Christian Mertes
| Snapshot Date: 2023-11-01 14:05:06 -0400 (Wed, 01 Nov 2023) |
| git_url: https://git.bioconductor.org/packages/OUTRIDER |
| git_branch: RELEASE_3_18 |
| git_last_commit: 0528b44 |
| git_last_commit_date: 2023-10-24 11:06:34 -0400 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-11-02 11:41:02 -0400 (Thu, 02 Nov 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4729 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4463 |
| lconway | macOS 12.6.5 Monterey | x86_64 | 4.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" | 4478 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4464 |
| 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 1480/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OUTRIDER 1.20.0 (landing page) Christian Mertes
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.6.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / 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: 1.20.0 |
| Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:OUTRIDER.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings OUTRIDER_1.20.0.tar.gz |
| StartedAt: 2023-11-02 12:51:46 -0000 (Thu, 02 Nov 2023) |
| EndedAt: 2023-11-02 13:01:22 -0000 (Thu, 02 Nov 2023) |
| EllapsedTime: 576.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: OUTRIDER.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:OUTRIDER.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings OUTRIDER_1.20.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/OUTRIDER.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
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 ‘1.20.0’
* 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++ (GCC) 10.3.1’
* 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 ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
padjOnSubset: no visible global function definition for ‘bpmapply’
Undefined global functions or variables:
bpmapply
* checking Rd files ... OK
* 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
OUTRIDER 13.715 3.471 15.481
findEncodingDim 16.096 0.472 16.628
plotFunctions 10.809 0.198 11.047
computePvalues 2.819 2.733 3.239
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/home/biocbuild/bbs-3.18-bioc/meat/OUTRIDER.Rcheck/00check.log’
for details.
OUTRIDER.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL OUTRIDER ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’ * installing *source* package ‘OUTRIDER’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (GCC) 10.3.1’ using C++11 g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/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-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/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-4.3.1/lib -L/usr/local/lib -o OUTRIDER.so RcppExports.o loss_n_gradient_functions.o -fopenmp -llapack -lblas -lgfortran -lm -L/home/biocbuild/R/R-4.3.1/lib -lR installing to /home/biocbuild/R/R-4.3.1/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)
OUTRIDER.Rcheck/tests/testthat.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)
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, setdiff, sort, 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 Nov 2 13:00:03 2023: Initial PCA loss: 6.31433371696729"
[1] "Thu Nov 2 13:00:04 2023: Iteration: 1 loss: 4.72536909502158"
[1] "Thu Nov 2 13:00:05 2023: Iteration: 2 loss: 4.62385434083743"
[1] "Thu Nov 2 13:00:06 2023: Iteration: 3 loss: 4.55506939950682"
