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This page was generated on 2025-10-16 11:41 -0400 (Thu, 16 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.6 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.7.5 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4555
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4586
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 1512/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OUTRIDER 1.26.3  (landing page)
Christian Mertes
Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025)
git_url: https://git.bioconductor.org/packages/OUTRIDER
git_branch: RELEASE_3_21
git_last_commit: 174dc26
git_last_commit_date: 2025-07-28 15:29:40 -0400 (Mon, 28 Jul 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.7.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    ERROR  


CHECK results for OUTRIDER on kunpeng2

To the developers/maintainers of the OUTRIDER package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/OUTRIDER.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: OUTRIDER
Version: 1.26.3
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:OUTRIDER.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings OUTRIDER_1.26.3.tar.gz
StartedAt: 2025-10-14 12:16:37 -0000 (Tue, 14 Oct 2025)
EndedAt: 2025-10-14 12:26:37 -0000 (Tue, 14 Oct 2025)
EllapsedTime: 600.8 seconds
RetCode: 1
Status:   ERROR  
CheckDir: OUTRIDER.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:OUTRIDER.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings OUTRIDER_1.26.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/OUTRIDER.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OUTRIDER/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OUTRIDER’ version ‘1.26.3’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 22 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 ‘OUTRIDER’ can be installed ... OK
* used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* 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 ... NOTE
Unexported object imported by a ':::' call: 'ggbio:::.buildFacetsFromArgs'
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'checkOutriderDataSet'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
estimateBestQ: no visible binding for global variable ‘oht’
plotEncDimSearch.OUTRIDER: no visible binding for global variable ‘oht’
plotEncDimSearch.OUTRIDER: no visible binding for global variable
  ‘singular_values’
plotEncDimSearch,OutriderDataSet: no visible binding for global
  variable ‘oht’
plotEncDimSearch,OutriderDataSet: no visible binding for global
  variable ‘singular_values’
Undefined global functions or variables:
  oht singular_values
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Non-topic package-anchored link(s) in Rd file 'getter_setter_functions.Rd':
  ‘[DESeq2]{estimateDispersions}’

