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This page was generated on 2024-03-18 11:36:22 -0400 (Mon, 18 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4665
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4401
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4425
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 2013/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
spatialHeatmap 2.8.5  (landing page)
Jianhai Zhang
Snapshot Date: 2024-03-15 14:05:07 -0400 (Fri, 15 Mar 2024)
git_url: https://git.bioconductor.org/packages/spatialHeatmap
git_branch: RELEASE_3_18
git_last_commit: 649defc
git_last_commit_date: 2024-02-15 15:17:04 -0400 (Thu, 15 Feb 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for spatialHeatmap on nebbiolo2


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: 2.8.5
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:spatialHeatmap.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings spatialHeatmap_2.8.5.tar.gz
StartedAt: 2024-03-16 02:46:30 -0400 (Sat, 16 Mar 2024)
EndedAt: 2024-03-16 02:57:43 -0400 (Sat, 16 Mar 2024)
EllapsedTime: 673.5 seconds
RetCode: 0
Status:   OK  
CheckDir: spatialHeatmap.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:spatialHeatmap.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings spatialHeatmap_2.8.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/spatialHeatmap.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘spatialHeatmap/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘spatialHeatmap’ version ‘2.8.5’
* 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 ... NOTE
  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 R 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 ... OK
* 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              15.123  0.439  15.576
covis             14.782  0.254  15.077
cell_group        10.741  0.112  10.849
process_cell_meta  7.412  0.073   7.482
reduce_dim         7.057  0.427   7.483
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘covisualize.Rmd’ using ‘UTF-8’... OK
  ‘custom_SVGs.Rmd’ using ‘UTF-8’... OK
  ‘spatialHeatmap.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/spatialHeatmap.Rcheck/00check.log’
for details.



Installation output

spatialHeatmap.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL spatialHeatmap
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘spatialHeatmap’ ...
** 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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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

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, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, 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 0.6217813 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 0.6217813 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 -- Sat Mar 16 02:53:03 2024 
*********************************************** 
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 
 25.489   1.214  26.693 

Example timings

spatialHeatmap.Rcheck/spatialHeatmap-Ex.timings

nameusersystemelapsed
Database0.3370.0000.338
SPHM15.123 0.43915.576
SPHMMethods1.3080.1041.434
SVG0.6460.0860.789
SVGMethods0.3610.0770.478
SpatialEnrichment3.8120.1353.950
aSVG.remote.repo0.0020.0000.002
adj_mod2.7660.1842.893
aggr_rep0.7970.0040.802
cell_group10.741 0.11210.849
cluster_cell1.2710.0121.284
coclus_opt0.2400.0130.253
cocluster0.1950.0040.199
com_factor0.1620.0030.165
covis14.782 0.25415.077
custom_shiny0.0160.0020.019
cut_dendro0.6010.0000.585
cvt_id0.4470.0080.454
data_ref0.7400.0080.749
edit_tar0.0020.0020.004
filter_data0.9020.0230.925
matrix_hm2.1360.0682.204
network1.9640.0442.008
norm_cell1.8160.0041.820
norm_data0.7750.0240.799
norm_srsc2.6560.0402.696
opt_bar0.1410.0000.141
opt_setting0.0070.0000.007
opt_violin0.1610.0000.160
optimal_k0.1080.0000.108
plot_dim1.5240.0271.552
plot_kmeans0.4820.0040.486
plot_meta2.3410.0762.470
process_cell_meta7.4120.0737.482
qc_cell1.0250.0001.025
read_cache2.2430.0712.315
read_fr0.0010.0020.004
read_svg0.4830.0760.640
reduce_dim7.0570.4277.483
reduce_rep0.0010.0000.002
return_feature0.5230.0310.558
save_cache2.1380.3232.461
shiny_shm000
shm3.0520.2053.289
spatialHeatmap-package000
spatial_hm4.3930.3494.798
submatrix3.5860.6164.203
true_bulk0.2790.0200.299
update_feature0.0010.0000.001
write_svg2.4460.0912.562