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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PCAtools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PCAtools_2.14.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/PCAtools.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PCAtools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PCAtools’ version ‘2.14.0’
* 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 ‘PCAtools’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 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 ... OK
* 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 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
pca       19.153  1.997  21.834
biplot     7.903  0.298   9.235
pairsplot  7.587  0.132   8.639
* 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. └─PCAtools::pca(lcounts, center = FALSE, rank = 10) at test-pca.R:49:5
    2.   ├─MatrixGenerics::colVars(DelayedArray(mat), center = .center)
    3.   └─DelayedMatrixStats::colVars(DelayedArray(mat), center = .center)
    4.     └─DelayedMatrixStats (local) .local(x, rows, cols, na.rm, center, ..., useNames = useNames)
    5.       └─DelayedMatrixStats:::.smart_seed_dispatcher(...)
    6.         └─MatrixGenerics (local) candidate(S, ..., useNames = useNames)
    7.           └─MatrixGenerics (local) .local(x, rows, cols, na.rm, center, ..., useNames = useNames)
    8.             └─matrixStats::colVars(...)
    9.               └─matrixStats:::validateScalarCenter(center, ncol(x), "columns")
   10.                 └─base (local) action(msg = msg, package = .packageName)
  
  [ FAIL 2 | WARN 0 | SKIP 1 | PASS 36 ]
  Error: Test failures
  Execution halted
* 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: 1 ERROR, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.18-bioc/meat/PCAtools.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL PCAtools
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘PCAtools’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/dqrng/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/dqrng/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c shuffle_matrix.cpp -o shuffle_matrix.o
clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o PCAtools.so RcppExports.o shuffle_matrix.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-PCAtools/00new/PCAtools/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 (PCAtools)

R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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(scran)
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

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

Loading required package: GenomicRanges
Loading required package: stats4
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

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: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

Loading required package: scuttle
> test_check("PCAtools")
Loading required package: PCAtools
Loading required package: ggplot2
Loading required package: ggrepel

Attaching package: 'PCAtools'

The following object is masked from 'package:scran':

    parallelPCA

The following objects are masked from 'package:stats':

    biplot, screeplot

[ FAIL 2 | WARN 0 | SKIP 1 | PASS 36 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• missing lots of things (1): 'test-datatypes.R:1:1'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-pca.R:12:5'): pca settings work as expected ────────────────────
<defunctError/error/condition>
Error: [matrixStats (>= 0.58.0)] Argument 'center' should be of the same length as number of columns of 'x'. Use of a scalar value is defunct: 1 != 1000 (See also ?matrixStats::matrixStats.options)
Backtrace:
     ▆
  1. └─PCAtools::pca(lcounts, center = FALSE, rank = 10) at test-pca.R:12:5
  2.   ├─MatrixGenerics::colVars(DelayedArray(mat), center = .center)
  3.   └─DelayedMatrixStats::colVars(DelayedArray(mat), center = .center)
  4.     └─DelayedMatrixStats (local) .local(x, rows, cols, na.rm, center, ..., useNames = useNames)
  5.       └─DelayedMatrixStats:::.smart_seed_dispatcher(...)
  6.         └─MatrixGenerics (local) candidate(S, ..., useNames = useNames)
  7.           └─MatrixGenerics (local) .local(x, rows, cols, na.rm, center, ..., useNames = useNames)
  8.             └─matrixStats::colVars(...)
  9.               └─matrixStats:::validateScalarCenter(center, ncol(x), "columns")
 10.                 └─base (local) action(msg = msg, package = .packageName)
── Error ('test-pca.R:49:5'): percentage of variance calculations are correct ──
<defunctError/error/condition>
Error: [matrixStats (>= 0.58.0)] Argument 'center' should be of the same length as number of columns of 'x'. Use of a scalar value is defunct: 1 != 1000 (See also ?matrixStats::matrixStats.options)
Backtrace:
     ▆
  1. └─PCAtools::pca(lcounts, center = FALSE, rank = 10) at test-pca.R:49:5
  2.   ├─MatrixGenerics::colVars(DelayedArray(mat), center = .center)
  3.   └─DelayedMatrixStats::colVars(DelayedArray(mat), center = .center)
  4.     └─DelayedMatrixStats (local) .local(x, rows, cols, na.rm, center, ..., useNames = useNames)
  5.       └─DelayedMatrixStats:::.smart_seed_dispatcher(...)
  6.         └─MatrixGenerics (local) candidate(S, ..., useNames = useNames)
  7.           └─MatrixGenerics (local) .local(x, rows, cols, na.rm, center, ..., useNames = useNames)
  8.             └─matrixStats::colVars(...)
  9.               └─matrixStats:::validateScalarCenter(center, ncol(x), "columns")
 10.                 └─base (local) action(msg = msg, package = .packageName)

[ FAIL 2 | WARN 0 | SKIP 1 | PASS 36 ]
Error: Test failures
Execution halted