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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:spatialHeatmap.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings spatialHeatmap_2.17.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/spatialHeatmap.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* 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 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘spatialHeatmap/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘spatialHeatmap’ version ‘2.17.3’
* 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 ‘spatialHeatmap’ can be installed ... OK
* checking installed package size ... INFO
  installed size is 26.9Mb
  sub-directories of 1Mb or more:
    R         1.2Mb
    extdata  25.3Mb
* 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 ... NOTE
Problems with news in ‘NEWS’:
  Cannot process chunk/lines:
    Changes in version 2.17.2 (2025-01-15)
     1. return_feature: replaced rols::Term with rols::olsTerm
     2. read_cache: If the cache is older than a certain number of days, the function returns NULL.
* 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 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
Non-topic package-anchored link(s) in Rd file 'norm_data.Rd':
  ‘[DESeq2]{estimateSizeFactors}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
covis             15.249  0.645  15.898
SPHM              15.342  0.464  15.810
cell_group        10.747  0.552  11.301
process_cell_meta  7.134  0.661   7.795
reduce_dim         6.963  0.696   7.659
spatial_hm         5.259  0.516   5.772
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/spatialHeatmap.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL spatialHeatmap
###
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘spatialHeatmap’ ...
** this is package ‘spatialHeatmap’ version ‘2.17.3’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘svg’ in package ‘spatialHeatmap’
Creating a new generic function for ‘match’ in package ‘spatialHeatmap’
** 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 (spatialHeatmap)

R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"
Copyright (C) 2026 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.

> BiocGenerics:::testPackage("spatialHeatmap")

Attaching package: 'spatialHeatmap'

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

    svg

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

    match

Loading required package: Biobase
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 object is masked from 'package:spatialHeatmap':

    match

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

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

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

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians


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

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

    rowMedians

Loading required package: GenomicRanges
Loading required package: stats4
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: Seqinfo
Loading required package: limma

Attaching package: 'limma'

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

    plotMA

Loading required package: xml2
Loading required package: RCurl
Loading required package: jsonlite
Loading required package: BiocStyle

Attaching package: 'BiocStyle'

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

    output

Normalising: ESF 
   type 
"ratio" 
Syntactically valid column names are made! 
Syntactically valid column names are made! 
All values before filtering:
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  0.000   0.000   0.287   2.442   4.268  19.991 
All coefficient of variances (CVs) before filtering:
     Min.   1st Qu.    Median      Mean   3rd Qu.      Max. 
0.0007742 0.0767696 0.4019655 0.6217814 0.9956157 2.0000000 
All values after filtering:
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  0.000   2.654   4.976   4.779   6.451  14.695 
All coefficient of variances (CVs) after filtering:
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
 0.3001  0.3648  0.4637  0.5651  0.7392  1.1548 

Warning: variables of sample/condition are less than 5! 
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
 ..done.
 ..done.
 ..done.
 ..done.
Normalising: ESF 
   type 
"ratio" 
Syntactically valid column names are made! 
Syntactically valid column names are made! 
All values before filtering:
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  0.000   0.000   0.287   2.442   4.268  19.991 
All coefficient of variances (CVs) before filtering:
     Min.   1st Qu.    Median      Mean   3rd Qu.      Max. 
0.0007742 0.0767696 0.4019655 0.6217814 0.9956157 2.0000000 
All values after filtering:
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  0.000   2.654   4.976   4.779   6.451  14.695 
All coefficient of variances (CVs) after filtering:
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
 0.3001  0.3648  0.4637  0.5651  0.7392  1.1548 


RUNIT TEST PROTOCOL -- Fri Jan 23 04:27:08 2026 
*********************************************** 
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
spatialHeatmap RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 23.912   0.915  24.821