[1] "Thu Nov 2 13:00:07 2023: Iteration: 4 loss: 4.52080033052811"
[1] "Thu Nov 2 13:00:08 2023: Iteration: 5 loss: 4.49908161991301"
[1] "Thu Nov 2 13:00:09 2023: Iteration: 6 loss: 4.49168690714068"
Time difference of 5.559535 secs
[1] "Thu Nov 2 13:00:09 2023: 6 Final nb-AE loss: 4.49168690714068"
[1] "Thu Nov 2 13:00:10 2023: Initial PCA loss: 6.31433371696729"
[1] "Thu Nov 2 13:00:12 2023: Iteration: 1 loss: 4.72536909502158"
[1] "Thu Nov 2 13:00:13 2023: Iteration: 2 loss: 4.62385434083743"
[1] "Thu Nov 2 13:00:14 2023: Iteration: 3 loss: 4.55506939950682"
[1] "Thu Nov 2 13:00:15 2023: Iteration: 4 loss: 4.52080033052811"
[1] "Thu Nov 2 13:00:16 2023: Iteration: 5 loss: 4.49908161991301"
[1] "Thu Nov 2 13:00:17 2023: Iteration: 6 loss: 4.49168690714068"
Time difference of 5.760125 secs
[1] "Thu Nov 2 13:00:17 2023: 6 Final nb-AE loss: 4.49168690714068"
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 Nov 2 13:00:35 2023: Initial PCA loss: 4.44405166274382"
[1] "Thu Nov 2 13:00:37 2023: Iteration: 1 loss: 4.10663685140188"
[1] "Thu Nov 2 13:00:38 2023: Iteration: 2 loss: 4.06910856295826"
Time difference of 1.871863 secs
[1] "Thu Nov 2 13:00:38 2023: 2 Final nb-AE loss: 4.06910856295826"
[1] "Evaluation loss: 0.618372367267823 for q=3"
[1] "Thu Nov 2 13:00:39 2023: Initial PCA loss: 4.42110032154062"
[1] "Thu Nov 2 13:00:41 2023: Iteration: 1 loss: 4.05329114110436"
[1] "Thu Nov 2 13:00:42 2023: Iteration: 2 loss: 4.02237895650388"
Time difference of 1.912955 secs
[1] "Thu Nov 2 13:00:42 2023: 2 Final nb-AE loss: 4.02237895650388"
[1] "Evaluation loss: 0.488507988686597 for q=4"
[1] "Thu Nov 2 13:00:43 2023: Initial PCA loss: 4.39666498568224"
[1] "Thu Nov 2 13:00:45 2023: Iteration: 1 loss: 3.97667250313389"
[1] "Thu Nov 2 13:00:46 2023: Iteration: 2 loss: 3.95514538511609"
Time difference of 1.885312 secs
[1] "Thu Nov 2 13:00:46 2023: 2 Final nb-AE loss: 3.95514538511609"
[1] "Evaluation loss: 0.493049157666591 for q=5"
[1] "Thu Nov 2 13:00:58 2023: Initial PCA loss: 6.46616282459584"
[1] "Thu Nov 2 13:01:00 2023: Iteration: 1 loss: 4.81528047990959"
[1] "Thu Nov 2 13:01:01 2023: Iteration: 2 loss: 4.78972022300971"
Time difference of 2.413595 secs
[1] "Thu Nov 2 13:01:01 2023: 2 Final nb-AE loss: 4.78972022300971"
[ FAIL 0 | WARN 32 | SKIP 0 | PASS 103 ]
[ FAIL 0 | WARN 32 | SKIP 0 | PASS 103 ]
>
> proc.time()
user system elapsed
97.633 1.669 99.480
OUTRIDER.Rcheck/OUTRIDER-Ex.timings
| name | user | system | elapsed | |
| OUTRIDER | 13.715 | 3.471 | 15.481 | |
| OutriderDataSet-class | 1.195 | 0.188 | 1.386 | |
| aberrant | 2.565 | 1.177 | 2.515 | |
| computeGeneLength | 1.977 | 0.346 | 2.330 | |
| computeLatentSpace | 1.160 | 0.079 | 1.242 | |
| computePvalues | 2.819 | 2.733 | 3.239 | |
| computeZscores | 1.256 | 0.168 | 1.427 | |
| controlForConfounders | 1.640 | 0.136 | 1.784 | |
| counts | 0.785 | 0.067 | 0.856 | |
| estimateBestQ | 0.591 | 0.032 | 0.624 | |
| filterExpression | 2.085 | 0.053 | 2.142 | |
| findEncodingDim | 16.096 | 0.472 | 16.628 | |
| fit | 1.237 | 0.005 | 1.245 | |
| fpkm | 1.052 | 0.008 | 1.062 | |
| getter_setter_functions | 4.268 | 0.023 | 4.303 | |
| makeExampleOutriderDataSet | 1.535 | 0.020 | 1.558 | |
| normalizationFactors | 1.000 | 0.001 | 1.003 | |
| plotFunctions | 10.809 | 0.198 | 11.047 | |
| results | 4.460 | 0.008 | 4.479 | |
| sampleExclusionMask | 0.602 | 0.004 | 0.608 | |
| sizeFactors | 0.897 | 0.000 | 0.899 | |