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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:alabaster.sfe.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings alabaster.sfe_1.1.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/alabaster.sfe.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘alabaster.sfe/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘alabaster.sfe’ version ‘1.1.0’
* 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 ‘alabaster.sfe’ 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:
  readBioFormatsImage.Rd: BioFormatsImage
  readExtImage.Rd: readImage, ExtImage
  readSpatRaster.Rd: SpatRasterImage
  saveObject-ExtImage-method.Rd: writeImage
  saveObject-SpatRaster-method.Rd: writeRaster
  saveObject-SpatialFeatureExperiment-method.Rd: colFeatureData,
    getParams
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
Examples with CPU (user + system) or elapsed time > 5s
                                             user system elapsed
readBioFormatsImage                        19.878  0.853  18.190
saveObject-SpatialFeatureExperiment-method  8.756  0.207   9.041
saveObject-ExtImage-method                  7.577  0.219   6.981
readExtImage                                7.377  0.379   6.432
saveObject-BioFormatsImage-method           7.474  0.270   6.746
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/alabaster.sfe.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL alabaster.sfe
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘alabaster.sfe’ ...
** this is package ‘alabaster.sfe’ version ‘1.1.0’
** using staged installation
** R
** 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.sfe)

R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(alabaster.sfe)
Loading required package: SpatialFeatureExperiment

Attaching package: 'SpatialFeatureExperiment'

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

    scale

Loading required package: alabaster.base
> 
> test_check("alabaster.sfe")
terra 1.8.60

Attaching package: 'terra'

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

    centroids, crop, origin, rotate

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

    compare, describe

Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following object is masked from 'package:alabaster.base':

    anyMissing


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:terra':

    as.factor, interpolate, intersect, union

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:terra':

    as.data.frame, match, saveRDS, unique, which.max, which.min, width

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 objects are masked from 'package:terra':

    values, values<-

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 objects are masked from 'package:terra':

    distance, gaps, nearest, shift, trim

Loading required package: Seqinfo
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

The following object is masked from 'package:alabaster.base':

    anyMissing

Loading required package: scuttle
Loading required package: ggplot2

Attaching package: 'ggplot2'

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

    unit

see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /tmp/RtmpfHcHy0/file25015c19d71528/vizgen/vizgen_cellbound_Cellpose 
>>> 1 `.parquet` files exist:
/tmp/RtmpfHcHy0/file25015c19d71528/vizgen/vizgen_cellbound_Cellpose/Cellpose/cellpose_micron_space.parquet
>>> using -> /tmp/RtmpfHcHy0/file25015c19d71528/vizgen/vizgen_cellbound_Cellpose/Cellpose/cellpose_micron_space.parquet
>>> Cell segmentations are found in `.parquet` file
Sanity checks on cell segmentation polygons:
>>> ..found 1 cells with (nested) polygon lists
>>> ..applying filtering
>>> Casting MULTIPOLYGON geometry to POLYGON
>>> Checking polygon validity
>>> Reading transcript coordinates
>>> Converting transcript spots to geometry
>>> Writing reformatted transcript spots to disk
>>> Saving SpatialExperiment
>>> Saving colgeometries
>>> Saving rowgeometries
>>> Reading SpatialExperiment
>>> Reading colgeometries
>>> Reading rowgeometries
>>> Saving SpatialExperiment
>>> Saving colgeometries
>>> Saving rowgeometries
>>> Saving localResults
>>> Saving spatial graphs
>>> Reading SpatialExperiment
>>> Reading colgeometries
>>> Reading rowgeometries
>>> Reading spatial graphs
>>> Reading localResults
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /tmp/RtmpfHcHy0/file25015c19d71528/xenium1/xenium_lr 
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
The downloaded files are in /tmp/RtmpfHcHy0/file25015c19d71528/xenium2/xenium2 
>>> Cell segmentations are found in `.csv` file(s)
>>> Reading cell and nucleus segmentations
>>> Making POLYGON geometries
>>> Checking polygon validity
>>> Saving geometries to parquet files
>>> Reading cell metadata -> `cells.csv`
>>> Reading h5 gene count matrix
>>> filtering cellSeg geometries to match 16324 cells with counts > 0
>>> filtering nucSeg geometries to match 16324 cells with counts > 0
>>> Cell segmentations are found in `.parquet` file(s)
>>> Reading cell and nucleus segmentations
>>> Making MULTIPOLYGON nuclei geometries
>>> Making POLYGON cell geometries
Sanity checks on cell segmentation polygons:
>>> ..found 132 cells with (nested) polygon lists
>>> ..applying filtering
>>> Checking polygon validity
>>> Saving geometries to parquet files
>>> Reading cell metadata -> `cells.parquet`
>>> Reading h5 gene count matrix
>>> filtering cellSeg geometries to match 6272 cells with counts > 0
>>> filtering nucSeg geometries to match 6158 cells with counts > 0
>>> Preprocessed sf segmentations found
>>> Reading cell and nucleus segmentations
>>> Reading cell metadata -> `cells.csv`
>>> Reading h5 gene count matrix
>>> filtering cellSeg geometries to match 16324 cells with counts > 0
>>> filtering nucSeg geometries to match 16324 cells with counts > 0
Resolution subscript out of bound, reading the lowest resolution
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 39 ]
> 
> proc.time()
   user  system elapsed 
 52.925   2.363  51.722