| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-05-31 05:44:39 -0000 (Wed, 31 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4219 |
| 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 | ||||
|
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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 1428/2197 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OUTRIDER 1.19.0 (landing page) Christian Mertes
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: OUTRIDER |
| Version: 1.19.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:OUTRIDER.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings OUTRIDER_1.19.0.tar.gz |
| StartedAt: 2023-05-30 14:31:15 -0000 (Tue, 30 May 2023) |
| EndedAt: 2023-05-30 14:48:36 -0000 (Tue, 30 May 2023) |
| EllapsedTime: 1040.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: OUTRIDER.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:OUTRIDER.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings OUTRIDER_1.19.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/OUTRIDER.Rcheck’
* using R version 4.3.0 (2023-04-21)
* 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 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘OUTRIDER/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OUTRIDER’ version ‘1.19.0’
* 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++ (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0’
* 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 ... 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 12.844 3.320 14.535
findEncodingDim 15.211 0.399 15.612
plotFunctions 10.572 0.172 10.738
computePvalues 2.709 2.431 3.082
* 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: 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-4.3.0/bin/R CMD INSTALL OUTRIDER ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’ * installing *source* package ‘OUTRIDER’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0’ using C++11 g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -DARMA_DONT_USE_OPENMP -fPIC -g -O2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -DARMA_DONT_USE_OPENMP -fPIC -g -O2 -c loss_n_gradient_functions.cpp -o loss_n_gradient_functions.o g++ -std=gnu++11 -shared -L/home/biocbuild/R/R-4.3.0/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-4.3.0/lib -lR installing to /home/biocbuild/R/R-4.3.0/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 4.3.0 (2023-04-21) -- "Already Tomorrow"
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] "Tue May 30 14:38:30 2023: Initial PCA loss: 6.16492132084264"
[1] "Tue May 30 14:38:31 2023: Iteration: 1 loss: 4.471072017112"
[1] "Tue May 30 14:38:32 2023: Iteration: 2 loss: 4.39601391403689"
[1] "Tue May 30 14:38:33 2023: Iteration: 3 loss: 4.37219132534751"
[1] "Tue May 30 14:38:34 2023: Iteration: 4 loss: 4.35596391619911"
[1] "Tue May 30 14:38:35 2023: Iteration: 5 loss: 4.35018099252254"
[1] "Tue May 30 14:38:36 2023: Iteration: 6 loss: 4.34558415010005"
Time difference of 5.258382 secs
[1] "Tue May 30 14:38:36 2023: 6 Final nb-AE loss: 4.34558415010005"
[1] "Tue May 30 14:38:37 2023: Initial PCA loss: 6.16492132084264"
[1] "Tue May 30 14:38:39 2023: Iteration: 1 loss: 4.471072017112"
[1] "Tue May 30 14:38:40 2023: Iteration: 2 loss: 4.39601391403689"
[1] "Tue May 30 14:38:40 2023: Iteration: 3 loss: 4.37219132534751"
[1] "Tue May 30 14:38:41 2023: Iteration: 4 loss: 4.35596391619911"
[1] "Tue May 30 14:38:42 2023: Iteration: 5 loss: 4.35018099252254"
[1] "Tue May 30 14:38:43 2023: Iteration: 6 loss: 4.34558415010005"
Time difference of 5.146813 secs
[1] "Tue May 30 14:38:43 2023: 6 Final nb-AE loss: 4.34558415010005"
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 May 30 14:39:01 2023: Initial PCA loss: 4.46445862592757"
[1] "Tue May 30 14:39:03 2023: Iteration: 1 loss: 4.10708294994175"
[1] "Tue May 30 14:39:04 2023: Iteration: 2 loss: 4.09235324737883"
Time difference of 1.834859 secs
[1] "Tue May 30 14:39:04 2023: 2 Final nb-AE loss: 4.09235324737883"
[1] "Evaluation loss: 0.307554196529873 for q=3"
[1] "Tue May 30 14:39:05 2023: Initial PCA loss: 4.44357889121228"
[1] "Tue May 30 14:39:06 2023: Iteration: 1 loss: 4.04321073229099"
[1] "Tue May 30 14:39:07 2023: Iteration: 2 loss: 4.02265468899381"
Time difference of 1.833918 secs
[1] "Tue May 30 14:39:07 2023: 2 Final nb-AE loss: 4.02265468899381"
[1] "Evaluation loss: 0.304222566398324 for q=4"
[1] "Tue May 30 14:39:08 2023: Initial PCA loss: 4.41873113535893"
[1] "Tue May 30 14:39:10 2023: Iteration: 1 loss: 3.95506220689944"
[1] "Tue May 30 14:39:12 2023: Iteration: 2 loss: 3.93487972730499"
Time difference of 2.944859 secs
[1] "Tue May 30 14:39:12 2023: 2 Final nb-AE loss: 3.93487972730499"
[1] "Evaluation loss: 0.377170033735722 for q=5"
[1] "Tue May 30 14:39:23 2023: Initial PCA loss: 6.46616282459584"
[1] "Tue May 30 14:39:25 2023: Iteration: 1 loss: 4.81528047990959"
[1] "Tue May 30 14:39:26 2023: Iteration: 2 loss: 4.78972022300971"
Time difference of 2.281905 secs
[1] "Tue May 30 14:39:26 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
91.475 2.033 93.495
OUTRIDER.Rcheck/OUTRIDER-Ex.timings
| name | user | system | elapsed | |
| OUTRIDER | 12.844 | 3.320 | 14.535 | |
| OutriderDataSet-class | 1.085 | 0.134 | 1.220 | |
| aberrant | 2.465 | 1.076 | 2.423 | |
| computeGeneLength | 1.887 | 0.217 | 2.104 | |
| computeLatentSpace | 1.035 | 0.076 | 1.111 | |
| computePvalues | 2.709 | 2.431 | 3.082 | |
| computeZscores | 1.178 | 0.236 | 1.413 | |
| controlForConfounders | 1.473 | 0.143 | 1.616 | |
| counts | 0.767 | 0.032 | 0.798 | |
| estimateBestQ | 0.541 | 0.000 | 0.541 | |
| filterExpression | 2.008 | 0.092 | 2.100 | |
| findEncodingDim | 15.211 | 0.399 | 15.612 | |
| fit | 1.162 | 0.044 | 1.208 | |
| fpkm | 1.013 | 0.004 | 1.017 | |
| getter_setter_functions | 3.987 | 0.052 | 4.039 | |
| makeExampleOutriderDataSet | 1.476 | 0.000 | 1.475 | |
| normalizationFactors | 0.95 | 0.00 | 0.95 | |
| plotFunctions | 10.572 | 0.172 | 10.738 | |
| results | 4.217 | 0.016 | 4.234 | |
| sampleExclusionMask | 0.585 | 0.000 | 0.585 | |
| sizeFactors | 0.839 | 0.008 | 0.847 | |