Back to Build/check report for BioC 3.15 experimental data |
|
This page was generated on 2022-10-18 14:50:14 -0400 (Tue, 18 Oct 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4386 |
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 spatialLIBD package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 362/410 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||||
spatialLIBD 1.8.11 (landing page) Leonardo Collado-Torres
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | ||||||||
Package: spatialLIBD |
Version: 1.8.11 |
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:spatialLIBD.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings spatialLIBD_1.8.11.tar.gz |
StartedAt: 2022-10-18 11:45:24 -0400 (Tue, 18 Oct 2022) |
EndedAt: 2022-10-18 11:55:13 -0400 (Tue, 18 Oct 2022) |
EllapsedTime: 588.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: spatialLIBD.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:spatialLIBD.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings spatialLIBD_1.8.11.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.15-data-experiment/meat/spatialLIBD.Rcheck’ * using R version 4.2.1 (2022-06-23) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘spatialLIBD/DESCRIPTION’ ... OK * this is package ‘spatialLIBD’ version ‘1.8.11’ * 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 ‘spatialLIBD’ can be installed ... OK * checking installed package size ... OK * 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 ... NOTE app_server: no visible binding for global variable ‘test’ layer_boxplot: no visible global function definition for ‘assay’ Undefined global functions or variables: assay test * 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 LazyData ... 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 add_images 22.406 2.016 28.157 vis_gene 19.872 2.361 22.931 img_update_all 19.910 1.223 21.533 check_spe 19.034 1.147 20.849 cluster_import 18.599 1.282 20.524 geom_spatial 17.878 1.658 20.239 vis_grid_gene 17.320 1.908 19.925 add_key 17.847 1.380 19.823 vis_clus 17.881 1.261 19.779 cluster_export 17.634 1.448 19.765 vis_gene_p 17.590 1.400 19.759 vis_grid_clus 16.849 2.078 20.812 img_edit 17.257 1.369 19.208 vis_clus_p 17.405 1.194 19.182 img_update 16.851 1.094 18.645 sce_to_spe 16.691 1.073 18.463 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... 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-3.15-data-experiment/meat/spatialLIBD.Rcheck/00check.log’ for details.
spatialLIBD.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL spatialLIBD ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’ * installing *source* package ‘spatialLIBD’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (spatialLIBD)
spatialLIBD.Rcheck/tests/testthat.Rout
R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid" Copyright (C) 2022 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. > library(testthat) > library(spatialLIBD) Loading required package: SpatialExperiment Loading required package: SingleCellExperiment Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats 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 Loading required package: GenomicRanges Loading required package: stats4 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, 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 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: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians > > test_check("spatialLIBD") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ] > > proc.time() user system elapsed 10.170 0.590 10.741
spatialLIBD.Rcheck/spatialLIBD-Ex.timings
name | user | system | elapsed | |
add10xVisiumAnalysis | 0.001 | 0.000 | 0.001 | |
add_images | 22.406 | 2.016 | 28.157 | |
add_key | 17.847 | 1.380 | 19.823 | |
check_modeling_results | 0.769 | 0.088 | 1.175 | |
check_sce | 2.702 | 0.180 | 3.188 | |
check_sce_layer | 0.965 | 0.060 | 1.349 | |
check_spe | 19.034 | 1.147 | 20.849 | |
cluster_export | 17.634 | 1.448 | 19.765 | |
cluster_import | 18.599 | 1.282 | 20.524 | |
enough_ram | 0.007 | 0.003 | 0.011 | |
fetch_data | 0.934 | 0.092 | 1.343 | |
gene_set_enrichment | 1.139 | 0.090 | 1.518 | |
gene_set_enrichment_plot | 1.088 | 0.133 | 1.418 | |
geom_spatial | 17.878 | 1.658 | 20.239 | |
get_colors | 0.932 | 0.096 | 1.366 | |
img_edit | 17.257 | 1.369 | 19.208 | |
img_update | 16.851 | 1.094 | 18.645 | |
img_update_all | 19.910 | 1.223 | 21.533 | |
layer_boxplot | 2.287 | 0.097 | 3.015 | |
layer_matrix_plot | 0.008 | 0.000 | 0.008 | |
layer_stat_cor | 0.789 | 0.032 | 1.110 | |
layer_stat_cor_plot | 0.901 | 0.032 | 1.245 | |
locate_images | 0 | 0 | 0 | |
read10xVisiumAnalysis | 0 | 0 | 0 | |
read10xVisiumWrapper | 0 | 0 | 0 | |
run_app | 0 | 0 | 0 | |
sce_to_spe | 16.691 | 1.073 | 18.463 | |
sig_genes_extract | 1.798 | 0.684 | 3.010 | |
sig_genes_extract_all | 2.245 | 0.124 | 2.948 | |
sort_clusters | 0.002 | 0.000 | 0.003 | |
vis_clus | 17.881 | 1.261 | 19.779 | |
vis_clus_p | 17.405 | 1.194 | 19.182 | |
vis_gene | 19.872 | 2.361 | 22.931 | |
vis_gene_p | 17.590 | 1.400 | 19.759 | |
vis_grid_clus | 16.849 | 2.078 | 20.812 | |
vis_grid_gene | 17.320 | 1.908 | 19.925 | |