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This page was generated on 2025-09-18 11:38 -0400 (Thu, 18 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4827
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4608
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4549
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4581
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 2062/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
spatialHeatmap 2.14.1  (landing page)
Jianhai Zhang
Snapshot Date: 2025-09-15 13:40 -0400 (Mon, 15 Sep 2025)
git_url: https://git.bioconductor.org/packages/spatialHeatmap
git_branch: RELEASE_3_21
git_last_commit: ef32f47
git_last_commit_date: 2025-06-19 22:10:56 -0400 (Thu, 19 Jun 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    NA  


CHECK results for spatialHeatmap on merida1

To the developers/maintainers of the spatialHeatmap package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/spatialHeatmap.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: spatialHeatmap
Version: 2.14.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:spatialHeatmap.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings spatialHeatmap_2.14.1.tar.gz
StartedAt: 2025-09-16 10:09:12 -0400 (Tue, 16 Sep 2025)
EndedAt: 2025-09-16 10:22:32 -0400 (Tue, 16 Sep 2025)
EllapsedTime: 800.4 seconds
RetCode: 0
Status:   OK  
CheckDir: spatialHeatmap.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:spatialHeatmap.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings spatialHeatmap_2.14.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/spatialHeatmap.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘spatialHeatmap/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘spatialHeatmap’ version ‘2.14.1’
* 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 ‘spatialHeatmap’ can be installed ... OK
* checking installed package size ... INFO
  installed size is 31.8Mb
  sub-directories of 1Mb or more:
    R         1.2Mb
    extdata  30.2Mb
* 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 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             24.144  1.550  27.704
SPHM              23.618  1.416  27.223
cell_group        14.736  0.341  15.842
spatial_hm        13.584  0.514  14.824
SpatialEnrichment 10.628  0.482  11.997
process_cell_meta  9.915  0.150  10.845
reduce_dim         9.238  0.167  10.580
shm                8.626  0.443   9.520
norm_srsc          6.509  0.339   7.179
plot_meta          5.588  0.836   6.599
write_svg          5.436  0.587   6.272
adj_mod            5.064  0.230   5.558
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/spatialHeatmap.Rcheck/00check.log’
for details.


Installation output

spatialHeatmap.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘spatialHeatmap’ ...
** this is package ‘spatialHeatmap’ version ‘2.14.1’
** 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)

Tests output

spatialHeatmap.Rcheck/tests/runTests.Rout


R version 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"
Copyright (C) 2025 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.

> 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: GenomeInfoDb
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 -- Tue Sep 16 10:22:12 2025 
*********************************************** 
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 
 49.533   2.028  54.204 

Example timings

spatialHeatmap.Rcheck/spatialHeatmap-Ex.timings

nameusersystemelapsed
SPHM23.618 1.41627.223
SPHMMethods3.0130.6263.902
SVG1.1350.3151.566
SVGMethods0.7580.1630.959
SpatialEnrichment10.628 0.48211.997
aSVG.remote.repo0.0030.0030.006
adj_mod5.0640.2305.558
aggr_rep1.9350.0822.141
cell_group14.736 0.34115.842
cluster_cell2.0250.0362.094
coclus_opt0.5070.0242.184
cocluster0.4000.0352.431
com_factor0.3510.0310.587
covis24.144 1.55027.704
custom_shiny0.0350.0110.046
cut_dendro1.7480.0412.253
cvt_id1.0000.0411.093
data_ref1.6380.0361.798
database0.6870.0420.755
edit_tar0.0080.0020.011
filter_data2.1580.1032.612
matrix_hm4.1040.1734.510
network3.9730.0954.244
norm_cell2.9240.0443.096
norm_data1.9360.0632.096
norm_srsc6.5090.3397.179
opt_bar0.4750.0040.503
opt_setting0.0190.0150.035
opt_violin0.5870.0060.616
optimal_k0.4490.0030.477
plot_dim2.9150.0493.156
plot_kmeans1.2000.0321.287
plot_meta5.5880.8366.599
process_cell_meta 9.915 0.15010.845
qc_cell1.6490.0512.125
read_cache2.5990.0813.194
read_fr0.0080.0020.011
read_svg0.7680.3711.690
reduce_dim 9.238 0.16710.580
reduce_rep0.0020.0020.004
return_feature1.4420.0241.602
save_cache2.5160.0342.693
shiny_shm0.0000.0000.001
shm8.6260.4439.520
spatialHeatmap-package0.0010.0030.002
spatial_hm13.584 0.51414.824
submatrix4.2340.0794.535
true_bulk0.5320.0250.587
update_feature0.0020.0030.009
write_svg5.4360.5876.272