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This page was generated on 2021-12-01 18:35:25 -0500 (Wed, 01 Dec 2021).

CHECK results for spatialLIBD on nebbiolo2

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.

raw results

Package 361/408HostnameOS / ArchINSTALLBUILDCHECK
spatialLIBD 1.6.2  (landing page)
Leonardo Collado-Torres
Snapshot Date: 2021-12-01 08:30:01 -0500 (Wed, 01 Dec 2021)
git_url: https://git.bioconductor.org/packages/spatialLIBD
git_branch: RELEASE_3_14
git_last_commit: 49f9935
git_last_commit_date: 2021-11-30 16:56:40 -0500 (Tue, 30 Nov 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  YES

Summary

Package: spatialLIBD
Version: 1.6.2
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:spatialLIBD.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings spatialLIBD_1.6.2.tar.gz
StartedAt: 2021-12-01 15:40:44 -0500 (Wed, 01 Dec 2021)
EndedAt: 2021-12-01 15:50:41 -0500 (Wed, 01 Dec 2021)
EllapsedTime: 596.7 seconds
RetCode: 0
Status:   OK  
CheckDir: spatialLIBD.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:spatialLIBD.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings spatialLIBD_1.6.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-data-experiment/meat/spatialLIBD.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘1.6.2’
* 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 ... 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 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            24.931  3.023  33.039
vis_gene              19.784  2.240  23.970
img_update_all        19.844  1.807  23.363
cluster_import        19.333  2.069  23.222
check_spe             19.012  1.531  22.523
vis_gene_p            18.045  2.031  23.179
cluster_export        17.986  1.750  21.815
vis_grid_gene         17.444  2.184  21.643
vis_grid_clus         17.306  2.232  21.522
vis_clus              17.451  1.808  21.112
vis_clus_p            17.248  1.998  21.103
geom_spatial          17.540  1.555  21.001
img_edit              17.284  1.704  20.878
img_update            16.215  1.650  19.918
sce_to_spe            16.101  1.382  19.419
layer_boxplot          4.649  0.536   5.694
check_sce              4.405  0.508   5.189
sig_genes_extract_all  4.242  0.524   5.235
* 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: OK


Installation output

spatialLIBD.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL spatialLIBD
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.14-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)

Tests output

spatialLIBD.Rcheck/tests/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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 
  9.437   0.489   9.908 

Example timings

spatialLIBD.Rcheck/spatialLIBD-Ex.timings

nameusersystemelapsed
add10xVisiumAnalysis000
add_images24.931 3.02333.039
check_modeling_results1.7320.1152.174
check_sce4.4050.5085.189
check_sce_layer2.0510.1662.496
check_spe19.012 1.53122.523
cluster_export17.986 1.75021.815
cluster_import19.333 2.06923.222
enough_ram0.0060.0060.012
fetch_data1.9430.1802.437
gene_set_enrichment1.8800.1802.356
gene_set_enrichment_plot2.7600.4153.363
geom_spatial17.540 1.55521.001
get_colors1.7570.1562.223
img_edit17.284 1.70420.878
img_update16.215 1.65019.918
img_update_all19.844 1.80723.363
layer_boxplot4.6490.5365.694
layer_matrix_plot0.0070.0000.008
layer_stat_cor1.4850.0901.765
layer_stat_cor_plot1.5320.1071.823
locate_images000
read10xVisiumAnalysis000
read10xVisiumWrapper000
run_app0.0000.0000.001
sce_to_spe16.101 1.38219.419
sig_genes_extract3.1830.4164.179
sig_genes_extract_all4.2420.5245.235
sort_clusters0.0030.0000.002
vis_clus17.451 1.80821.112
vis_clus_p17.248 1.99821.103
vis_gene19.784 2.24023.970
vis_gene_p18.045 2.03123.179
vis_grid_clus17.306 2.23221.522
vis_grid_gene17.444 2.18421.643