Non-topic package-anchored link(s) in Rd file 'sizeFactors.Rd':
  ‘[DESeq2]{estimateSizeFactors}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘OUTRIDER-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: OUTRIDER
> ### Title: OUTRIDER - Finding expression outlier events
> ### Aliases: OUTRIDER
> 
> ### ** Examples
> 
> ods <- makeExampleOutriderDataSet()
> implementation <- 'autoencoder'
> ## Don't show: 
>     ods <- ods[1:10,1:10]
>     implementation <- 'pca'
> ## End(Don't show)
> ods <- OUTRIDER(ods, implementation=implementation)
Tue Oct 14 12:24:39 2025: SizeFactor estimation ...
Tue Oct 14 12:24:39 2025: Controlling for confounders ...
Using provided q with: 10
Tue Oct 14 12:24:39 2025: Using the pca implementation for controlling.
Tue Oct 14 12:24:40 2025: Used the pca implementation for controlling.
Tue Oct 14 12:24:40 2025: Fitting the data ...
Tue Oct 14 12:24:44 2025: P-value calculation ...
Tue Oct 14 12:24:45 2025: Zscore calculation ...
> 
> pValue(ods)[1:10,1:10]
            sample_1  sample_2  sample_3  sample_4  sample_5  sample_6
feature_1  0.9708112 0.9673898 1.0000000 1.0000000 0.9682199 0.9715971
feature_2  1.0000000 0.9645359 0.9956326 0.9691272 0.9565509 1.0000000
feature_3  0.9956214 1.0000000 0.9817906 0.9714409 0.9874758 1.0000000
feature_4  0.9172160 1.0000000 0.8531784 0.9520697 0.9681790 0.9964730
feature_5  0.9341059 0.9465044 0.8974455 0.9659065 1.0000000 1.0000000
feature_6  0.9589618 0.9899073 0.8672567 1.0000000 1.0000000 0.8466523
feature_7  0.9996636 0.9941701 0.9987946 0.9951733 0.9949322 0.9736942
feature_8  1.0000000 0.9589015 0.8852728 1.0000000 0.9101463 0.8960677
feature_9  0.9944175 0.9819508 0.9432241 1.0000000 0.9670230 1.0000000
feature_10 1.0000000 0.9713634 1.0000000 0.9862026 0.9942747 0.9858947
            sample_7  sample_8  sample_9 sample_10
feature_1  0.9654920 1.0000000 0.9479204 0.9599123
feature_2  1.0000000 0.9600617 0.9691272 0.9950102
feature_3  0.9944387 0.9835739 1.0000000 1.0000000
feature_4  0.9738876 0.9834010 0.9285130 0.9901875
feature_5  0.9985055 1.0000000 0.9314466 1.0000000
feature_6  0.9361394 0.9962628 0.9703490 0.9706844
feature_7  1.0000000 1.0000000 0.9939868 0.9878672
feature_8  0.9879651 0.9976097 0.9930988 0.9906877
feature_9  1.0000000 0.9898412 0.9810968 1.0000000
feature_10 0.9773213 0.9988272 1.0000000 1.0000000
> res <- results(ods, all=TRUE)
> res
Key: <geneID, sampleID>
         geneID  sampleID    pValue padjust zScore  l2fc rawcounts
         <char>    <char>     <num>   <num>  <num> <num>     <int>
  1:  feature_1  sample_1 0.9708112       1  -0.26 -0.02        58
  2:  feature_1 sample_10 0.9599123       1  -0.99 -0.04        35
  3:  feature_1  sample_2 0.9673898       1  -0.46 -0.03        49
  4:  feature_1  sample_3 1.0000000       1   0.74  0.00       434
  5:  feature_1  sample_4 1.0000000       1   0.83  0.00      1052
  6:  feature_1  sample_5 0.9682199       1  -0.41 -0.03        51
  7:  feature_1  sample_6 0.9715971       1   0.88  0.00      4121
  8:  feature_1  sample_7 0.9654920       1   0.89  0.00      5031
  9:  feature_1  sample_8 1.0000000       1   0.80  0.00       691
 10:  feature_1  sample_9 0.9479204       1  -2.03 -0.06        22
 11: feature_10  sample_1 1.0000000       1   0.54  0.00      1449
 12: feature_10 sample_10 1.0000000       1   0.66  0.00      2818
 13: feature_10  sample_2 0.9713634       1   0.77  0.00     27702
 14: feature_10  sample_3 1.0000000       1   0.57  0.00      1673
 15: feature_10  sample_4 0.9862026       1  -0.71 -0.01       238
 16: feature_10  sample_5 0.9942747       1   0.17  0.00       580
 17: feature_10  sample_6 0.9858947       1  -0.75 -0.01       231
 18: feature_10  sample_7 0.9773213       1  -2.37 -0.01       112
 19: feature_10  sample_8 0.9988272       1   0.44  0.00      1036
 20: feature_10  sample_9 1.0000000       1   0.67  0.00      2984
 21:  feature_2  sample_1 1.0000000       1   0.76  0.00      1033
 22:  feature_2 sample_10 0.9950102       1   0.50 -0.01       241
 23:  feature_2  sample_2 0.9645359       1  -1.10 -0.03        42
 24:  feature_2  sample_3 0.9956326       1   0.79  0.00      1592
 25:  feature_2  sample_4 0.9691272       1  -0.74 -0.03        52
 26:  feature_2  sample_5 0.9565509       1  -1.84 -0.05        30
