Christian Mertes
| Snapshot Date: 2025-07-31 13:40 -0400 (Thu, 31 Jul 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) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-08-04 11:48 -0400 (Mon, 04 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4823 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4565 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4603 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4544 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4579 |
| 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 1512/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OUTRIDER 1.26.3 (landing page) Christian Mertes
| nebbiolo1 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
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. |
| 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: 2025-08-01 12:41:29 -0000 (Fri, 01 Aug 2025) |
| EndedAt: 2025-08-01 12:53:19 -0000 (Fri, 01 Aug 2025) |
| EllapsedTime: 709.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: OUTRIDER.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotFunctions 20.019 0.268 24.035
estimateBestQ 16.666 0.278 18.862
OUTRIDER 13.331 3.012 17.517
results 6.164 0.153 6.864
computePvalues 2.679 2.343 4.042
* 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
‘/home/biocbuild/bbs-3.21-bioc/meat/OUTRIDER.Rcheck/00check.log’
for details.
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)
OUTRIDER.Rcheck/tests/testthat.Rout
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] "Fri Aug 1 12:51:27 2025: Initial PCA loss: 6.36111953068794"
[1] "Fri Aug 1 12:51:29 2025: Iteration: 1 loss: 4.55833885872901"
[1] "Fri Aug 1 12:51:30 2025: Iteration: 2 loss: 4.49653424389275"
[1] "Fri Aug 1 12:51:31 2025: Iteration: 3 loss: 4.47230031353285"
[1] "Fri Aug 1 12:51:32 2025: Iteration: 4 loss: 4.46298785406586"
[1] "Fri Aug 1 12:51:33 2025: Iteration: 5 loss: 4.45703015157447"
[1] "Fri Aug 1 12:51:34 2025: Iteration: 6 loss: 4.45120835777032"
Time difference of 6.501202 secs
[1] "Fri Aug 1 12:51:34 2025: 6 Final nb-AE loss: 4.45120835777032"
[1] "Fri Aug 1 12:51:36 2025: Initial PCA loss: 6.36111953068794"
[1] "Fri Aug 1 12:51:38 2025: Iteration: 1 loss: 4.55833885872901"
[1] "Fri Aug 1 12:51:39 2025: Iteration: 2 loss: 4.49653424389275"
[1] "Fri Aug 1 12:51:40 2025: Iteration: 3 loss: 4.47230031353285"
[1] "Fri Aug 1 12:51:41 2025: Iteration: 4 loss: 4.46298785406586"
[1] "Fri Aug 1 12:51:42 2025: Iteration: 5 loss: 4.45703015157447"
[1] "Fri Aug 1 12:51:43 2025: Iteration: 6 loss: 4.45120835777032"
Time difference of 6.563656 secs
[1] "Fri Aug 1 12:51:43 2025: 6 Final nb-AE loss: 4.45120835777032"
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 1 12:51:52 2025: Initial PCA loss: 4.44447939329331"
[1] "Fri Aug 1 12:51:54 2025: Iteration: 1 loss: 4.11631151074453"
[1] "Fri Aug 1 12:51:54 2025: Iteration: 2 loss: 4.09104773642096"
Time difference of 1.873613 secs
[1] "Fri Aug 1 12:51:54 2025: 2 Final nb-AE loss: 4.09104773642096"
[1] "Evaluation loss: 0.621327446918882 for q=3"
[1] "Fri Aug 1 12:51:56 2025: Initial PCA loss: 4.41622992570441"
[1] "Fri Aug 1 12:51:58 2025: Iteration: 1 loss: 4.02559291257259"
[1] "Fri Aug 1 12:51:59 2025: Iteration: 2 loss: 3.98176083463679"
Time difference of 2.430996 secs
[1] "Fri Aug 1 12:51:59 2025: 2 Final nb-AE loss: 3.98176083463679"
[1] "Evaluation loss: 0.528511358956533 for q=4"
[1] "Fri Aug 1 12:52:00 2025: Initial PCA loss: 4.39839323353949"
[1] "Fri Aug 1 12:52:02 2025: Iteration: 1 loss: 3.95424466230371"
[1] "Fri Aug 1 12:52:03 2025: Iteration: 2 loss: 3.9093379788628"
Time difference of 2.003571 secs
[1] "Fri Aug 1 12:52:03 2025: 2 Final nb-AE loss: 3.9093379788628"
[1] "Evaluation loss: 0.52872260465708 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 1 12:52:43 2025: Initial PCA loss: 7.16457134714849"
[1] "Fri Aug 1 12:52:45 2025: Iteration: 1 loss: 6.82913931405131"
[1] "Fri Aug 1 12:52:46 2025: Iteration: 2 loss: 6.82749008590827"
Time difference of 2.289966 secs
[1] "Fri Aug 1 12:52:46 2025: 2 Final nb-AE loss: 6.82749008590827"
[ FAIL 0 | WARN 11 | SKIP 0 | PASS 131 ]
[ FAIL 0 | WARN 11 | SKIP 0 | PASS 131 ]
>
> proc.time()
user system elapsed
119.088 1.595 133.481
OUTRIDER.Rcheck/OUTRIDER-Ex.timings
| name | user | system | elapsed | |
| OUTRIDER | 13.331 | 3.012 | 17.517 | |
| OutriderDataSet-class | 1.123 | 0.060 | 1.367 | |
| aberrant | 2.532 | 1.038 | 2.898 | |
| computeGeneLength | 1.924 | 0.251 | 2.394 | |
| computeLatentSpace | 1.011 | 0.024 | 1.058 | |
| computePvalues | 2.679 | 2.343 | 4.042 | |
| computeZscores | 1.218 | 0.147 | 1.543 | |
| controlForConfounders | 1.555 | 0.120 | 1.784 | |
| counts | 0.789 | 0.020 | 0.816 | |
| estimateBestQ | 16.666 | 0.278 | 18.862 | |
| filterExpression | 2.051 | 0.019 | 2.170 | |
| fit | 1.258 | 0.001 | 1.377 | |
| fpkm | 1.054 | 0.000 | 1.072 | |
| getter_setter_functions | 4.155 | 0.004 | 4.779 | |
| makeExampleOutriderDataSet | 1.585 | 0.000 | 1.689 | |
| normalizationFactors | 1.043 | 0.008 | 1.053 | |
| plotFunctions | 20.019 | 0.268 | 24.035 | |
| results | 6.164 | 0.153 | 6.864 | |
| sampleExclusionMask | 0.598 | 0.064 | 0.817 | |
| sizeFactors | 0.863 | 0.060 | 0.926 | |