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

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4818
lconway	macOS 12.7.1 Monterey	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4596
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4538
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4535
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 lconway

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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:OUTRIDER.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings OUTRIDER_1.27.2.tar.gz

StartedAt: 2025-08-15 22:37:10 -0400 (Fri, 15 Aug 2025)

EndedAt: 2025-08-15 22:47:30 -0400 (Fri, 15 Aug 2025)

EllapsedTime: 619.3 seconds

RetCode: 0

Status: OK

CheckDir: OUTRIDER.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:OUTRIDER.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings OUTRIDER_1.27.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/OUTRIDER.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OUTRIDER/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OUTRIDER’ version ‘1.27.2’
* 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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
plotFunctions 16.500  0.975  17.716
OUTRIDER      12.593  2.590  14.068
estimateBestQ 14.463  0.266  14.816
results        5.599  0.071   5.694
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/OUTRIDER.Rcheck/00check.log’
for details.

Installation output

OUTRIDER.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL OUTRIDER
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘OUTRIDER’ ...
** this is package ‘OUTRIDER’ version ‘1.27.2’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include    -DARMA_DONT_USE_OPENMP -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include    -DARMA_DONT_USE_OPENMP -fPIC  -falign-functions=64 -Wall -g -O2   -c loss_n_gradient_functions.cpp -o loss_n_gradient_functions.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o OUTRIDER.so RcppExports.o loss_n_gradient_functions.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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

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

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

> 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] "Fri Aug 15 22:46:05 2025: Initial PCA loss: 6.21511006248101"
[1] "Fri Aug 15 22:46:06 2025: Iteration: 1 loss: 4.47436228133543"
[1] "Fri Aug 15 22:46:07 2025: Iteration: 2 loss: 4.40736162071084"
[1] "Fri Aug 15 22:46:08 2025: Iteration: 3 loss: 4.37179677260978"
[1] "Fri Aug 15 22:46:09 2025: Iteration: 4 loss: 4.36062860008022"
[1] "Fri Aug 15 22:46:09 2025: Iteration: 5 loss: 4.35910238996652"
[1] "Fri Aug 15 22:46:10 2025: Iteration: 6 loss: 4.35906981639062"
Time difference of 4.913308 secs
[1] "Fri Aug 15 22:46:10 2025: 6 Final nb-AE loss: 4.35906981639062"
[1] "Fri Aug 15 22:46:12 2025: Initial PCA loss: 6.21511006248101"
[1] "Fri Aug 15 22:46:13 2025: Iteration: 1 loss: 4.47436228133543"
[1] "Fri Aug 15 22:46:14 2025: Iteration: 2 loss: 4.40736162071084"
[1] "Fri Aug 15 22:46:15 2025: Iteration: 3 loss: 4.37179677260978"
[1] "Fri Aug 15 22:46:15 2025: Iteration: 4 loss: 4.36062860008022"
[1] "Fri Aug 15 22:46:16 2025: Iteration: 5 loss: 4.35910238996652"
[1] "Fri Aug 15 22:46:17 2025: Iteration: 6 loss: 4.35906981639062"
Time difference of 4.328234 secs
[1] "Fri Aug 15 22:46:17 2025: 6 Final nb-AE loss: 4.35906981639062"
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] "Fri Aug 15 22:46:23 2025: Initial PCA loss: 4.45172630517027"
[1] "Fri Aug 15 22:46:25 2025: Iteration: 1 loss: 4.11751859693499"
[1] "Fri Aug 15 22:46:26 2025: Iteration: 2 loss: 4.10578154058379"
Time difference of 1.651229 secs
[1] "Fri Aug 15 22:46:26 2025: 2 Final nb-AE loss: 4.10578154058379"
[1] "Evaluation loss: 0.607542059158957 for q=3"
[1] "Fri Aug 15 22:46:27 2025: Initial PCA loss: 4.42686835795732"
[1] "Fri Aug 15 22:46:28 2025: Iteration: 1 loss: 4.05045306043668"
[1] "Fri Aug 15 22:46:29 2025: Iteration: 2 loss: 4.03907678332436"
Time difference of 1.545231 secs
[1] "Fri Aug 15 22:46:29 2025: 2 Final nb-AE loss: 4.03907678332436"
[1] "Evaluation loss: 0.631384098785458 for q=4"
[1] "Fri Aug 15 22:46:30 2025: Initial PCA loss: 4.40635335429994"
[1] "Fri Aug 15 22:46:31 2025: Iteration: 1 loss: 3.97222727491397"
[1] "Fri Aug 15 22:46:32 2025: Iteration: 2 loss: 3.95958592583294"
Time difference of 1.538261 secs
[1] "Fri Aug 15 22:46:32 2025: 2 Final nb-AE loss: 3.95958592583294"
[1] "Evaluation loss: 0.612228495421609 for q=5"
Optimal encoding dimension: 4 
Optimal encoding dimension: 50 
Optimal encoding dimension: 20 
Optimal encoding dimension: 2 
Optimal encoding dimension: 4 
[1] "Fri Aug 15 22:46:57 2025: Initial PCA loss: 7.16457134714849"
[1] "Fri Aug 15 22:46:58 2025: Iteration: 1 loss: 6.82913712406641"
[1] "Fri Aug 15 22:46:59 2025: Iteration: 2 loss: 6.82748357330359"
Time difference of 1.815381 secs
[1] "Fri Aug 15 22:46:59 2025: 2 Final nb-AE loss: 6.82748357330359"
[ FAIL 0 | WARN 11 | SKIP 0 | PASS 131 ]

[ FAIL 0 | WARN 11 | SKIP 0 | PASS 131 ]
> 
> proc.time()
   user  system elapsed 
 94.084   2.599  97.446

Example timings

OUTRIDER.Rcheck/OUTRIDER-Ex.timings

name	user	system	elapsed
OUTRIDER	12.593	2.590	14.068
OutriderDataSet-class	0.859	0.055	0.920
aberrant	2.185	0.722	2.091
computeGeneLength	1.785	0.153	1.953
computeLatentSpace	0.951	0.010	0.970
computePvalues	2.908	1.802	3.233
computeZscores	1.181	0.103	1.294
controlForConfounders	1.415	0.051	1.476
counts	0.724	0.008	0.736
estimateBestQ	14.463	0.266	14.816
filterExpression	1.525	0.016	1.547
fit	0.994	0.013	1.011
fpkm	0.900	0.011	0.914
getter_setter_functions	3.568	0.046	3.650
makeExampleOutriderDataSet	1.332	0.011	1.349
normalizationFactors	0.821	0.020	0.857
plotFunctions	16.500	0.975	17.716
results	5.599	0.071	5.694
sampleExclusionMask	0.580	0.051	0.635
sizeFactors	0.886	0.039	0.936