 27:  feature_2  sample_6 1.0000000       1   0.78  0.00      1247
 28:  feature_2  sample_7 1.0000000       1   0.76  0.00      1041
 29:  feature_2  sample_8 0.9600617       1   0.83  0.00      5113
 30:  feature_2  sample_9 0.9691272       1  -0.74 -0.03        52
 31:  feature_3  sample_1 0.9956214       1  -0.04  0.00       404
 32:  feature_3 sample_10 1.0000000       1   0.59  0.00      1238
 33:  feature_3  sample_2 1.0000000       1   0.67  0.00      1690
 34:  feature_3  sample_3 0.9817906       1  -1.96 -0.01       130
 35:  feature_3  sample_4 0.9714409       1   0.84  0.00      8658
 36:  feature_3  sample_5 0.9874758       1   0.80  0.00      4329
 37:  feature_3  sample_6 1.0000000       1   0.32  0.00       657
 38:  feature_3  sample_7 0.9944387       1  -0.14  0.00       363
 39:  feature_3  sample_8 0.9835739       1  -1.62 -0.01       148
 40:  feature_3  sample_9 1.0000000       1   0.54  0.00      1062
 41:  feature_4  sample_1 0.9172160       1  -0.67 -0.17         7
 42:  feature_4 sample_10 0.9901875       1   0.39 -0.03        48
 43:  feature_4  sample_2 1.0000000       1   0.57 -0.01       235
 44:  feature_4  sample_3 0.8531784       1  -2.53 -0.42         2
 45:  feature_4  sample_4 0.9520697       1   0.59  0.00       541
 46:  feature_4  sample_5 0.9681790       1   0.59  0.00       427
 47:  feature_4  sample_6 0.9964730       1   0.57 -0.01       278
 48:  feature_4  sample_7 0.9738876       1   0.58  0.00       392
 49:  feature_4  sample_8 0.9834010       1   0.34 -0.04        39
 50:  feature_4  sample_9 0.9285130       1  -0.43 -0.14         9
 51:  feature_5  sample_1 0.9341059       1   0.88  0.00       336
 52:  feature_5 sample_10 1.0000000       1   0.73 -0.01       120
 53:  feature_5  sample_2 0.9465044       1  -1.33 -0.12        11
 54:  feature_5  sample_3 0.8974455       1   0.91  0.00       497
 55:  feature_5  sample_4 0.9659065       1  -0.58 -0.08        17
 56:  feature_5  sample_5 1.0000000       1   0.29 -0.03        41
 57:  feature_5  sample_6 1.0000000       1   0.45 -0.03        54
 58:  feature_5  sample_7 0.9985055       1   0.22 -0.04        37
 59:  feature_5  sample_8 1.0000000       1   0.47 -0.03        56
 60:  feature_5  sample_9 0.9314466       1  -2.05 -0.15         8
 61:  feature_6  sample_1 0.9589618       1   0.35 -0.04        39
 62:  feature_6 sample_10 0.9706844       1   0.45 -0.02        74
 63:  feature_6  sample_2 0.9899073       1   0.56  0.00       398
 64:  feature_6  sample_3 0.8672567       1  -1.54 -0.32         3
 65:  feature_6  sample_4 1.0000000       1   0.58  0.00      2050
 66:  feature_6  sample_5 1.0000000       1   0.58  0.00      2075
 67:  feature_6  sample_6 0.8466523       1  -2.16 -0.42         2
 68:  feature_6  sample_7 0.9361394       1   0.04 -0.08        16
 69:  feature_6  sample_8 0.9962628       1   0.57  0.00       939
 70:  feature_6  sample_9 0.9703490       1   0.58  0.00     59866
 71:  feature_7  sample_1 0.9996636       1   0.27  0.00      1095
 72:  feature_7 sample_10 0.9878672       1  -2.29 -0.01       275
 73:  feature_7  sample_2 0.9941701       1   0.99  0.00      6690
 74:  feature_7  sample_3 0.9987946       1   0.16  0.00       980
 75:  feature_7  sample_4 0.9951733       1  -0.39  0.00       623
 76:  feature_7  sample_5 0.9949322       1  -0.43  0.00       605
 77:  feature_7  sample_6 0.9736942       1   1.09  0.00     23938
 78:  feature_7  sample_7 1.0000000       1   0.67  0.00      2051
 79:  feature_7  sample_8 1.0000000       1   0.56  0.00      1647
 80:  feature_7  sample_9 0.9939868       1  -0.62  0.00       540
 81:  feature_8  sample_1 1.0000000       1   0.56 -0.01       217
 82:  feature_8 sample_10 0.9906877       1   0.46 -0.02        90
 83:  feature_8  sample_2 0.9589015       1   0.09 -0.05        26
 84:  feature_8  sample_3 0.8852728       1  -2.08 -0.26         4
 85:  feature_8  sample_4 1.0000000       1   0.58  0.00       323
 86:  feature_8  sample_5 0.9101463       1   0.62  0.00      3174
 87:  feature_8  sample_6 0.8960677       1  -1.66 -0.22         5
 88:  feature_8  sample_7 0.9879651       1   0.44 -0.02        80
 89:  feature_8  sample_8 0.9976097       1   0.51 -0.01       122
 90:  feature_8  sample_9 0.9930988       1   0.48 -0.01       100
