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###
### 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 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 ... WARNING
Invalid citation information in ‘inst/CITATION’:
  Error in tools:::.parse_CITATION_file(file, meta$Encoding): non-ASCII input in a CITATION file without a declared encoding
  Warning message:
  In utils::packageDescription(basename(dir), dirname(dir)) :
    no package 'OUTRIDER' was found
* 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 ... WARNING
Error in library(OUTRIDER, lib.loc = "/home/biocbuild/bbs-3.17-bioc/R/library") : 
  there is no package called ‘OUTRIDER’
Execution halted

It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
* 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 ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  [1] "Evaluation loss: 0.460212271656785 for q=3"
  [1] "Sun Jan 29 05:45:21 2023: Initial PCA loss: 4.43176861864039"
  [1] "Sun Jan 29 05:45:23 2023: Iteration: 1 loss: 4.06063376579377"
  [1] "Sun Jan 29 05:45:23 2023: Iteration: 2 loss: 4.04476978018496"
  Time difference of 1.956957 secs
  [1] "Sun Jan 29 05:45:23 2023: 2 Final nb-AE loss: 4.04476978018496"
  [1] "Evaluation loss: 0.390843039383055 for q=4"
  [1] "Sun Jan 29 05:45:25 2023: Initial PCA loss: 4.41197623767674"
  [1] "Sun Jan 29 05:45:27 2023: Iteration: 1 loss: 3.97891544194152"
  [1] "Sun Jan 29 05:45:29 2023: Iteration: 2 loss: 3.95220884636681"
  Time difference of 3.042551 secs
  [1] "Sun Jan 29 05:45:29 2023: 2 Final nb-AE loss: 3.95220884636681"
  [1] "Evaluation loss: 0.37400553871916 for q=5"
  [1] "Sun Jan 29 05:45:43 2023: Initial PCA loss: 6.46616282459584"
  Killed
* 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 ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘OUTRIDER.Rnw’ using knitr
The magick package is required to crop "figure/deVsOutlier-1.png" but not available.
Killed

* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 2 WARNINGs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/OUTRIDER.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL OUTRIDER
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-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/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/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/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/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)

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] "Sun Jan 29 05:44:29 2023: Initial PCA loss: 6.13713117720576"
[1] "Sun Jan 29 05:44:31 2023: Iteration: 1 loss: 4.57875064446764"
[1] "Sun Jan 29 05:44:32 2023: Iteration: 2 loss: 4.4433775932415"
[1] "Sun Jan 29 05:44:33 2023: Iteration: 3 loss: 4.38970792208347"
[1] "Sun Jan 29 05:44:35 2023: Iteration: 4 loss: 4.37434558608913"
[1] "Sun Jan 29 05:44:36 2023: Iteration: 5 loss: 4.36265738600777"
[1] "Sun Jan 29 05:44:37 2023: Iteration: 6 loss: 4.35726803750825"
Time difference of 7.203659 secs
[1] "Sun Jan 29 05:44:37 2023: 6 Final nb-AE loss: 4.35726803750825"
[1] "Sun Jan 29 05:44:40 2023: Initial PCA loss: 6.13713117720576"
[1] "Sun Jan 29 05:44:43 2023: Iteration: 1 loss: 4.57875064446764"
[1] "Sun Jan 29 05:44:44 2023: Iteration: 2 loss: 4.4433775932415"
[1] "Sun Jan 29 05:44:45 2023: Iteration: 3 loss: 4.38970792208347"
[1] "Sun Jan 29 05:44:46 2023: Iteration: 4 loss: 4.37434558608913"
[1] "Sun Jan 29 05:44:47 2023: Iteration: 5 loss: 4.36265738600777"
[1] "Sun Jan 29 05:44:48 2023: Iteration: 6 loss: 4.35726803750825"
Time difference of 7.09121 secs
[1] "Sun Jan 29 05:44:48 2023: 6 Final nb-AE loss: 4.35726803750825"
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] "Sun Jan 29 05:45:16 2023: Initial PCA loss: 4.47329327202986"
[1] "Sun Jan 29 05:45:19 2023: Iteration: 1 loss: 4.15593162525625"
[1] "Sun Jan 29 05:45:19 2023: Iteration: 2 loss: 4.13959226406972"
Time difference of 2.061629 secs
[1] "Sun Jan 29 05:45:19 2023: 2 Final nb-AE loss: 4.13959226406972"
[1] "Evaluation loss: 0.460212271656785 for q=3"
[1] "Sun Jan 29 05:45:21 2023: Initial PCA loss: 4.43176861864039"
[1] "Sun Jan 29 05:45:23 2023: Iteration: 1 loss: 4.06063376579377"
[1] "Sun Jan 29 05:45:23 2023: Iteration: 2 loss: 4.04476978018496"
Time difference of 1.956957 secs
[1] "Sun Jan 29 05:45:23 2023: 2 Final nb-AE loss: 4.04476978018496"
[1] "Evaluation loss: 0.390843039383055 for q=4"
[1] "Sun Jan 29 05:45:25 2023: Initial PCA loss: 4.41197623767674"
[1] "Sun Jan 29 05:45:27 2023: Iteration: 1 loss: 3.97891544194152"
[1] "Sun Jan 29 05:45:29 2023: Iteration: 2 loss: 3.95220884636681"
Time difference of 3.042551 secs
[1] "Sun Jan 29 05:45:29 2023: 2 Final nb-AE loss: 3.95220884636681"
[1] "Evaluation loss: 0.37400553871916 for q=5"
[1] "Sun Jan 29 05:45:43 2023: Initial PCA loss: 6.46616282459584"
Killed