| Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-01 07:38:46 -0000 (Wed, 01 Mar 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4266 |
| 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 | ||||
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To the developers/maintainers of the OUTRIDER package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1411/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OUTRIDER 1.17.1 (landing page) Christian Mertes
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: OUTRIDER |
| Version: 1.17.1 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:OUTRIDER.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings OUTRIDER_1.17.1.tar.gz |
| StartedAt: 2023-02-28 10:37:30 -0000 (Tue, 28 Feb 2023) |
| EndedAt: 2023-02-28 10:54:59 -0000 (Tue, 28 Feb 2023) |
| EllapsedTime: 1048.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: OUTRIDER.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:OUTRIDER.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings OUTRIDER_1.17.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/OUTRIDER.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘OUTRIDER/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OUTRIDER’ version ‘1.17.1’
* 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++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* 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 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 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
findEncodingDim 16.137 0.492 16.630
OUTRIDER 12.877 3.271 14.478
plotFunctions 11.037 0.224 11.254
computePvalues 2.942 2.555 3.238
* 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 ...
‘OUTRIDER.Rnw’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/OUTRIDER.Rcheck/00check.log’
for details.
OUTRIDER.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL OUTRIDER ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘OUTRIDER’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ using C++11 g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/lib -L/usr/local/lib -o OUTRIDER.so RcppExports.o loss_n_gradient_functions.o -fopenmp -llapack -L/home/biocbuild/bbs-3.17-bioc/R/lib -lRblas -lgfortran -lm -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.17-bioc/R/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) (2023-01-14 r83615) -- "Unsuffered Consequences"
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 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] "Tue Feb 28 10:44:28 2023: Initial PCA loss: 6.09323600303724"
[1] "Tue Feb 28 10:44:30 2023: Iteration: 1 loss: 4.40428776947674"
[1] "Tue Feb 28 10:44:31 2023: Iteration: 2 loss: 4.34599302117502"
[1] "Tue Feb 28 10:44:32 2023: Iteration: 3 loss: 4.31672991648811"
[1] "Tue Feb 28 10:44:32 2023: Iteration: 4 loss: 4.29604380373066"
[1] "Tue Feb 28 10:44:33 2023: Iteration: 5 loss: 4.28734851492187"
[1] "Tue Feb 28 10:44:34 2023: Iteration: 6 loss: 4.28210195166819"
Time difference of 5.549039 secs
[1] "Tue Feb 28 10:44:34 2023: 6 Final nb-AE loss: 4.28210195166819"
[1] "Tue Feb 28 10:44:36 2023: Initial PCA loss: 6.09323600303724"
[1] "Tue Feb 28 10:44:37 2023: Iteration: 1 loss: 4.40428776947674"
[1] "Tue Feb 28 10:44:38 2023: Iteration: 2 loss: 4.34599302117502"
[1] "Tue Feb 28 10:44:39 2023: Iteration: 3 loss: 4.31672991648811"
[1] "Tue Feb 28 10:44:40 2023: Iteration: 4 loss: 4.29604380373066"
[1] "Tue Feb 28 10:44:41 2023: Iteration: 5 loss: 4.28734851492187"
[1] "Tue Feb 28 10:44:42 2023: Iteration: 6 loss: 4.28210195166819"
Time difference of 5.416043 secs
[1] "Tue Feb 28 10:44:42 2023: 6 Final nb-AE loss: 4.28210195166819"
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] "Tue Feb 28 10:45:00 2023: Initial PCA loss: 4.4630502469877"
[1] "Tue Feb 28 10:45:02 2023: Iteration: 1 loss: 4.09007751879649"
[1] "Tue Feb 28 10:45:04 2023: Iteration: 2 loss: 4.07013980939294"
Time difference of 3.594708 secs
[1] "Tue Feb 28 10:45:04 2023: 2 Final nb-AE loss: 4.07013980939294"
[1] "Evaluation loss: 0.310542572721048 for q=3"
[1] "Tue Feb 28 10:45:06 2023: Initial PCA loss: 4.42479622048517"
[1] "Tue Feb 28 10:45:08 2023: Iteration: 1 loss: 4.01568668095595"
[1] "Tue Feb 28 10:45:09 2023: Iteration: 2 loss: 4.00478213069462"
Time difference of 1.928108 secs
[1] "Tue Feb 28 10:45:09 2023: 2 Final nb-AE loss: 4.00478213069462"
[1] "Evaluation loss: 0.15971905221399 for q=4"
[1] "Tue Feb 28 10:45:10 2023: Initial PCA loss: 4.40655833902657"
[1] "Tue Feb 28 10:45:12 2023: Iteration: 1 loss: 3.94590459660366"
[1] "Tue Feb 28 10:45:13 2023: Iteration: 2 loss: 3.93288438156989"
Time difference of 1.876698 secs
[1] "Tue Feb 28 10:45:13 2023: 2 Final nb-AE loss: 3.93288438156989"
[1] "Evaluation loss: 0.158666289442955 for q=5"
[1] "Tue Feb 28 10:45:27 2023: Initial PCA loss: 6.46616282459584"
[1] "Tue Feb 28 10:45:29 2023: Iteration: 1 loss: 4.81540001449887"
[1] "Tue Feb 28 10:45:30 2023: Iteration: 2 loss: 4.78983075795365"
Time difference of 2.429173 secs
[1] "Tue Feb 28 10:45:30 2023: 2 Final nb-AE loss: 4.78983075795365"
[ FAIL 0 | WARN 32 | SKIP 0 | PASS 103 ]
[ FAIL 0 | WARN 32 | SKIP 0 | PASS 103 ]
>
> proc.time()
user system elapsed
93.428 1.506 101.180
OUTRIDER.Rcheck/OUTRIDER-Ex.timings
| name | user | system | elapsed | |
| OUTRIDER | 12.877 | 3.271 | 14.478 | |
| OutriderDataSet-class | 1.107 | 0.168 | 1.276 | |
| aberrant | 2.535 | 1.108 | 2.472 | |
| computeGeneLength | 1.956 | 0.288 | 2.246 | |
| computeLatentSpace | 1.124 | 0.076 | 1.199 | |
| computePvalues | 2.942 | 2.555 | 3.238 | |
| computeZscores | 1.289 | 0.203 | 1.493 | |
| controlForConfounders | 1.508 | 0.208 | 1.717 | |
| counts | 0.821 | 0.032 | 0.853 | |
| estimateBestQ | 0.576 | 0.008 | 0.585 | |
| filterExpression | 2.094 | 0.060 | 2.154 | |
| findEncodingDim | 16.137 | 0.492 | 16.630 | |
| fit | 1.220 | 0.032 | 1.252 | |
| fpkm | 1.042 | 0.004 | 1.046 | |
| getter_setter_functions | 4.211 | 0.004 | 4.215 | |
| makeExampleOutriderDataSet | 1.525 | 0.016 | 1.542 | |
| normalizationFactors | 0.977 | 0.032 | 1.009 | |
| plotFunctions | 11.037 | 0.224 | 11.254 | |
| results | 4.453 | 0.020 | 4.474 | |
| sampleExclusionMask | 0.606 | 0.004 | 0.610 | |
| sizeFactors | 0.879 | 0.000 | 0.880 | |