 91:  feature_9  sample_1 0.9944175       1   0.34  0.00       503
 92:  feature_9 sample_10 1.0000000       1   0.45  0.00      2206
 93:  feature_9  sample_2 0.9819508       1   0.02 -0.01       152
 94:  feature_9  sample_3 0.9432241       1  -2.80 -0.07        20
 95:  feature_9  sample_4 1.0000000       1   0.44  0.00      1830
 96:  feature_9  sample_5 0.9670230       1   0.47  0.00     22553
 97:  feature_9  sample_6 1.0000000       1   0.41  0.00      1030
 98:  feature_9  sample_7 1.0000000       1   0.44  0.00      1934
 99:  feature_9  sample_8 0.9898412       1   0.25  0.00       310
100:  feature_9  sample_9 0.9810968       1  -0.01 -0.01       142
         geneID  sampleID    pValue padjust zScore  l2fc rawcounts
     meanRawcounts normcounts meanCorrected     theta aberrant AberrantBySample
             <num>      <num>         <num>     <num>   <lgcl>            <num>
  1:        1154.4     242.52        243.43 120191.17    FALSE                0
  2:        1154.4     239.85        243.43 120191.17    FALSE                0
  3:        1154.4     241.77        243.43 120191.17    FALSE                0
  4:        1154.4     246.13        243.43 120191.17    FALSE                0
  5:        1154.4     246.47        243.43 120191.17    FALSE                0
  6:        1154.4     241.96        243.43 120191.17    FALSE                0
  7:        1154.4     246.64        243.43 120191.17    FALSE                0
  8:        1154.4     246.65        243.43 120191.17    FALSE                0
  9:        1154.4     246.35        243.43 120191.17    FALSE                0
 10:        1154.4     235.98        243.43 120191.17    FALSE                0
 11:        3882.3    1078.11       1076.47 244289.23    FALSE                0
 12:        3882.3    1078.47       1076.47 244289.23    FALSE                0
 13:        3882.3    1078.81       1076.47 244289.23    FALSE                0
 14:        3882.3    1078.21       1076.47 244289.23    FALSE                0
 15:        3882.3    1074.34       1076.47 244289.23    FALSE                0
 16:        3882.3    1076.99       1076.47 244289.23    FALSE                0
 17:        3882.3    1074.20       1076.47 244289.23    FALSE                0
 18:        3882.3    1069.30       1076.47 244289.23    FALSE                0
 19:        3882.3    1077.81       1076.47 244289.23    FALSE                0
 20:        3882.3    1078.49       1076.47 244289.23    FALSE                0
 21:        1044.3     315.69        312.80 124394.23    FALSE                0
 22:        1044.3     314.69        312.80 124394.23    FALSE                0
 23:        1044.3     308.64        312.80 124394.23    FALSE                0
 24:        1044.3     315.79        312.80 124394.23    FALSE                0
 25:        1044.3     310.03        312.80 124394.23    FALSE                0
 26:        1044.3     305.80        312.80 124394.23    FALSE                0
 27:        1044.3     315.74        312.80 124394.23    FALSE                0
 28:        1044.3     315.69        312.80 124394.23    FALSE                0
 29:        1044.3     315.93        312.80 124394.23    FALSE                0
 30:        1044.3     310.03        312.80 124394.23    FALSE                0
 31:        1867.9     829.51        829.59 144900.44    FALSE                0
 32:        1867.9     830.89        829.59 144900.44    FALSE                0
 33:        1867.9     831.07        829.59 144900.44    FALSE                0
 34:        1867.9     825.21        829.59 144900.44    FALSE                0
 35:        1867.9     831.47        829.59 144900.44    FALSE                0
 36:        1867.9     831.37        829.59 144900.44    FALSE                0
 37:        1867.9     830.30        829.59 144900.44    FALSE                0
 38:        1867.9     829.28        829.59 144900.44    FALSE                0
 39:        1867.9     825.98        829.59 144900.44    FALSE                0
 40:        1867.9     830.78        829.59 144900.44    FALSE                0
 41:         197.8      61.25         65.67 102654.97    FALSE                0
 42:         197.8      68.57         65.67 102654.97    FALSE                0
 43:         197.8      69.70         65.67 102654.97    FALSE                0
