNorm.limma.createRmd | 0.126 | 0.004 | 0.130 | |
lengthNorm.sva.limma.createRmd | 0.412 | 0.031 | 0.442 | |
listcreateRmd | 0.004 | 0.000 | 0.004 | |
logcpm.limma.createRmd | 0.137 | 0.010 | 0.147 | |
nEffRatio | 0.095 | 0.001 | 0.098 | |
phyloCompData | 0.002 | 0.000 | 0.002 | |
phylolm.createRmd | 0.139 | 0.005 | 0.144 | |
runComparison | 0.303 | 0.025 | 0.328 | |
runComparisonGUI | 0.001 | 0.000 | 0.001 | |
runComparisonShiny | 0 | 0 | 0 | |
runDiffExp | 0.177 | 0.013 | 0.190 | |
show-compData-method | 0.837 | 0.021 | 0.858 | |
show-phyloCompData-method | 0.131 | 0.004 | 0.135 | |
sqrtcpm.limma.createRmd | 0.143 | 0.011 | 0.154 | |
summarizeSyntheticDataSet | 0.087 | 0.002 | 0.089 | |
ttest.createRmd | 0.147 | 0.009 | 0.156 | |
voom.limma.createRmd | 0.176 | 0.012 | 0.188 | |
voom.ttest.createRmd | 0.151 | 0.011 | 0.161 | |