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This page was generated on 2022-10-18 14:50:14 -0400 (Tue, 18 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (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

CHECK results for spatialLIBD on nebbiolo1


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 362/410HostnameOS / ArchINSTALLBUILDCHECK
spatialLIBD 1.8.11  (landing page)
Leonardo Collado-Torres
Snapshot Date: 2022-10-18 07:30:03 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/spatialLIBD
git_branch: RELEASE_3_15
git_last_commit: aae8775
git_last_commit_date: 2022-09-02 10:56:55 -0400 (Fri, 02 Sep 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published

Summary

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

Command output

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###
### 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.



Installation output

spatialLIBD.Rcheck/00install.out

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###
### 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)

Tests output

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 

Example timings

spatialLIBD.Rcheck/spatialLIBD-Ex.timings

nameusersystemelapsed
add10xVisiumAnalysis0.0010.0000.001
add_images22.406 2.01628.157
add_key17.847 1.38019.823
check_modeling_results0.7690.0881.175
check_sce2.7020.1803.188
check_sce_layer0.9650.0601.349
check_spe19.034 1.14720.849
cluster_export17.634 1.44819.765
cluster_import18.599 1.28220.524
enough_ram0.0070.0030.011
fetch_data0.9340.0921.343
gene_set_enrichment1.1390.0901.518
gene_set_enrichment_plot1.0880.1331.418
geom_spatial17.878 1.65820.239
get_colors0.9320.0961.366
img_edit17.257 1.36919.208
img_update16.851 1.09418.645
img_update_all19.910 1.22321.533
layer_boxplot2.2870.0973.015
layer_matrix_plot0.0080.0000.008
layer_stat_cor0.7890.0321.110
layer_stat_cor_plot0.9010.0321.245
locate_images000
read10xVisiumAnalysis000
read10xVisiumWrapper000
run_app000
sce_to_spe16.691 1.07318.463
sig_genes_extract1.7980.6843.010
sig_genes_extract_all2.2450.1242.948
sort_clusters0.0020.0000.003
vis_clus17.881 1.26119.779
vis_clus_p17.405 1.19419.182
vis_gene19.872 2.36122.931
vis_gene_p17.590 1.40019.759
vis_grid_clus16.849 2.07820.812
vis_grid_gene17.320 1.90819.925