 44:         197.8      46.66         65.67 102654.97    FALSE                0
 45:         197.8      69.87         65.67 102654.97    FALSE                0
 46:         197.8      69.83         65.67 102654.97    FALSE                0
 47:         197.8      69.75         65.67 102654.97    FALSE                0
 48:         197.8      69.82         65.67 102654.97    FALSE                0
 49:         197.8      68.25         65.67 102654.97    FALSE                0
 50:         197.8      63.00         65.67 102654.97    FALSE                0
 51:         117.7      53.49         51.78  64681.51    FALSE                0
 52:         117.7      53.21         51.78  64681.51    FALSE                0
 53:         117.7      49.18         51.78  64681.51    FALSE                0
 54:         117.7      53.54         51.78  64681.51    FALSE                0
 55:         117.7      50.67         51.78  64681.51    FALSE                0
 56:         117.7      52.37         51.78  64681.51    FALSE                0
 57:         117.7      52.67         51.78  64681.51    FALSE                0
 58:         117.7      52.24         51.78  64681.51    FALSE                0
 59:         117.7      52.71         51.78  64681.51    FALSE                0
 60:         117.7      47.69         51.78  64681.51    FALSE                0
 61:        6546.2     184.39        176.16 153439.14    FALSE                0
 62:        6546.2     186.59        176.16 153439.14    FALSE                0
 63:        6546.2     188.64        176.16 153439.14    FALSE                0
 64:        6546.2     141.84        176.16 153439.14    FALSE                0
 65:        6546.2     189.02        176.16 153439.14    FALSE                0
 66:        6546.2     189.02        176.16 153439.14    FALSE                0
 67:        6546.2     126.08        176.16 153439.14    FALSE                0
 68:        6546.2     177.99        176.16 153439.14    FALSE                0
 69:        6546.2     188.91        176.16 153439.14    FALSE                0
 70:        6546.2     189.11        176.16 153439.14    FALSE                0
 71:        3844.4    1416.78       1416.38 107550.29    FALSE                0
 72:        3844.4    1412.93       1416.38 107550.29    FALSE                0
 73:        3844.4    1417.86       1416.38 107550.29    FALSE                0
 74:        3844.4    1416.62       1416.38 107550.29    FALSE                0
 75:        3844.4    1415.80       1416.38 107550.29    FALSE                0
 76:        3844.4    1415.73       1416.38 107550.29    FALSE                0
 77:        3844.4    1418.01       1416.38 107550.29    FALSE                0
 78:        3844.4    1417.38       1416.38 107550.29    FALSE                0
 79:        3844.4    1417.21       1416.38 107550.29    FALSE                0
 80:        3844.4    1415.45       1416.38 107550.29    FALSE                0
 81:         414.1      83.20         79.79 176319.66    FALSE                0
 82:         414.1      82.66         79.79 176319.66    FALSE                0
 83:         414.1      80.48         79.79 176319.66    FALSE                0
 84:         414.1      66.86         79.79 176319.66    FALSE                0
 85:         414.1      83.32         79.79 176319.66    FALSE                0
 86:         414.1      83.55         79.79 176319.66    FALSE                0
 87:         414.1      69.65         79.79 176319.66    FALSE                0
 88:         414.1      82.55         79.79 176319.66    FALSE                0
 89:         414.1      82.90         79.79 176319.66    FALSE                0
 90:         414.1      82.75         79.79 176319.66    FALSE                0
 91:        3068.0     646.91        643.74 201806.58    FALSE                0
 92:        3068.0     647.91        643.74 201806.58    FALSE                0
 93:        3068.0     643.96        643.74 201806.58    FALSE                0
 94:        3068.0     617.33        643.74 201806.58    FALSE                0
 95:        3068.0     647.85        643.74 201806.58    FALSE                0
 96:        3068.0     648.17        643.74 201806.58    FALSE                0
