Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 2020/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
spatialHeatmap 2.12.1 (landing page) Jianhai Zhang
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | 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. |
Package: spatialHeatmap |
Version: 2.12.1 |
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_2.12.1.tar.gz |
StartedAt: 2024-12-20 10:02:33 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 10:15:14 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 760.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: spatialHeatmap.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_2.12.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/spatialHeatmap.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * 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 ‘2.12.1’ * 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 ... NOTE 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 ... 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 24.022 1.533 26.085 covis 22.798 1.338 24.941 cell_group 14.658 0.297 16.439 spatial_hm 10.430 0.506 11.120 process_cell_meta 9.732 0.118 9.993 SpatialEnrichment 9.035 0.553 9.934 reduce_dim 9.276 0.099 9.464 shm 7.364 0.484 7.938 norm_srsc 6.719 0.324 7.096 plot_meta 5.525 0.882 6.479 write_svg 5.332 0.572 6.149 submatrix 5.309 0.099 5.581 adj_mod 4.924 0.222 5.193 * 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-3.20-bioc/meat/spatialHeatmap.Rcheck/00check.log’ for details.
spatialHeatmap.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL spatialHeatmap ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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)
spatialHeatmap.Rcheck/tests/runTests.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 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 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, saveRDS, setdiff, 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 -- Fri Dec 20 10:14:53 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 49.786 2.366 53.123
spatialHeatmap.Rcheck/spatialHeatmap-Ex.timings
name | user | system | elapsed | |
SPHM | 24.022 | 1.533 | 26.085 | |
SPHMMethods | 3.023 | 0.658 | 4.014 | |
SVG | 1.254 | 0.353 | 1.653 | |
SVGMethods | 0.831 | 0.172 | 1.028 | |
SpatialEnrichment | 9.035 | 0.553 | 9.934 | |
aSVG.remote.repo | 0.004 | 0.003 | 0.006 | |
adj_mod | 4.924 | 0.222 | 5.193 | |
aggr_rep | 1.916 | 0.077 | 2.013 | |
cell_group | 14.658 | 0.297 | 16.439 | |
cluster_cell | 2.042 | 0.034 | 2.213 | |
coclus_opt | 0.492 | 0.013 | 0.521 | |
cocluster | 0.369 | 0.023 | 0.414 | |
com_factor | 0.318 | 0.020 | 0.360 | |
covis | 22.798 | 1.338 | 24.941 | |
custom_shiny | 0.038 | 0.010 | 0.054 | |
cut_dendro | 1.700 | 0.030 | 1.865 | |
cvt_id | 1.024 | 0.038 | 1.119 | |
data_ref | 1.618 | 0.028 | 1.671 | |
database | 0.679 | 0.042 | 0.733 | |
edit_tar | 0.009 | 0.002 | 0.011 | |
filter_data | 2.113 | 0.085 | 2.385 | |
matrix_hm | 4.178 | 0.136 | 4.362 | |
network | 3.853 | 0.088 | 4.097 | |
norm_cell | 2.899 | 0.052 | 2.983 | |
norm_data | 1.936 | 0.071 | 2.040 | |
norm_srsc | 6.719 | 0.324 | 7.096 | |
opt_bar | 0.255 | 0.002 | 0.257 | |
opt_setting | 0.019 | 0.010 | 0.030 | |
opt_violin | 0.425 | 0.007 | 0.433 | |
optimal_k | 0.302 | 0.003 | 0.307 | |
plot_dim | 2.590 | 0.038 | 2.658 | |
plot_kmeans | 1.033 | 0.017 | 1.057 | |
plot_meta | 5.525 | 0.882 | 6.479 | |
process_cell_meta | 9.732 | 0.118 | 9.993 | |
qc_cell | 1.638 | 0.032 | 1.685 | |
read_cache | 2.527 | 0.049 | 2.604 | |
read_fr | 0.009 | 0.002 | 0.011 | |
read_svg | 0.891 | 0.344 | 1.277 | |
reduce_dim | 9.276 | 0.099 | 9.464 | |
reduce_rep | 0.002 | 0.002 | 0.004 | |
return_feature | 1.477 | 0.026 | 1.594 | |
save_cache | 2.350 | 0.030 | 2.495 | |
shiny_shm | 0.000 | 0.001 | 0.001 | |
shm | 7.364 | 0.484 | 7.938 | |
spatialHeatmap-package | 0.001 | 0.001 | 0.002 | |
spatial_hm | 10.430 | 0.506 | 11.120 | |
submatrix | 5.309 | 0.099 | 5.581 | |
true_bulk | 0.516 | 0.024 | 0.551 | |
update_feature | 0.002 | 0.003 | 0.005 | |
write_svg | 5.332 | 0.572 | 6.149 | |