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This page was generated on 2025-03-14 11:47 -0400 (Fri, 14 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4781
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" 4537
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4567
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4519
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4451
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 2034/2309HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
spatialHeatmap 2.13.1  (landing page)
Jianhai Zhang
Snapshot Date: 2025-03-13 13:40 -0400 (Thu, 13 Mar 2025)
git_url: https://git.bioconductor.org/packages/spatialHeatmap
git_branch: devel
git_last_commit: 0485a13
git_last_commit_date: 2024-11-24 02:19:14 -0400 (Sun, 24 Nov 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for spatialHeatmap on kunpeng2

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: spatialHeatmap
Version: 2.13.1
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:spatialHeatmap.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings spatialHeatmap_2.13.1.tar.gz
StartedAt: 2025-03-14 12:01:04 -0000 (Fri, 14 Mar 2025)
EndedAt: 2025-03-14 12:12:25 -0000 (Fri, 14 Mar 2025)
EllapsedTime: 680.4 seconds
RetCode: 0
Status:   OK  
CheckDir: spatialHeatmap.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:spatialHeatmap.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings spatialHeatmap_2.13.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/spatialHeatmap.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* 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-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘spatialHeatmap/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘spatialHeatmap’ version ‘2.13.1’
* 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 31.9Mb
  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 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
SPHM              26.000  0.269  36.539
covis             23.567  0.580  32.112
cell_group        17.054  0.267  22.890
reduce_dim         9.085  0.412  13.147
process_cell_meta  9.233  0.083  11.840
spatial_hm         6.502  0.468   8.057
SpatialEnrichment  5.732  0.344   9.262
shm                4.811  0.374   5.869
norm_srsc          4.109  0.064   5.825
plot_meta          3.513  0.094   5.424
submatrix          3.383  0.168   5.445
write_svg          3.374  0.177   5.389
matrix_hm          3.094  0.140   5.123
* 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
  ‘/home/biocbuild/bbs-3.21-bioc/meat/spatialHeatmap.Rcheck/00check.log’
for details.


Installation output

spatialHeatmap.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘spatialHeatmap’ ...
** this is package ‘spatialHeatmap’ version ‘2.13.1’
** 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 Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 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.

> 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 -- Fri Mar 14 12:12:13 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 
 33.886   0.890  42.789 

Example timings

spatialHeatmap.Rcheck/spatialHeatmap-Ex.timings

nameusersystemelapsed
SPHM26.000 0.26936.539
SPHMMethods1.9010.1582.912
SVG0.8510.1521.678
SVGMethods0.5310.0730.996
SpatialEnrichment5.7320.3449.262
aSVG.remote.repo0.0030.0000.003
adj_mod3.8590.2604.753
aggr_rep1.2310.0361.604
cell_group17.054 0.26722.890
cluster_cell1.7010.0362.439
coclus_opt0.3590.0130.715
cocluster0.2940.0190.635
com_factor0.2640.0160.450
covis23.567 0.58032.112
custom_shiny0.0230.0000.028
cut_dendro0.8990.0481.166
cvt_id0.6890.0240.858
data_ref1.0450.0241.126
database0.4830.0040.592
edit_tar0.0060.0000.015
filter_data1.3870.0522.015
matrix_hm3.0940.1405.123
network3.0370.0244.848
norm_cell2.5530.0253.924
norm_data1.2730.0081.491
norm_srsc4.1090.0645.825
opt_bar0.1590.0000.159
opt_setting0.0090.0000.010
opt_violin0.3090.0000.313
optimal_k0.1820.0000.182
plot_dim2.1540.0082.748
plot_kmeans0.8020.0001.521
plot_meta3.5130.0945.424
process_cell_meta 9.233 0.08311.840
qc_cell1.1570.0282.356
read_cache2.6760.0243.532
read_fr0.0050.0000.005
read_svg0.6190.0851.138
reduce_dim 9.085 0.41213.147
reduce_rep0.0010.0000.006
return_feature0.6730.0161.401
save_cache2.6890.0683.623
shiny_shm000
shm4.8110.3745.869
spatialHeatmap-package000
spatial_hm6.5020.4688.057
submatrix3.3830.1685.445
true_bulk0.4110.0040.764
update_feature0.0010.0000.002
write_svg3.3740.1775.389