 97:        3068.0     647.57        643.74 201806.58    FALSE                0
 98:        3068.0     647.87        643.74 201806.58    FALSE                0
 99:        3068.0     646.12        643.74 201806.58    FALSE                0
100:        3068.0     643.67        643.74 201806.58    FALSE                0
     meanRawcounts normcounts meanCorrected     theta aberrant AberrantBySample
     AberrantByGene padj_rank
              <num>     <num>
  1:              0       5.5
  2:              0       5.5
  3:              0       5.5
  4:              0       5.5
  5:              0       5.5
  6:              0       5.5
  7:              0       5.5
  8:              0       5.5
  9:              0       5.5
 10:              0       5.5
 11:              0       5.5
 12:              0       5.5
 13:              0       5.5
 14:              0       5.5
 15:              0       5.5
 16:              0       5.5
 17:              0       5.5
 18:              0       5.5
 19:              0       5.5
 20:              0       5.5
 21:              0       5.5
 22:              0       5.5
 23:              0       5.5
 24:              0       5.5
 25:              0       5.5
 26:              0       5.5
 27:              0       5.5
 28:              0       5.5
 29:              0       5.5
 30:              0       5.5
 31:              0       5.5
 32:              0       5.5
 33:              0       5.5
 34:              0       5.5
 35:              0       5.5
 36:              0       5.5
 37:              0       5.5
 38:              0       5.5
 39:              0       5.5
 40:              0       5.5
 41:              0       5.5
 42:              0       5.5
 43:              0       5.5
 44:              0       5.5
 45:              0       5.5
 46:              0       5.5
 47:              0       5.5
 48:              0       5.5
 49:              0       5.5
 50:              0       5.5
 51:              0       5.5
 52:              0       5.5
 53:              0       5.5
 54:              0       5.5
 55:              0       5.5
 56:              0       5.5
 57:              0       5.5
 58:              0       5.5
 59:              0       5.5
 60:              0       5.5
 61:              0       5.5
 62:              0       5.5
 63:              0       5.5
 64:              0       5.5
 65:              0       5.5
 66:              0       5.5
 67:              0       5.5
 68:              0       5.5
 69:              0       5.5
 70:              0       5.5
 71:              0       5.5
 72:              0       5.5
 73:              0       5.5
 74:              0       5.5
 75:              0       5.5
 76:              0       5.5
 77:              0       5.5
 78:              0       5.5
 79:              0       5.5
 80:              0       5.5
 81:              0       5.5
 82:              0       5.5
 83:              0       5.5
 84:              0       5.5
 85:              0       5.5
 86:              0       5.5
 87:              0       5.5
 88:              0       5.5
 89:              0       5.5
 90:              0       5.5
 91:              0       5.5
 92:              0       5.5
 93:              0       5.5
 94:              0       5.5
 95:              0       5.5
 96:              0       5.5
 97:              0       5.5
 98:              0       5.5
 99:              0       5.5
100:              0       5.5
     AberrantByGene padj_rank
> 
> plotAberrantPerSample(ods)
Warning in scale_y_log10(limits = c(oneOffset, NA)) :
  log-10 transformation introduced infinite values.
Warning: Removed 10 rows containing missing values or values outside the scale range
(`geom_bar()`).
> plotVolcano(ods, 1)
Error in pm[[2]] : subscript out of bounds
Calls: plotVolcano ... plotVolcano -> .local -> ggplotly -> ggplotly.ggplot -> gg2list
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Backtrace:
      ▆
   1. ├─testthat::expect_equal(...) at test_plotting.R:21:5
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. ├─OUTRIDER::plotVolcano(ods, 30)
   5. └─OUTRIDER::plotVolcano(ods, 30)
   6.   └─OUTRIDER (local) .local(object, ...)
   7.     ├─plotly::ggplotly(p, tooltip = "text")
   8.     └─plotly:::ggplotly.ggplot(p, tooltip = "text")
   9.       └─plotly::gg2list(...)
  
