Christian Mertes
| Snapshot Date: 2025-01-02 13:00 -0500 (Thu, 02 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/OUTRIDER |
| git_branch: RELEASE_3_20 |
| git_last_commit: cf28bbe |
| git_last_commit_date: 2024-10-29 10:29:54 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-01-09 12:11 -0500 (Thu, 09 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4358 |
| 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 1483/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OUTRIDER 1.24.0 (landing page) Christian Mertes
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | 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 | | ||||||||
| taishan | 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: 1.24.0 |
| 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_1.24.0.tar.gz |
| StartedAt: 2025-01-09 00:36:40 -0000 (Thu, 09 Jan 2025) |
| EndedAt: 2025-01-09 00:45:10 -0000 (Thu, 09 Jan 2025) |
| EllapsedTime: 509.8 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_1.24.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/OUTRIDER.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 12.3.1 (openEuler 12.3.1-36.oe2403)
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OUTRIDER/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OUTRIDER’ version ‘1.24.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
checkRd: (-1) results.Rd:48-50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) results.Rd:51-52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) results.Rd:53-54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) results.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) results.Rd:56-57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) results.Rd:58-60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) results.Rd:61-62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) results.Rd:63-64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) results.Rd:65-66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) results.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) results.Rd:68-71: Lost braces in \itemize; \value handles \item{}{} directly
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... 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 18.083 0.622 18.750
findEncodingDim 14.347 0.734 15.123
OUTRIDER 11.423 3.194 13.110
results 5.359 0.116 5.489
computePvalues 2.647 2.593 3.083
* 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: 5 NOTEs
See
‘/home/biocbuild/bbs-3.20-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-4.4.2/site-library’ * installing *source* package ‘OUTRIDER’ ... ** using staged installation ** libs using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’ using C++11 /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.2/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.2/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++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.2/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.2/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++11 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o OUTRIDER.so RcppExports.o loss_n_gradient_functions.o -fopenmp -lopenblas -L/usr/lib/gcc/aarch64-openEuler-linux/12 -lgfortran -lm -L/home/biocbuild/R/R/lib -lR installing to /home/biocbuild/R/R-4.4.2/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 version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 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
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, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table,
tapply, union, 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] "Thu Jan 9 00:43:49 2025: Initial PCA loss: 6.13903267380848"
