##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:netSmooth.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings netSmooth_1.25.0.tar.gz
###
##############################################################################
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* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/netSmooth.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'netSmooth/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'netSmooth' version '1.25.0'
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'netSmooth' can be installed ... OK
* 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 code 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 ... NOTE
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
* 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 ... NOTE
checkRd: (-1) human.ppi.Rd:7: Lost braces; missing escapes or markup?
     7 | \format{A square matrix where A_{ij}=1 if gene i interacts with gene j}
       |                                 ^
checkRd: (-1) mouse.ppi.Rd:7: Lost braces; missing escapes or markup?
     7 | \format{A square matrix where A_{ij}=1 if gene i interacts with gene j}
       |                                 ^
checkRd: (-1) randomWalkByMatrixInv-matrix-method.Rd:29: Lost braces; missing escapes or markup?
    29 |   f_{ss} = (1 - alpha) * (I - alpha * A)^{-1} * f_0
       |     ^
checkRd: (-1) randomWalkByMatrixInv-matrix-method.Rd:29: Lost braces; missing escapes or markup?
    29 |   f_{ss} = (1 - alpha) * (I - alpha * A)^{-1} * f_0
       |                                          ^
* 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 ... NOTE
Documented arguments not in \usage in Rd file 'projectFromNetworkRecombine-matrix-method.Rd':
  'filepath'

Documented arguments not in \usage in Rd file 'smoothAndRecombine-matrix-method.Rd':
  'filepath'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
robustClusters   7.75   0.38    8.19
pickDimReduction 5.77   0.14    5.91
* 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:
   23.                             └─BiocSingular (local) .local(x, ...)
   24.                               ├─BiocSingular::runSVD(...)
   25.                               └─BiocSingular::runSVD(...)
   26.                                 ├─BiocSingular::runSVD(...)
   27.                                 └─BiocSingular::runSVD(...)
   28.                                   ├─base::do.call(...)
   29.                                   └─BiocSingular (local) `<fn>`(...)
   30.                                     └─BiocSingular:::.compute_center_and_scale(x, center, scale, nthreads = bpnworkers(BPPARAM))
   31.                                       ├─beachmat::initializeCpp(x)
   32.                                       └─beachmat::initializeCpp(x)
   33.                                         └─beachmat:::initialize_dense_matrix(x@x, nrow(x), ncol(x))
  
  [ FAIL 1 | WARN 1 | SKIP 2 | PASS 13 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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, 4 NOTEs
See
  'F:/biocbuild/bbs-3.20-bioc/meat/netSmooth.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL netSmooth
###
##############################################################################
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* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'netSmooth' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (netSmooth)

R version 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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(netSmooth)
Loading required package: scater
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, 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

Attaching package: 'IRanges'

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

    windows

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
Loading required package: ggplot2
Loading required package: clusterExperiment

Attaching package: 'clusterExperiment'

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

    plotHeatmap

> 
> test_check("netSmooth")
[ FAIL 1 | WARN 1 | SKIP 2 | PASS 13 ]

══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• empty test (2): 'test_netsmooth.R:7:1', 'test_netsmooth.R:55:1'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_netsmooth.R:19:5'): netSmooth accepts sparse matrices ──────────
<Rcpp::not_a_matrix/C++Error/error/condition>
Error: Not a matrix.
Backtrace:
     ▆
  1. ├─netSmooth::netSmooth(...) at test_netsmooth.R:19:5
  2. └─netSmooth::netSmooth(...)
  3.   └─netSmooth (local) .local(x, ...)
  4.     ├─netSmooth::pickDimReduction(x, is.counts = is.counts)
  5.     └─netSmooth::pickDimReduction(x, is.counts = is.counts)
  6.       └─netSmooth (local) .local(x, ...)
  7.         └─base::sapply(...)
  8.           └─base::lapply(X = X, FUN = FUN, ...)
  9.             └─netSmooth (local) FUN(X[[i]], ...)
 10.               ├─netSmooth:::calc2DEntropy(dimReduce(x, flavor = flavor, is.counts = is.counts))
 11.               │ └─entropy::discretize2d(x[, 1], x[, 2], numBins1, numBins2)
 12.               │   └─base::seq(from = r1[1], to = r1[2], length.out = numBins1 + 1)
 13.               └─netSmooth:::dimReduce(x, flavor = flavor, is.counts = is.counts)
 14.                 ├─BiocSingular (local) function.to.call(sce, ncomponents = k, ntop = ntop)
 15.                 └─scater (local) function.to.call(sce, ncomponents = k, ntop = ntop)
 16.                   └─scater (local) .local(x, ...)
 17.                     ├─scater::calculatePCA(y, ...)
 18.                     └─scater::calculatePCA(y, ...)
 19.                       └─scater (local) .local(x, ...)
 20.                         └─scater:::.calculate_pca(mat, transposed = !is.null(dimred), ...)
 21.                           ├─BiocSingular::runPCA(...)
 22.                           └─BiocSingular::runPCA(...)
 23.                             └─BiocSingular (local) .local(x, ...)
 24.                               ├─BiocSingular::runSVD(...)
 25.                               └─BiocSingular::runSVD(...)
 26.                                 ├─BiocSingular::runSVD(...)
 27.                                 └─BiocSingular::runSVD(...)
 28.                                   ├─base::do.call(...)
 29.                                   └─BiocSingular (local) `<fn>`(...)
 30.                                     └─BiocSingular:::.compute_center_and_scale(x, center, scale, nthreads = bpnworkers(BPPARAM))
 31.                                       ├─beachmat::initializeCpp(x)
 32.                                       └─beachmat::initializeCpp(x)
 33.                                         └─beachmat:::initialize_dense_matrix(x@x, nrow(x), ncol(x))

[ FAIL 1 | WARN 1 | SKIP 2 | PASS 13 ]
Error: Test failures
Execution halted