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 99 ]
  Error: Test failures
  Execution halted
* 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 ERRORs, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/OUTRIDER.Rcheck/00check.log’
for details.


Installation output

OUTRIDER.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL OUTRIDER
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘OUTRIDER’ ...
** this is package ‘OUTRIDER’ version ‘1.26.3’
** using staged installation
** libs
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppArmadillo/include' -I/usr/local/include   -fopenmp -DARMA_DONT_USE_OPENMP -fPIC  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppArmadillo/include' -I/usr/local/include   -fopenmp -DARMA_DONT_USE_OPENMP -fPIC  -g -O2  -Wall -Werror=format-security  -c loss_n_gradient_functions.cpp -o loss_n_gradient_functions.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o OUTRIDER.so RcppExports.o loss_n_gradient_functions.o -fopenmp -L/home/biocbuild/R/R/lib -lRlapack -L/home/biocbuild/R/R/lib -lRblas -lgfortran -lm -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/R/R-devel_2025-02-19/site-library/00LOCK-OUTRIDER/00new/OUTRIDER/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (OUTRIDER)

Tests output

OUTRIDER.Rcheck/tests/testthat.Rout.fail


R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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.

> library(testthat)
> library(OUTRIDER)
Loading required package: BiocParallel
Loading required package: GenomicFeatures
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians


Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

The following object is masked from 'package:Biobase':

    rowMedians

Loading required package: data.table

Attaching package: 'data.table'

The following object is masked from 'package:SummarizedExperiment':

    shift

The following object is masked from 'package:GenomicRanges':

    shift

The following object is masked from 'package:IRanges':

    shift

The following objects are masked from 'package:S4Vectors':

