##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:visiumStitched.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings visiumStitched_0.99.15.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/visiumStitched.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 ‘visiumStitched/DESCRIPTION’ ... OK
* this is package ‘visiumStitched’ version ‘0.99.15’
* 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 ‘visiumStitched’ can be installed ... WARNING
Found the following significant warnings:
  Warning: program compiled against libxml 212 using older 211
See ‘/home/biocbuild/bbs-3.21-bioc/meat/visiumStitched.Rcheck/00install.out’ for details.
* 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 ...Warning: program compiled against libxml 212 using older 211
 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 ... NOTE
Warning: program compiled against libxml 212 using older 211

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Warning: program compiled against libxml 212 using older 211
* checking S3 generic/method consistency ... WARNING
Warning: program compiled against libxml 212 using older 211
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... WARNING
Warning: program compiled against libxml 212 using older 211
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
* checking foreign function calls ... NOTE
Warning: program compiled against libxml 212 using older 211
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
Warning: program compiled against libxml 212 using older 211
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Warning: program compiled against libxml 212 using older 211
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
* checking Rd \usage sections ... NOTE
Warning: program compiled against libxml 212 using older 211
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
build_SpatialExperiment 96.655  4.073 147.122
add_array_coords        35.441  4.240 243.990
merge_overlapping       25.389  0.332  27.903
prep_fiji               19.022  2.861  25.249
as.Seurat               17.165  2.256 125.835
rescale_fiji_inputs     13.478  1.443  19.420
add_overlap_info         4.809  0.502   7.369
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 5 WARNINGs, 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/visiumStitched.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL visiumStitched
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘visiumStitched’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: program compiled against libxml 212 using older 211
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: program compiled against libxml 212 using older 211
** testing if installed package can be loaded from final location
Warning: program compiled against libxml 212 using older 211
** testing if installed package keeps a record of temporary installation path
* DONE (visiumStitched)

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.

> # 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(visiumStitched)
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

Warning: program compiled against libxml 212 using older 211
> 
> test_check("visiumStitched")
2025-01-11 12:45:39.671898 loading file /home/biocbuild/.cache/R/BiocFileCache/3d2f0067dfe4ef_visiumStitched_brain_spe.rds%3Frlkey%3Dnq6a82u23xuu9hohr86oodwdi%26dl%3D1
2025-01-11 12:45:48.499757 loading file /home/biocbuild/.cache/R/BiocFileCache/3d2f006de42bff_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1
2025-01-11 12:45:52.649411 loading file /home/biocbuild/.cache/R/BiocFileCache/3d2f001d65b98c_visiumStitched_brain_fiji_out.zip%3Frlkey%3Dptwal8f5zxakzejwd0oqw0lhj%26dl%3D1
2025-01-11 12:46:16.359944 loading file /home/biocbuild/.cache/R/BiocFileCache/3d2f0067dfe4ef_visiumStitched_brain_spe.rds%3Frlkey%3Dnq6a82u23xuu9hohr86oodwdi%26dl%3D1
2025-01-11 12:46:25.290273 loading file /home/biocbuild/.cache/R/BiocFileCache/3d2f0067dfe4ef_visiumStitched_brain_spe.rds%3Frlkey%3Dnq6a82u23xuu9hohr86oodwdi%26dl%3D1
2025-01-11 12:46:30.206918 loading file /home/biocbuild/.cache/R/BiocFileCache/3d2f001ce4b81a_spatialDLPFC_spe_subset_example.rds%3Fdl%3D1
Overwriting 'spe$key'. Set 'overwrite = FALSE' if you do not want to overwrite it.
2025-01-11 12:46:42.698833 loading file /home/biocbuild/.cache/R/BiocFileCache/3d2f006de42bff_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1
2025-01-11 12:46:47.52028 loading file /home/biocbuild/.cache/R/BiocFileCache/3d2f001d65b98c_visiumStitched_brain_fiji_out.zip%3Frlkey%3Dptwal8f5zxakzejwd0oqw0lhj%26dl%3D1
Building SpatialExperiment using capture area as sample ID
2025-01-11 12:47:01.156301 SpatialExperiment::read10xVisium: reading basic data from SpaceRanger
2025-01-11 12:47:13.190413 read10xVisiumAnalysis: reading analysis output from SpaceRanger
2025-01-11 12:47:13.95816 add10xVisiumAnalysis: adding analysis output from SpaceRanger
2025-01-11 12:47:14.608135 rtracklayer::import: reading the reference GTF file
2025-01-11 12:48:11.603022 adding gene information to the SPE object
2025-01-11 12:48:12.16146 adding information used by spatialLIBD
Overwriting imgData(spe) with merged images (one per group)
Adding array coordinates and overlap info
2025-01-11 12:48:21.044615 loading file /home/biocbuild/.cache/R/BiocFileCache/3d2f0067dfe4ef_visiumStitched_brain_spe.rds%3Frlkey%3Dnq6a82u23xuu9hohr86oodwdi%26dl%3D1
'sample_id's are duplicated across 'SpatialExperiment' objects to cbind; appending sample indices.
2025-01-11 12:48:51.910614 loading file /home/biocbuild/.cache/R/BiocFileCache/3d2f006de42bff_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1
2025-01-11 12:48:56.504664 loading file /home/biocbuild/.cache/R/BiocFileCache/3d2f001d65b98c_visiumStitched_brain_fiji_out.zip%3Frlkey%3Dptwal8f5zxakzejwd0oqw0lhj%26dl%3D1
2025-01-11 12:49:12.716766 loading file /home/biocbuild/.cache/R/BiocFileCache/3d2f006de42bff_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 30 ]
> 
> proc.time()
   user  system elapsed 
215.186  11.073 250.023