Multiple platform build/check report for BioC 3.22 - CHECK results for OUTRIDER on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"	4814
lconway	macOS 12.7.1 Monterey	x86_64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4603
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4547
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4553
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*

CHECK results for OUTRIDER on nebbiolo2

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.

raw results

Summary

Package: OUTRIDER

Version: 1.27.2

Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:OUTRIDER.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings OUTRIDER_1.27.2.tar.gz

StartedAt: 2025-09-20 02:38:10 -0400 (Sat, 20 Sep 2025)

EndedAt: 2025-09-20 02:54:10 -0400 (Sat, 20 Sep 2025)

EllapsedTime: 959.5 seconds

RetCode: 0

Status: OK

CheckDir: OUTRIDER.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:OUTRIDER.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings OUTRIDER_1.27.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/OUTRIDER.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘OUTRIDER/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OUTRIDER’ version ‘1.27.2’
* 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: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
plotFunctions           35.506  1.026  32.459
estimateBestQ           19.654  1.640  23.135
OUTRIDER                12.205  3.247  13.788
results                  8.567  0.357  10.373
getter_setter_functions  6.130  0.212   6.503
computePvalues           2.301  3.555   3.225
* 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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/OUTRIDER.Rcheck/00check.log’
for details.

Installation output

OUTRIDER.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL OUTRIDER
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘OUTRIDER’ ...
** this is package ‘OUTRIDER’ version ‘1.27.2’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/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
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/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
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o OUTRIDER.so RcppExports.o loss_n_gradient_functions.o -fopenmp -llapack -L/home/biocbuild/bbs-3.22-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc/R/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


R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 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.

> 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: Seqinfo
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] "Sat Sep 20 02:49:08 2025: Initial PCA loss: 6.04750155535923"
[1] "Sat Sep 20 02:49:09 2025: Iteration: 1 loss: 4.69105333777073"
[1] "Sat Sep 20 02:49:09 2025: Iteration: 2 loss: 4.58314515550612"
[1] "Sat Sep 20 02:49:10 2025: Iteration: 3 loss: 4.4614050075459"
[1] "Sat Sep 20 02:49:11 2025: Iteration: 4 loss: 4.36667346178104"
[1] "Sat Sep 20 02:49:11 2025: Iteration: 5 loss: 4.32659115734563"
[1] "Sat Sep 20 02:49:12 2025: Iteration: 6 loss: 4.30762213248866"
Time difference of 3.868661 secs
[1] "Sat Sep 20 02:49:12 2025: 6 Final nb-AE loss: 4.30762213248866"
[1] "Sat Sep 20 02:49:13 2025: Initial PCA loss: 6.04750155535923"
[1] "Sat Sep 20 02:49:14 2025: Iteration: 1 loss: 4.69105333777073"
[1] "Sat Sep 20 02:49:15 2025: Iteration: 2 loss: 4.58314515550612"
[1] "Sat Sep 20 02:49:15 2025: Iteration: 3 loss: 4.4614050075459"
[1] "Sat Sep 20 02:49:16 2025: Iteration: 4 loss: 4.36667346178104"
[1] "Sat Sep 20 02:49:17 2025: Iteration: 5 loss: 4.32659115734563"
[1] "Sat Sep 20 02:49:18 2025: Iteration: 6 loss: 4.30762213248866"
Time difference of 3.970001 secs
[1] "Sat Sep 20 02:49:18 2025: 6 Final nb-AE loss: 4.30762213248866"
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] "Sat Sep 20 02:49:23 2025: Initial PCA loss: 4.53544652881035"
[1] "Sat Sep 20 02:49:24 2025: Iteration: 1 loss: 4.21234228761977"
[1] "Sat Sep 20 02:49:25 2025: Iteration: 2 loss: 4.20736193889198"
Time difference of 1.228807 secs
[1] "Sat Sep 20 02:49:25 2025: 2 Final nb-AE loss: 4.20736193889198"
[1] "Evaluation loss: 0.709933943033538 for q=3"
[1] "Sat Sep 20 02:49:26 2025: Initial PCA loss: 4.49418948225558"
[1] "Sat Sep 20 02:49:27 2025: Iteration: 1 loss: 4.13498104714674"
[1] "Sat Sep 20 02:49:27 2025: Iteration: 2 loss: 4.12579499707119"
Time difference of 1.231851 secs
[1] "Sat Sep 20 02:49:27 2025: 2 Final nb-AE loss: 4.12579499707119"
[1] "Evaluation loss: 0.648946229713413 for q=4"
[1] "Sat Sep 20 02:49:28 2025: Initial PCA loss: 4.47057488675883"
[1] "Sat Sep 20 02:49:29 2025: Iteration: 1 loss: 4.05672576727024"
[1] "Sat Sep 20 02:49:30 2025: Iteration: 2 loss: 4.04458854835696"
Time difference of 1.240403 secs
[1] "Sat Sep 20 02:49:30 2025: 2 Final nb-AE loss: 4.04458854835696"
[1] "Evaluation loss: 0.68468640646659 for q=5"
Optimal encoding dimension: 4 
Optimal encoding dimension: 50 
Optimal encoding dimension: 20 
Optimal encoding dimension: 2 
Optimal encoding dimension: 4 
[1] "Sat Sep 20 02:49:51 2025: Initial PCA loss: 7.16457134714849"
[1] "Sat Sep 20 02:49:53 2025: Iteration: 1 loss: 6.82914112812595"
[1] "Sat Sep 20 02:49:54 2025: Iteration: 2 loss: 6.82749097859465"
Time difference of 1.519399 secs
[1] "Sat Sep 20 02:49:54 2025: 2 Final nb-AE loss: 6.82749097859465"
[ FAIL 0 | WARN 12 | SKIP 0 | PASS 131 ]

[ FAIL 0 | WARN 12 | SKIP 0 | PASS 131 ]
> 
> proc.time()
   user  system elapsed 
 88.820   2.245  93.386

Example timings

OUTRIDER.Rcheck/OUTRIDER-Ex.timings

name	user	system	elapsed
OUTRIDER	12.205	3.247	13.788
OutriderDataSet-class	0.801	0.062	0.864
aberrant	1.959	1.260	2.107
computeGeneLength	1.454	0.209	1.662
computeLatentSpace	0.797	0.101	0.897
computePvalues	2.301	3.555	3.225
computeZscores	1.210	0.176	1.385
controlForConfounders	1.475	0.243	1.719
counts	1.196	0.070	1.266
estimateBestQ	19.654	1.640	23.135
filterExpression	1.528	0.061	1.588
fit	0.915	0.019	0.934
fpkm	1.023	0.039	1.062
getter_setter_functions	6.130	0.212	6.503
makeExampleOutriderDataSet	2.448	0.059	4.297
normalizationFactors	1.275	0.074	1.348
plotFunctions	35.506	1.026	32.459
results	8.567	0.357	10.373
sampleExclusionMask	0.988	0.089	1.332
sizeFactors	1.526	0.099	1.925