Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-17 12:23 -0400 (Mon, 17 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4685 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4400 |
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 1981/2242 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
spatialHeatmap 2.11.0 (landing page) Jianhai Zhang
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | 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: 2.11.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:spatialHeatmap.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings spatialHeatmap_2.11.0.tar.gz |
StartedAt: 2024-06-17 03:53:26 -0400 (Mon, 17 Jun 2024) |
EndedAt: 2024-06-17 04:04:06 -0400 (Mon, 17 Jun 2024) |
EllapsedTime: 640.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: spatialHeatmap.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:spatialHeatmap.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings spatialHeatmap_2.11.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/spatialHeatmap.Rcheck’ * using R version 4.4.0 RC (2024-04-16 r86468) * using platform: x86_64-pc-linux-gnu * 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 ‘2.11.0’ * 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 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 ... 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 14.899 0.480 15.395 covis 14.747 0.567 15.348 cell_group 10.454 0.439 10.890 process_cell_meta 7.361 0.776 8.135 reduce_dim 7.096 0.356 7.450 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.20-bioc/meat/spatialHeatmap.Rcheck/00check.log’ for details.
spatialHeatmap.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL spatialHeatmap ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-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)
spatialHeatmap.Rcheck/tests/runTests.Rout
R version 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-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 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, 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 -- Mon Jun 17 03:59:59 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 24.377 0.930 25.295
spatialHeatmap.Rcheck/spatialHeatmap-Ex.timings
name | user | system | elapsed | |
Database | 0.329 | 0.012 | 0.340 | |
SPHM | 14.899 | 0.480 | 15.395 | |
SPHMMethods | 1.208 | 0.098 | 1.328 | |
SVG | 0.581 | 0.106 | 0.767 | |
SVGMethods | 0.356 | 0.101 | 0.493 | |
SpatialEnrichment | 3.862 | 0.233 | 4.100 | |
aSVG.remote.repo | 0.000 | 0.003 | 0.003 | |
adj_mod | 2.697 | 0.381 | 3.019 | |
aggr_rep | 0.801 | 0.064 | 0.865 | |
cell_group | 10.454 | 0.439 | 10.890 | |
cluster_cell | 1.275 | 0.060 | 1.336 | |
coclus_opt | 0.232 | 0.023 | 0.255 | |
cocluster | 0.193 | 0.012 | 0.205 | |
com_factor | 0.159 | 0.020 | 0.179 | |
covis | 14.747 | 0.567 | 15.348 | |
custom_shiny | 0.013 | 0.004 | 0.018 | |
cut_dendro | 0.597 | 0.005 | 0.583 | |
cvt_id | 0.458 | 0.000 | 0.458 | |
data_ref | 0.656 | 0.016 | 0.671 | |
edit_tar | 0.004 | 0.000 | 0.004 | |
filter_data | 0.883 | 0.012 | 0.895 | |
matrix_hm | 2.152 | 0.115 | 2.268 | |
network | 2.066 | 0.077 | 2.143 | |
norm_cell | 1.779 | 0.007 | 1.786 | |
norm_data | 0.781 | 0.008 | 0.789 | |
norm_srsc | 2.549 | 0.068 | 2.617 | |
opt_bar | 0.097 | 0.000 | 0.098 | |
opt_setting | 0.007 | 0.000 | 0.007 | |
opt_violin | 0.166 | 0.003 | 0.170 | |
optimal_k | 0.155 | 0.011 | 0.167 | |
plot_dim | 1.439 | 0.009 | 1.447 | |
plot_kmeans | 0.516 | 0.004 | 0.519 | |
plot_meta | 2.329 | 0.191 | 2.576 | |
process_cell_meta | 7.361 | 0.776 | 8.135 | |
qc_cell | 1.003 | 0.048 | 1.051 | |
read_cache | 2.260 | 0.188 | 2.449 | |
read_fr | 0.000 | 0.004 | 0.004 | |
read_svg | 0.401 | 0.109 | 0.550 | |
reduce_dim | 7.096 | 0.356 | 7.450 | |
reduce_rep | 0.001 | 0.000 | 0.001 | |
return_feature | 0.539 | 0.000 | 0.541 | |
save_cache | 2.093 | 0.136 | 2.228 | |
shiny_shm | 0 | 0 | 0 | |
shm | 3.092 | 0.102 | 3.229 | |
spatialHeatmap-package | 0 | 0 | 0 | |
spatial_hm | 4.295 | 0.132 | 4.481 | |
submatrix | 3.229 | 0.128 | 3.357 | |
true_bulk | 0.274 | 0.000 | 0.274 | |
update_feature | 0.001 | 0.000 | 0.001 | |
write_svg | 2.288 | 0.099 | 2.424 | |