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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:alabaster.spatial.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings alabaster.spatial_1.7.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/alabaster.spatial.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘alabaster.spatial/DESCRIPTION’ ... OK
* this is package ‘alabaster.spatial’ version ‘1.7.1’
* 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 ‘alabaster.spatial’ 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  loadSpatialImage.Rd: SpatialImage-class
  readSpatialExperiment.Rd: SpatialExperiment-class, saveObject,
    readObjectFile, readSingleCellExperiment, altReadObject
  saveSpatialExperiment.Rd: SpatialExperiment-class, imgData
  stageSpatialImage.Rd: SpatialImage-class, RemoteSpatialImage-class,
    StoredSpatialImage-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 ... OK
* 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:
    5.     └─alabaster.sce (local) .local(x, dir, path, child, ...)
    6.       ├─methods::callNextMethod()
    7.       └─alabaster.se (local) .nextMethod(x = x, dir = dir, path = path)
    8.         └─alabaster.se (local) .local(x, dir, path, child, ...)
    9.           ├─methods::callNextMethod()
   10.           └─alabaster.se (local) .nextMethod(x = x, dir = dir, path = path)
   11.             └─alabaster.se (local) .local(x, dir, path, child, ...)
   12.               └─base::tryCatch(...)
   13.                 └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   14.                   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   15.                     └─value[[3L]](cond)
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 16 ]
  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, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/alabaster.spatial.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL alabaster.spatial
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘alabaster.spatial’ ...
** 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 (alabaster.spatial)

R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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(alabaster.spatial)
Loading required package: 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
Loading required package: generics

Attaching package: 'generics'

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

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, 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: alabaster.base

Attaching package: 'alabaster.base'

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

    anyMissing

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

    anyMissing

> test_check("alabaster.spatial")
[ FAIL 3 | WARN 0 | SKIP 0 | PASS 16 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-image.R:13:5'): local saves work correctly ─────────────────────
Error in `dyn.load(file, DLLpath = DLLpath, ...)`: unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
  libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
    ▆
 1. ├─alabaster.base::.writeMetadata(meta, tmp) at test-image.R:13:5
 2. │ └─alabaster.base::writeMetadata(...)
 3. │   └─jsonvalidate::json_validate(...)
 4. │     └─jsonvalidate::json_validator(...)
 5. │       └─jsonvalidate:::jsonvalidate_js()
 6. └─base::loadNamespace(x)
 7.   └─base::library.dynam(lib, package, package.lib)
 8.     └─base::dyn.load(file, DLLpath = DLLpath, ...)
── Error ('test-image.R:34:5'): forcible resaves work correctly ────────────────
Error in `dyn.load(file, DLLpath = DLLpath, ...)`: unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
  libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
    ▆
 1. ├─alabaster.base::.writeMetadata(meta, tmp) at test-image.R:34:5
 2. │ └─alabaster.base::writeMetadata(...)
 3. │   └─jsonvalidate::json_validate(...)
 4. │     └─jsonvalidate::json_validator(...)
 5. │       └─jsonvalidate:::jsonvalidate_js()
 6. └─base::loadNamespace(x)
 7.   └─base::library.dynam(lib, package, package.lib)
 8.     └─base::dyn.load(file, DLLpath = DLLpath, ...)
── Error ('test-spe.R:12:5'): staging and loading works correctly ──────────────
Error in `value[[3L]](cond)`: failed to stage 'colData(<SpatialExperiment>)'
  - unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
  libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
     ▆
  1. ├─alabaster.base::stageObject(spe, tmp, "experiment-1") at test-spe.R:12:5
  2. └─alabaster.spatial::stageObject(spe, tmp, "experiment-1")
  3.   ├─methods::callNextMethod()
  4.   └─alabaster.sce (local) .nextMethod(x = x, dir = dir, path = path)
  5.     └─alabaster.sce (local) .local(x, dir, path, child, ...)
  6.       ├─methods::callNextMethod()
  7.       └─alabaster.se (local) .nextMethod(x = x, dir = dir, path = path)
  8.         └─alabaster.se (local) .local(x, dir, path, child, ...)
  9.           ├─methods::callNextMethod()
 10.           └─alabaster.se (local) .nextMethod(x = x, dir = dir, path = path)
 11.             └─alabaster.se (local) .local(x, dir, path, child, ...)
 12.               └─base::tryCatch(...)
 13.                 └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 14.                   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 15.                     └─value[[3L]](cond)

[ FAIL 3 | WARN 0 | SKIP 0 | PASS 16 ]
Error: Test failures
Execution halted