Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-01 07:38:51 -0000 (Wed, 01 Mar 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4266 |
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 |
To the developers/maintainers of the spatialHeatmap package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1922/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
spatialHeatmap 2.5.3 (landing page) Jianhai Zhang
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
Package: spatialHeatmap |
Version: 2.5.3 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:spatialHeatmap.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings spatialHeatmap_2.5.3.tar.gz |
StartedAt: 2023-02-28 16:13:04 -0000 (Tue, 28 Feb 2023) |
EndedAt: 2023-02-28 16:27:49 -0000 (Tue, 28 Feb 2023) |
EllapsedTime: 885.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: spatialHeatmap.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:spatialHeatmap.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings spatialHeatmap_2.5.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/spatialHeatmap.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘spatialHeatmap/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘spatialHeatmap’ version ‘2.5.3’ * 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 19.3Mb sub-directories of 1Mb or more: R 1.1Mb extdata 17.8Mb * 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 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 read_hdf5 17.595 0.784 18.402 write_hdf5 15.036 0.604 15.641 covis 12.334 0.551 12.842 spatialHeatmap-package 9.985 0.962 10.925 spatial_hm 10.077 0.663 10.716 manual_group 9.136 0.384 9.519 reduce_dim 8.791 0.663 9.453 process_cell_meta 8.605 0.292 8.896 spatial_enrich 4.686 0.398 5.082 * 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 ‘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-3.17-bioc/meat/spatialHeatmap.Rcheck/00check.log’ for details.
spatialHeatmap.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL spatialHeatmap ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/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’ ** 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) (2023-01-14 r83615) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-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 Loading required package: Biobase Loading required package: BiocGenerics Attaching package: 'BiocGenerics' 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 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 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. 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 -- Tue Feb 28 16:21:11 2023 *********************************************** 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 34.511 1.771 36.269
spatialHeatmap.Rcheck/spatialHeatmap-Ex.timings
name | user | system | elapsed | |
SVG | 0.854 | 0.126 | 0.990 | |
SVGMethods | 0.453 | 0.077 | 0.527 | |
aSVG.remote.repo | 0.000 | 0.003 | 0.003 | |
adj_mod | 3.405 | 0.328 | 3.737 | |
aggr_rep | 0.348 | 0.008 | 0.355 | |
cluster_cell | 2.138 | 0.088 | 2.225 | |
coclus_opt | 0.328 | 0.028 | 0.360 | |
cocluster | 0.250 | 0.023 | 0.275 | |
com_factor | 0.198 | 0.017 | 0.215 | |
covis | 12.334 | 0.551 | 12.842 | |
custom_shiny | 0.014 | 0.000 | 0.014 | |
deg.table | 0.017 | 0.000 | 0.016 | |
deg_ovl | 1.936 | 0.128 | 2.064 | |
edit_tar | 0.008 | 0.000 | 0.008 | |
filter_data | 0.904 | 0.048 | 0.951 | |
graph_line | 0.271 | 0.008 | 0.279 | |
lis.deg.up.down | 0.002 | 0.000 | 0.001 | |
manual_group | 9.136 | 0.384 | 9.519 | |
matrix_hm | 1.721 | 0.072 | 1.735 | |
network | 2.296 | 0.132 | 2.428 | |
norm_cell | 2.667 | 0.064 | 2.731 | |
norm_data | 0.581 | 0.016 | 0.597 | |
opt_bar | 0.150 | 0.008 | 0.157 | |
opt_setting | 0.010 | 0.000 | 0.011 | |
opt_violin | 0.239 | 0.000 | 0.238 | |
plot_dim | 2.243 | 0.040 | 2.283 | |
process_cell_meta | 8.605 | 0.292 | 8.896 | |
qc_cell | 1.387 | 0.044 | 1.431 | |
read_cache | 2.191 | 0.084 | 2.278 | |
read_fr | 0.004 | 0.000 | 0.004 | |
read_hdf5 | 17.595 | 0.784 | 18.402 | |
read_svg | 0.466 | 0.132 | 0.592 | |
reduce_dim | 8.791 | 0.663 | 9.453 | |
reduce_rep | 0.001 | 0.000 | 0.001 | |
refine_cluster | 1.779 | 0.036 | 1.815 | |
return_feature | 0.981 | 0.068 | 1.063 | |
save_cache | 2.229 | 0.216 | 2.445 | |
shiny_shm | 0.000 | 0.000 | 0.001 | |
spatialHeatmap-package | 9.985 | 0.962 | 10.925 | |
spatial_enrich | 4.686 | 0.398 | 5.082 | |
spatial_hm | 10.077 | 0.663 | 10.716 | |
submatrix | 1.023 | 0.040 | 1.063 | |
tar_ref | 0.898 | 0.040 | 0.937 | |
true_bulk | 0.398 | 0.008 | 0.407 | |
update_feature | 0.001 | 0.000 | 0.002 | |
write_hdf5 | 15.036 | 0.604 | 15.641 | |