Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-03-14 11:47 -0400 (Fri, 14 Mar 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4781 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" | 4537 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4567 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4519 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R 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 2034/2309 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
spatialHeatmap 2.13.1 (landing page) Jianhai Zhang
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
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. |
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 |
############################################################################## ############################################################################## ### ### 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.
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)
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
spatialHeatmap.Rcheck/spatialHeatmap-Ex.timings
name | user | system | elapsed | |
SPHM | 26.000 | 0.269 | 36.539 | |
SPHMMethods | 1.901 | 0.158 | 2.912 | |
SVG | 0.851 | 0.152 | 1.678 | |
SVGMethods | 0.531 | 0.073 | 0.996 | |
SpatialEnrichment | 5.732 | 0.344 | 9.262 | |
aSVG.remote.repo | 0.003 | 0.000 | 0.003 | |
adj_mod | 3.859 | 0.260 | 4.753 | |
aggr_rep | 1.231 | 0.036 | 1.604 | |
cell_group | 17.054 | 0.267 | 22.890 | |
cluster_cell | 1.701 | 0.036 | 2.439 | |
coclus_opt | 0.359 | 0.013 | 0.715 | |
cocluster | 0.294 | 0.019 | 0.635 | |
com_factor | 0.264 | 0.016 | 0.450 | |
covis | 23.567 | 0.580 | 32.112 | |
custom_shiny | 0.023 | 0.000 | 0.028 | |
cut_dendro | 0.899 | 0.048 | 1.166 | |
cvt_id | 0.689 | 0.024 | 0.858 | |
data_ref | 1.045 | 0.024 | 1.126 | |
database | 0.483 | 0.004 | 0.592 | |
edit_tar | 0.006 | 0.000 | 0.015 | |
filter_data | 1.387 | 0.052 | 2.015 | |
matrix_hm | 3.094 | 0.140 | 5.123 | |
network | 3.037 | 0.024 | 4.848 | |
norm_cell | 2.553 | 0.025 | 3.924 | |
norm_data | 1.273 | 0.008 | 1.491 | |
norm_srsc | 4.109 | 0.064 | 5.825 | |
opt_bar | 0.159 | 0.000 | 0.159 | |
opt_setting | 0.009 | 0.000 | 0.010 | |
opt_violin | 0.309 | 0.000 | 0.313 | |
optimal_k | 0.182 | 0.000 | 0.182 | |
plot_dim | 2.154 | 0.008 | 2.748 | |
plot_kmeans | 0.802 | 0.000 | 1.521 | |
plot_meta | 3.513 | 0.094 | 5.424 | |
process_cell_meta | 9.233 | 0.083 | 11.840 | |
qc_cell | 1.157 | 0.028 | 2.356 | |
read_cache | 2.676 | 0.024 | 3.532 | |
read_fr | 0.005 | 0.000 | 0.005 | |
read_svg | 0.619 | 0.085 | 1.138 | |
reduce_dim | 9.085 | 0.412 | 13.147 | |
reduce_rep | 0.001 | 0.000 | 0.006 | |
return_feature | 0.673 | 0.016 | 1.401 | |
save_cache | 2.689 | 0.068 | 3.623 | |
shiny_shm | 0 | 0 | 0 | |
shm | 4.811 | 0.374 | 5.869 | |
spatialHeatmap-package | 0 | 0 | 0 | |
spatial_hm | 6.502 | 0.468 | 8.057 | |
submatrix | 3.383 | 0.168 | 5.445 | |
true_bulk | 0.411 | 0.004 | 0.764 | |
update_feature | 0.001 | 0.000 | 0.002 | |
write_svg | 3.374 | 0.177 | 5.389 | |