##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SpatialFeatureExperiment.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SpatialFeatureExperiment_1.5.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-apple-darwin20
* 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 ‘SpatialFeatureExperiment/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SpatialFeatureExperiment’ version ‘1.5.1’
* 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 ‘SpatialFeatureExperiment’ 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 ... NOTE
Unexported objects imported by ':::' calls:
  ‘S4Vectors:::disableValidity’ ‘spdep:::minmax.listw’
  See the note in ?`:::` about the use of this operator.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘SpatialFeatureExperiment-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: readVizgen
> ### Title: Read Vizgen MERFISH output as SpatialFeatureExperiment
> ### Aliases: readVizgen
> 
> ### ** Examples
> 
> dir_use <- system.file("extdata/vizgen", package = "SpatialFeatureExperiment")
> sfe <- readVizgen(dir_use, z = 0L, use_cellpose = TRUE, image = "PolyT",
+ flip = "geometry")
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/arrow/libs/arrow.so':
  dlopen(/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/arrow/libs/arrow.so, 0x0006): symbol not found in flat namespace (_utf8proc_category)
Calls: readVizgen ... <Anonymous> -> loadNamespace -> library.dynam -> dyn.load
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:
   4.   └─base::library.dynam(lib, package, package.lib)
   5.     └─base::dyn.load(file, DLLpath = DLLpath, ...)
  ── Error ('test-read.R:224:1'): (code run outside of `test_that()`) ────────────
  Error in `dyn.load(file, DLLpath = DLLpath, ...)`: unable to load shared object '/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/arrow/libs/arrow.so':
    dlopen(/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/arrow/libs/arrow.so, 0x0006): symbol not found in flat namespace (_utf8proc_category)
  Backtrace:
      ▆
   1. ├─sfarrow::st_read_parquet(file.path(dir_use, "cellpose_micron_space.parquet")) at test-read.R:224:1
   2. └─base::loadNamespace(x)
   3.   └─base::library.dynam(lib, package, package.lib)
   4.     └─base::dyn.load(file, DLLpath = DLLpath, ...)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 561 ]
  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: 2 ERRORs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SpatialFeatureExperiment
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘SpatialFeatureExperiment’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for ‘saveRDS’ from package ‘base’ in package ‘SpatialFeatureExperiment’
** 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 (SpatialFeatureExperiment)

R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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(SpatialFeatureExperiment)
> 
> test_check("SpatialFeatureExperiment")
Linking to GEOS 3.11.0, GDAL 3.5.3, PROJ 9.1.0; sf_use_s2() is TRUE
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 objects are masked from 'package:Matrix':

    expand, unname

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

see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
trying URL 'https://cf.10xgenomics.com/samples/spatial-exp/2.0.0/Visium_Mouse_Olfactory_Bulb/Visium_Mouse_Olfactory_Bulb_filtered_feature_bc_matrix.h5'
Content type 'binary/octet-stream' length 7521734 bytes (7.2 MB)
==================================================
downloaded 7.2 MB

trying URL 'https://cf.10xgenomics.com/samples/spatial-exp/2.0.0/Visium_Mouse_Olfactory_Bulb/Visium_Mouse_Olfactory_Bulb_spatial.tar.gz'
Content type 'application/x-tar' length 7806681 bytes (7.4 MB)
==================================================
downloaded 7.4 MB

terra 1.7.71

Attaching package: 'terra'

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

    distance, nearest, shift, trim, values, values<-, width

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

    distance, gaps, nearest, shift, trim, values, values<-, width

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

    distance, gaps, nearest, shift, trim, width

The following objects are masked from 'package:S4Vectors':

    values, values<-, width

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

    width

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

    centroids, crop

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

    compare, describe

see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
Testing dist_type none style W 
Testing dist_type idw style W 
Testing dist_type exp style W 
Testing dist_type dpd style W 
Testing dist_type idw style raw 
Testing dist_type idw style W 
Testing dist_type idw style B 
Testing dist_type idw style C 
Testing dist_type idw style U 
Testing dist_type idw style minmax 
Testing dist_type idw style S 
Testing dist_type none style W 
Testing dist_type idw style W 
Testing dist_type exp style W 
Testing dist_type dpd style W 
Testing dist_type idw style raw 
Testing dist_type idw style W 
Testing dist_type idw style B 
Testing dist_type idw style C 
Testing dist_type idw style U 
Testing dist_type idw style minmax 
Testing dist_type idw style S 
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
trying URL 'https://cf.10xgenomics.com/samples/spatial-exp/1.0.0/V1_Mouse_Kidney/V1_Mouse_Kidney_filtered_feature_bc_matrix.h5'
Content type 'binary/octet-stream' length 10785331 bytes (10.3 MB)
==================================================
downloaded 10.3 MB

trying URL 'https://cf.10xgenomics.com/samples/spatial-exp/1.0.0/V1_Mouse_Kidney/V1_Mouse_Kidney_spatial.tar.gz'
Content type 'application/x-tar' length 8531653 bytes (8.1 MB)
==================================================
downloaded 8.1 MB

