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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:nnSVG.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings nnSVG_1.5.4.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/nnSVG.Rcheck’
* using R version 4.3.0 RC (2023-04-13 r84266)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘nnSVG/DESCRIPTION’ ... OK
* this is package ‘nnSVG’ version ‘1.5.4’
* 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 ‘nnSVG’ 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 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘nnSVG-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: filter_genes
> ### Title: Preprocessing function to filter genes
> ### Aliases: filter_genes
> 
> ### ** Examples
> 
> library(SpatialExperiment)
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

> library(STexampleData)
Loading required package: ExperimentHub
Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr

Attaching package: ‘AnnotationHub’

The following object is masked from ‘package:Biobase’:

    cache

> 
> # load example dataset from STexampleData package
> spe <- Visium_humanDLPFC()
see ?STexampleData and browseVignettes('STexampleData') for documentation
downloading 1 resources
retrieving 1 resource
loading from cache
Error: failed to load resource
  name: EH7538
  title: Visium_humanDLPFC
  reason: unknown input format
Execution halted
* 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:
    9.     └─ExperimentHub (local) .local(x, i, j = j, ...)
   10.       ├─methods::callNextMethod(x, i, j, ..., force = force, verbose = verbose)
   11.       │ └─base::eval(call, callEnv)
   12.       │   └─base::eval(call, callEnv)
   13.       └─AnnotationHub (local) .nextMethod(x, i, j, ..., force = force, verbose = verbose)
   14.         └─AnnotationHub (local) .local(x, i, j = j, ...)
   15.           └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
   16.             └─base::tryCatch(...)
   17.               └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   18.                 └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   19.                   └─value[[3L]](cond)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  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: 2 ERRORs
See
  ‘/Users/biocbuild/bbs-3.18-bioc/meat/nnSVG.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL nnSVG
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘nnSVG’ ...
** using staged installation
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (nnSVG)

R version 4.3.0 RC (2023-04-13 r84266) -- "Already Tomorrow"
Copyright (C) 2023 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(nnSVG)
> 
> test_check("nnSVG")
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_example.R:2:1'): (code run outside of `test_that()`) ───────────
Error: failed to load resource
  name: EH7538
  title: Visium_humanDLPFC
  reason: unknown input format
Backtrace:
     ▆
  1. ├─utils::example(nnSVG, echo = FALSE) at test_example.R:2:0
  2. │ └─base::source(...)
  3. │   ├─base::withVisible(eval(ei, envir))
  4. │   └─base::eval(ei, envir)
  5. │     └─base::eval(ei, envir)
  6. └─ExperimentHub (local) Visium_humanDLPFC() at tmp/Rtmp0KPbqX/Rex173de43c9ccf8:16:0
  7.   ├─eh[[ehid]]
  8.   └─eh[[ehid]]
  9.     └─ExperimentHub (local) .local(x, i, j = j, ...)
 10.       ├─methods::callNextMethod(x, i, j, ..., force = force, verbose = verbose)
 11.       │ └─base::eval(call, callEnv)
 12.       │   └─base::eval(call, callEnv)
 13.       └─AnnotationHub (local) .nextMethod(x, i, j, ..., force = force, verbose = verbose)
 14.         └─AnnotationHub (local) .local(x, i, j = j, ...)
 15.           └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
 16.             └─base::tryCatch(...)
 17.               └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 18.                 └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 19.                   └─value[[3L]](cond)

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