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This page was generated on 2024-11-20 12:08 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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 1483/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OUTRIDER 1.24.0  (landing page)
Christian Mertes
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
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)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


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: 1.24.0
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: 2024-11-20 10:46:39 -0000 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 10:56:28 -0000 (Wed, 20 Nov 2024)
EllapsedTime: 589.1 seconds
RetCode: 0
Status:   OK  
CheckDir: OUTRIDER.Rcheck
Warnings: 0

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_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/OUTRIDER.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (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 ‘1.24.0’
* 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: ‘g++ (conda-forge gcc 14.2.0-1) 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   19.214  0.292  19.442
findEncodingDim 16.386  0.471  16.891
OUTRIDER        13.368  3.373  15.084
computePvalues   2.679  2.518   3.079
* 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.


Installation output

OUTRIDER.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’
* installing *source* package ‘OUTRIDER’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppArmadillo/include' -I/usr/local/include   -fopenmp -DARMA_DONT_USE_OPENMP -fPIC  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppArmadillo/include' -I/usr/local/include   -fopenmp -DARMA_DONT_USE_OPENMP -fPIC  -g -O2  -Wall  -c loss_n_gradient_functions.cpp -o loss_n_gradient_functions.o
g++ -std=gnu++11 -shared -L/home/biocbuild/R/R-4.4.1/lib -L/usr/local/lib -o OUTRIDER.so RcppExports.o loss_n_gradient_functions.o -fopenmp -lopenblas -L/usr/lib/gcc/aarch64-linux-gnu/10.3.1 -lgfortran -lm -L/home/biocbuild/R/R-4.4.1/lib -lR
installing to /home/biocbuild/R/R-4.4.1/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 4.4.1 (2024-06-14) -- "Race for Your Life"
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] "Wed Nov 20 10:55:02 2024: Initial PCA loss: 6.15865769891326"
[1] "Wed Nov 20 10:55:04 2024: Iteration: 1 loss: 4.41165015346574"
[1] "Wed Nov 20 10:55:05 2024: Iteration: 2 loss: 4.34173081118159"
[1] "Wed Nov 20 10:55:06 2024: Iteration: 3 loss: 4.31502802048498"
[1] "Wed Nov 20 10:55:07 2024: Iteration: 4 loss: 4.29925216320403"
[1] "Wed Nov 20 10:55:08 2024: Iteration: 5 loss: 4.28151986364134"
[1] "Wed Nov 20 10:55:09 2024: Iteration: 6 loss: 4.27245210951687"
Time difference of 5.627782 secs
[1] "Wed Nov 20 10:55:09 2024: 6 Final nb-AE loss: 4.27245210951687"
[1] "Wed Nov 20 10:55:10 2024: Initial PCA loss: 6.15865769891326"
[1] "Wed Nov 20 10:55:12 2024: Iteration: 1 loss: 4.41165015346574"
[1] "Wed Nov 20 10:55:13 2024: Iteration: 2 loss: 4.34173081118159"
[1] "Wed Nov 20 10:55:14 2024: Iteration: 3 loss: 4.31502802048498"
[1] "Wed Nov 20 10:55:15 2024: Iteration: 4 loss: 4.29925216320403"
[1] "Wed Nov 20 10:55:16 2024: Iteration: 5 loss: 4.28151986364134"
[1] "Wed Nov 20 10:55:17 2024: Iteration: 6 loss: 4.27245210951687"
Time difference of 5.724263 secs
[1] "Wed Nov 20 10:55:17 2024: 6 Final nb-AE loss: 4.27245210951687"
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] "Wed Nov 20 10:55:35 2024: Initial PCA loss: 4.48754895386196"
[1] "Wed Nov 20 10:55:37 2024: Iteration: 1 loss: 4.0998233883726"
[1] "Wed Nov 20 10:55:38 2024: Iteration: 2 loss: 4.08131818063444"
Time difference of 1.874628 secs
[1] "Wed Nov 20 10:55:38 2024: 2 Final nb-AE loss: 4.08131818063444"
[1] "Evaluation loss: 0.414727775554702 for q=3"
[1] "Wed Nov 20 10:55:39 2024: Initial PCA loss: 4.45935005225991"
[1] "Wed Nov 20 10:55:40 2024: Iteration: 1 loss: 4.0199119929381"
[1] "Wed Nov 20 10:55:41 2024: Iteration: 2 loss: 3.98148949398081"
Time difference of 1.882937 secs
[1] "Wed Nov 20 10:55:41 2024: 2 Final nb-AE loss: 3.98148949398081"
[1] "Evaluation loss: 0.441930947651278 for q=4"
[1] "Wed Nov 20 10:55:42 2024: Initial PCA loss: 4.43151938124969"
[1] "Wed Nov 20 10:55:44 2024: Iteration: 1 loss: 3.94613491376044"
[1] "Wed Nov 20 10:55:45 2024: Iteration: 2 loss: 3.91537049737599"
Time difference of 1.852607 secs
[1] "Wed Nov 20 10:55:45 2024: 2 Final nb-AE loss: 3.91537049737599"
[1] "Evaluation loss: 0.440569359268371 for q=5"
[1] "Wed Nov 20 10:55:57 2024: Initial PCA loss: 7.16457134714849"
[1] "Wed Nov 20 10:55:59 2024: Iteration: 1 loss: 6.82915718001769"
[1] "Wed Nov 20 10:56:00 2024: Iteration: 2 loss: 6.82749821997582"
Time difference of 2.373358 secs
[1] "Wed Nov 20 10:56:00 2024: 2 Final nb-AE loss: 6.82749821997582"
[ FAIL 0 | WARN 10 | SKIP 0 | PASS 115 ]

[ FAIL 0 | WARN 10 | SKIP 0 | PASS 115 ]
> 
> proc.time()
   user  system elapsed 
104.635   2.154 106.799 

Example timings

OUTRIDER.Rcheck/OUTRIDER-Ex.timings

nameusersystemelapsed
OUTRIDER13.368 3.37315.084
OutriderDataSet-class1.1290.0521.184
aberrant2.5111.1492.353
computeGeneLength1.8330.3122.150
computeLatentSpace1.0000.0791.082
computePvalues2.6792.5183.079
computeZscores1.3040.1941.412
controlForConfounders1.5730.1521.728
counts0.7980.0200.821
estimateBestQ0.5990.0080.608
filterExpression2.0500.0602.114
findEncodingDim16.386 0.47116.891
fit1.1520.0161.169
fpkm0.9610.0040.967
getter_setter_functions3.9100.0113.928
makeExampleOutriderDataSet1.4050.0121.419
normalizationFactors0.9140.0440.960
plotFunctions19.214 0.29219.442
results4.9220.0084.939
sampleExclusionMask0.6280.0280.657
sizeFactors2.3540.0962.455