[updateObject] DFrame object is current.
[updateObject] Nothing to update.
updateObject(object="ANY") default for object of class 'NULL'
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
[updateObject] DFrame object is current.
[updateObject] Nothing to update.
updateObject(object="ANY") default for object of class 'NULL'
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
updateObject(object="ANY") default for object of class 'dgCMatrix'
updateObjectFromSlots(object = 'dgCMatrix' class = 'dgCMatrix')
updateObject(object="ANY") default for object of class 'integer'
[updateObject] Validating the updated object ... OK
updateObject(object="ANY") default for object of class 'integer'
[updateObject] Validating the updated object ... OK
updateObject(object="ANY") default for object of class 'integer'
[updateObject] Validating the updated object ... OK
updateObject(object = 'list')
updateObject(object="ANY") default for object of class 'character'
[updateObject] Validating the updated object ... OK
updateObject(object="ANY") default for object of class 'character'
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
updateObject(object="ANY") default for object of class 'numeric'
[updateObject] Validating the updated object ... OK
updateObject(object = 'list')
[updateObject] Validating the updated object ... OK
heuristic updateObjectFromSlots, method 1
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
[updateObject] DFrame object is current.
[updateObject] Nothing to update.
updateObject(object="ANY") default for object of class 'NULL'
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
[updateObject] DFrame object is current.
[updateObject] Nothing to update.
updateObject(object="ANY") default for object of class 'NULL'
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
[updateObject] CompressedGRangesList object is current.
[updateObject] Nothing to update.
[updateObject] Internal representation of GRanges object is current.
[updateObject] Nothing to update.
[updateObject] Internal representation of IRanges object is current.
[updateObject] Nothing to update.
updateObject(object="ANY") default for object of class 'NULL'
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
[updateObject] DFrame object is current.
[updateObject] Nothing to update.
updateObject(object="ANY") default for object of class 'NULL'
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
[updateObject] Internal representation of GRanges object is current.
[updateObject] Nothing to update.
[updateObject] Internal representation of IRanges object is current.
[updateObject] Nothing to update.
updateObject(object="ANY") default for object of class 'NULL'
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
[updateObject] DFrame object is current.
[updateObject] Nothing to update.
updateObject(object="ANY") default for object of class 'NULL'
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
[updateObject] Internal representation of PartitioningByEnd object is current.
[updateObject] Nothing to update.
updateObject(object="ANY") default for object of class 'NULL'
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
[updateObject] DFrame object is current.
[updateObject] Nothing to update.
updateObject(object="ANY") default for object of class 'NULL'
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 561 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-read.R:141:5'): readVizgen flip geometry, use cellpose ─────────
Error in `dyn.load(file, DLLpath = DLLpath, ...)`: unable to load shared object '/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/arrow/libs/arrow.so':
  dlopen(/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/arrow/libs/arrow.so, 0x0006): symbol not found in flat namespace (_utf8proc_category)
Backtrace:
    ▆
 1. ├─SpatialFeatureExperiment::readVizgen(...) at test-read.R:141:5
 2. │ └─sfarrow::st_read_parquet(fn)
 3. └─base::loadNamespace(x)
 4.   └─base::library.dynam(lib, package, package.lib)
 5.     └─base::dyn.load(file, DLLpath = DLLpath, ...)
── Error ('test-read.R:224:1'): (code run outside of `test_that()`) ────────────
Error in `dyn.load(file, DLLpath = DLLpath, ...)`: unable to load shared object '/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/arrow/libs/arrow.so':
  dlopen(/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/arrow/libs/arrow.so, 0x0006): symbol not found in flat namespace (_utf8proc_category)
Backtrace:
    ▆
 1. ├─sfarrow::st_read_parquet(file.path(dir_use, "cellpose_micron_space.parquet")) at test-read.R:224:1
 2. └─base::loadNamespace(x)
 3.   └─base::library.dynam(lib, package, package.lib)
 4.     └─base::dyn.load(file, DLLpath = DLLpath, ...)

[ FAIL 2 | WARN 0 | SKIP 0 | PASS 561 ]
Error: Test failures
Execution halted