[1] "Thu Jan 9 00:43:51 2025: Iteration: 1 loss: 4.38527627401679"
[1] "Thu Jan 9 00:43:52 2025: Iteration: 2 loss: 4.29360037615479"
[1] "Thu Jan 9 00:43:53 2025: Iteration: 3 loss: 4.27915940910782"
[1] "Thu Jan 9 00:43:53 2025: Iteration: 4 loss: 4.27660968118756"
[1] "Thu Jan 9 00:43:54 2025: Iteration: 5 loss: 4.2740531135349"
[1] "Thu Jan 9 00:43:55 2025: Iteration: 6 loss: 4.27331091290323"
Time difference of 5.480555 secs
[1] "Thu Jan 9 00:43:55 2025: 6 Final nb-AE loss: 4.27331091290323"
[1] "Thu Jan 9 00:43:57 2025: Initial PCA loss: 6.13903267380848"
[1] "Thu Jan 9 00:43:59 2025: Iteration: 1 loss: 4.38527627401679"
[1] "Thu Jan 9 00:43:59 2025: Iteration: 2 loss: 4.29360037615479"
[1] "Thu Jan 9 00:44:00 2025: Iteration: 3 loss: 4.27915940910782"
[1] "Thu Jan 9 00:44:01 2025: Iteration: 4 loss: 4.27660968118756"
[1] "Thu Jan 9 00:44:02 2025: Iteration: 5 loss: 4.2740531135349"
[1] "Thu Jan 9 00:44:03 2025: Iteration: 6 loss: 4.27331091290323"
Time difference of 5.253475 secs
[1] "Thu Jan 9 00:44:03 2025: 6 Final nb-AE loss: 4.27331091290323"
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] "Thu Jan 9 00:44:20 2025: Initial PCA loss: 4.56667474387158"
[1] "Thu Jan 9 00:44:22 2025: Iteration: 1 loss: 4.21992091630024"
[1] "Thu Jan 9 00:44:23 2025: Iteration: 2 loss: 4.19516506601898"
Time difference of 1.785035 secs
[1] "Thu Jan 9 00:44:23 2025: 2 Final nb-AE loss: 4.19516506601898"
[1] "Evaluation loss: 0.467219589545543 for q=3"
[1] "Thu Jan 9 00:44:24 2025: Initial PCA loss: 4.50687192680207"
[1] "Thu Jan 9 00:44:26 2025: Iteration: 1 loss: 4.1364090263702"
[1] "Thu Jan 9 00:44:26 2025: Iteration: 2 loss: 4.09713871586475"
Time difference of 1.738496 secs
[1] "Thu Jan 9 00:44:26 2025: 2 Final nb-AE loss: 4.09713871586475"
[1] "Evaluation loss: 0.434097940701226 for q=4"
[1] "Thu Jan 9 00:44:28 2025: Initial PCA loss: 4.45493554697596"
[1] "Thu Jan 9 00:44:29 2025: Iteration: 1 loss: 4.04141712322441"
[1] "Thu Jan 9 00:44:30 2025: Iteration: 2 loss: 4.02386866385593"
Time difference of 1.793874 secs
[1] "Thu Jan 9 00:44:30 2025: 2 Final nb-AE loss: 4.02386866385593"
[1] "Evaluation loss: 0.415360990441045 for q=5"
[1] "Thu Jan 9 00:44:41 2025: Initial PCA loss: 7.16457134714849"
[1] "Thu Jan 9 00:44:43 2025: Iteration: 1 loss: 6.82914904822917"
[1] "Thu Jan 9 00:44:44 2025: Iteration: 2 loss: 6.82749374530494"
Time difference of 2.120293 secs
[1] "Thu Jan 9 00:44:44 2025: 2 Final nb-AE loss: 6.82749374530494"
[ FAIL 0 | WARN 10 | SKIP 0 | PASS 115 ]
[ FAIL 0 | WARN 10 | SKIP 0 | PASS 115 ]
>
> proc.time()
user system elapsed
96.170 2.198 98.565
OUTRIDER.Rcheck/OUTRIDER-Ex.timings
| name | user | system | elapsed | |
| OUTRIDER | 11.423 | 3.194 | 13.110 | |
| OutriderDataSet-class | 1.010 | 0.108 | 1.121 | |
| aberrant | 2.425 | 1.413 | 2.476 | |
| computeGeneLength | 1.743 | 0.435 | 2.185 | |
| computeLatentSpace | 0.947 | 0.064 | 1.013 | |
| computePvalues | 2.647 | 2.593 | 3.083 | |
| computeZscores | 1.136 | 0.175 | 1.315 | |
| controlForConfounders | 1.424 | 0.203 | 1.633 | |
| counts | 0.719 | 0.052 | 0.773 | |
| estimateBestQ | 0.569 | 0.063 | 0.635 | |
| filterExpression | 1.873 | 0.116 | 1.994 | |
| findEncodingDim | 14.347 | 0.734 | 15.123 | |
| fit | 1.098 | 0.044 | 1.144 | |
| fpkm | 0.952 | 0.028 | 0.982 | |
| getter_setter_functions | 3.820 | 0.147 | 3.978 | |
| makeExampleOutriderDataSet | 1.309 | 0.044 | 1.357 | |
| normalizationFactors | 0.884 | 0.007 | 0.894 | |
| plotFunctions | 18.083 | 0.622 | 18.750 | |
| results | 5.359 | 0.116 | 5.489 | |
| sampleExclusionMask | 0.511 | 0.008 | 0.521 | |
| sizeFactors | 0.761 | 0.064 | 0.828 | |