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This page was generated on 2024-12-24 11:39 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4373
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 409/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
compcodeR 1.43.0  (landing page)
Charlotte Soneson
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/compcodeR
git_branch: devel
git_last_commit: e1b50cd
git_last_commit_date: 2024-12-21 12:49:41 -0500 (Sat, 21 Dec 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for compcodeR on nebbiolo1

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.

raw results


Summary

Package: compcodeR
Version: 1.43.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:compcodeR.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings compcodeR_1.43.0.tar.gz
StartedAt: 2024-12-23 20:50:59 -0500 (Mon, 23 Dec 2024)
EndedAt: 2024-12-23 20:56:09 -0500 (Mon, 23 Dec 2024)
EllapsedTime: 309.4 seconds
RetCode: 0
Status:   OK  
CheckDir: compcodeR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:compcodeR.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings compcodeR_1.43.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/compcodeR.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* 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 ... 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 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 ... 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 20.216  0.847  21.065
DESeq2.createRmd 12.514  0.591  13.110
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/compcodeR.Rcheck/00check.log’
for details.


Installation output

compcodeR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL compcodeR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/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)

Tests output

compcodeR.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 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
 [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.4.5.1.exact.TMM.movingave.tagwise on Mon Dec 23 20:53:38 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.4.5.1.exact.TMM.movingave.tagwise on Mon Dec 23 20:53:38 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 Mon Dec 23 20:54:02 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 Mon Dec 23 20:54:02 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 Mon Dec 23 20:54:18 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 length(s).

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 Mon Dec 23 20:54:18 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 length(s).

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 1401 ]
> 
> proc.time()
   user  system elapsed 
167.987   8.854 176.993 

Example timings

compcodeR.Rcheck/compcodeR-Ex.timings

nameusersystemelapsed
DESeq2.createRmd12.514 0.59113.110
DESeq2.length.createRmd0.5870.0400.626
DSS.createRmd0.0010.0000.001
EBSeq.createRmd1.1060.0281.134
NBPSeq.createRmd20.216 0.84721.065
NOISeq.prenorm.createRmd2.0540.0502.106
TCC.createRmd1.9680.0312.003
checkDataObject0.1940.0000.194
checkTableConsistency0.8150.0280.843
check_compData0.1920.0040.195
check_compData_results0.4830.0140.498
check_phyloCompData0.5140.0160.532
compData0.0010.0010.002
convertListTocompData0.0020.0010.004
convertListTophyloCompData0.0090.0010.011
convertcompDataToList2.5150.0952.610
convertphyloCompDataToList0.1970.0000.197
edgeR.GLM.createRmd0.760.010.77
edgeR.exact.createRmd0.5610.0140.576
generateCodeHTMLs0.6780.0720.760
generateSyntheticData0.5260.0050.531
lengthNorm.limma.createRmd0.3360.0050.340
lengthNorm.sva.limma.createRmd1.6040.0851.689
listcreateRmd0.0070.0010.008
logcpm.limma.createRmd0.3980.0200.419
nEffRatio0.2890.0290.318
phyloCompData0.0060.0000.006
phylolm.createRmd0.4000.0160.417
runComparison0.8090.0150.824
runComparisonGUI0.0010.0000.001
runComparisonShiny0.0000.0010.000
runDiffExp0.4760.0220.498
show-compData-method2.5530.0192.572
show-phyloCompData-method0.5110.0090.520
sqrtcpm.limma.createRmd0.3870.0050.392
summarizeSyntheticDataSet0.2110.0000.212
ttest.createRmd0.4080.0070.415
voom.limma.createRmd0.4700.0070.476
voom.ttest.createRmd0.4510.0210.471