    first, second

> 
> register(SerialParam())
> 
> test_check("OUTRIDER")
[1] "Tue Oct 14 12:25:12 2025: Initial PCA loss: 6.269466444026"
[1] "Tue Oct 14 12:25:14 2025: Iteration: 1 loss: 4.61577601938473"
[1] "Tue Oct 14 12:25:15 2025: Iteration: 2 loss: 4.55515474101613"
[1] "Tue Oct 14 12:25:16 2025: Iteration: 3 loss: 4.51373526295885"
[1] "Tue Oct 14 12:25:17 2025: Iteration: 4 loss: 4.48283487981497"
[1] "Tue Oct 14 12:25:17 2025: Iteration: 5 loss: 4.46743909110935"
[1] "Tue Oct 14 12:25:18 2025: Iteration: 6 loss: 4.46542241472605"
Time difference of 5.551991 secs
[1] "Tue Oct 14 12:25:18 2025: 6 Final nb-AE loss: 4.46542241472605"
[1] "Tue Oct 14 12:25:20 2025: Initial PCA loss: 6.269466444026"
[1] "Tue Oct 14 12:25:21 2025: Iteration: 1 loss: 4.61577601938473"
[1] "Tue Oct 14 12:25:22 2025: Iteration: 2 loss: 4.55515474101613"
[1] "Tue Oct 14 12:25:23 2025: Iteration: 3 loss: 4.51373526295885"
[1] "Tue Oct 14 12:25:24 2025: Iteration: 4 loss: 4.48283487981497"
[1] "Tue Oct 14 12:25:25 2025: Iteration: 5 loss: 4.46743909110935"
[1] "Tue Oct 14 12:25:26 2025: Iteration: 6 loss: 4.46542241472605"
Time difference of 5.365014 secs
[1] "Tue Oct 14 12:25:26 2025: 6 Final nb-AE loss: 4.46542241472605"
class: OutriderDataSet
class: RangedSummarizedExperiment 
dim: 100 50 
metadata(1): version
assays(1): counts
rownames(100): ENSG00000223972.4 ENSG00000227232.4 ...
  ENSG00000107404.13 ENSG00000162576.12
rowData names(0):
colnames(50): GTEX.UPK5.0426.SM.3GAEK GTEX.WFG7.2026.SM.3GIL7 ...
  GTEX.11UD2.2526.SM.5CVNU GTEX.13O61.1426.SM.5KM3D
colData names(1): sampleID
[1] "Tue Oct 14 12:25:34 2025: Initial PCA loss: 4.45497702648287"
[1] "Tue Oct 14 12:25:36 2025: Iteration: 1 loss: 4.10212714917902"
[1] "Tue Oct 14 12:25:37 2025: Iteration: 2 loss: 4.08520151065717"
Time difference of 1.875806 secs
[1] "Tue Oct 14 12:25:37 2025: 2 Final nb-AE loss: 4.08520151065717"
[1] "Evaluation loss: 0.409365624668786 for q=3"
[1] "Tue Oct 14 12:25:38 2025: Initial PCA loss: 4.42698071615731"
[1] "Tue Oct 14 12:25:40 2025: Iteration: 1 loss: 4.02209565570526"
[1] "Tue Oct 14 12:25:41 2025: Iteration: 2 loss: 4.00839830497134"
Time difference of 1.933573 secs
[1] "Tue Oct 14 12:25:41 2025: 2 Final nb-AE loss: 4.00839830497134"
[1] "Evaluation loss: 0.422585264564871 for q=4"
[1] "Tue Oct 14 12:25:42 2025: Initial PCA loss: 4.40759694007152"
[1] "Tue Oct 14 12:25:43 2025: Iteration: 1 loss: 3.94101914633159"
[1] "Tue Oct 14 12:25:44 2025: Iteration: 2 loss: 3.92229871820955"
Time difference of 1.899659 secs
[1] "Tue Oct 14 12:25:44 2025: 2 Final nb-AE loss: 3.92229871820955"
[1] "Evaluation loss: 0.380595225546335 for q=5"
Optimal encoding dimension: 4 
Optimal encoding dimension: 50 
Optimal encoding dimension: 20 
Optimal encoding dimension: 2 
Optimal encoding dimension: 4 
[1] "Tue Oct 14 12:26:22 2025: Initial PCA loss: 7.16457134714849"
[1] "Tue Oct 14 12:26:24 2025: Iteration: 1 loss: 6.82913931405131"
[1] "Tue Oct 14 12:26:25 2025: Iteration: 2 loss: 6.82749008590827"
Time difference of 2.423867 secs
[1] "Tue Oct 14 12:26:25 2025: 2 Final nb-AE loss: 6.82749008590827"
[ FAIL 1 | WARN 2 | SKIP 0 | PASS 99 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_plotting.R:21:5'): plotting ────────────────────────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `pm[[2]]`: subscript out of bounds
Backtrace:
    ▆
 1. ├─testthat::expect_equal(...) at test_plotting.R:21:5
 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
 3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
 4. ├─OUTRIDER::plotVolcano(ods, 30)
 5. └─OUTRIDER::plotVolcano(ods, 30)
 6.   └─OUTRIDER (local) .local(object, ...)
 7.     ├─plotly::ggplotly(p, tooltip = "text")
 8.     └─plotly:::ggplotly.ggplot(p, tooltip = "text")
 9.       └─plotly::gg2list(...)

[ FAIL 1 | WARN 2 | SKIP 0 | PASS 99 ]
Error: Test failures
Execution halted

Example timings

OUTRIDER.Rcheck/OUTRIDER-Ex.timings

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