Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-03-04 11:40:09 -0500 (Mon, 04 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4676
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4414
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4441
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4417
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 2218/2251HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Voyager 1.5.0  (landing page)
Lambda Moses
Snapshot Date: 2024-03-01 14:00:22 -0500 (Fri, 01 Mar 2024)
git_url: https://git.bioconductor.org/packages/Voyager
git_branch: devel
git_last_commit: b67f40d
git_last_commit_date: 2023-10-24 11:44:36 -0500 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for Voyager on merida1


To the developers/maintainers of the Voyager package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Voyager.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.

raw results


Summary

Package: Voyager
Version: 1.5.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Voyager.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Voyager_1.5.0.tar.gz
StartedAt: 2024-03-02 12:21:17 -0500 (Sat, 02 Mar 2024)
EndedAt: 2024-03-02 12:43:00 -0500 (Sat, 02 Mar 2024)
EllapsedTime: 1303.1 seconds
RetCode: 0
Status:   OK  
CheckDir: Voyager.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Voyager.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Voyager_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/Voyager.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Voyager/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Voyager’ version ‘1.5.0’
* 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 ‘Voyager’ 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 data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
calculateMultivariate 68.471  1.597  74.368
calculateBivariate    23.368  0.857  27.481
clusterVariograms     16.744  0.403  17.537
ElbowPlot             13.237  1.587  23.407
plotGeometry          10.298  0.445  11.088
moranPlot              9.027  0.344   9.612
plotVariogram          8.475  0.217   8.879
plotCellBin2D          8.011  0.439   8.637
calculateUnivariate    7.395  0.386   8.051
plotLocalResult        6.578  0.235   7.023
plotColDataHistogram   6.503  0.303   6.987
plotCrossVariogramMap  6.384  0.264   6.853
plotCrossVariogram     6.179  0.247   6.602
plotCorrelogram        5.536  0.208   5.935
plotSpatialFeature     5.502  0.216   5.920
plotColDataFreqpoly    5.092  0.236   5.560
plotVariogramMap       5.043  0.201   5.452
plotColGraph           4.767  0.215   5.246
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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

Voyager.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Voyager
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘Voyager’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** 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 (Voyager)

Tests output

Voyager.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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(Voyager)
> 
> test_check("Voyager")
Loading required package: spData
To access larger datasets in this package, install the spDataLarge
package with: `install.packages('spDataLarge',
repos='https://nowosad.github.io/drat/', type='source')`
Loading required package: sf
Linking to GEOS 3.11.0, GDAL 3.5.3, PROJ 9.1.0; sf_use_s2() is TRUE
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, 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

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: 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

Loading required package: scuttle
Loading required package: ggplot2

Attaching package: 'SpatialFeatureExperiment'

The following object is masked from 'package:ggplot2':

    unit

see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache

Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand

see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
gstat does not fit anisotropic variograms. Variogram model is fitted to the whole dataset.
Only one cluster is present. Not using color_by.
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
Coordinate system already present. Adding new coordinate system, which will replace the existing one.
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
beginning bbox testssee ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
Please use linewidth instead of size for thickness of polygon outlines.
trying URL 'https://cf.10xgenomics.com/samples/spatial-exp/2.0.0/Visium_Mouse_Olfactory_Bulb/Visium_Mouse_Olfactory_Bulb_filtered_feature_bc_matrix.h5'
Content type 'binary/octet-stream' length 7521734 bytes (7.2 MB)
==================================================
downloaded 7.2 MB

trying URL 'https://cf.10xgenomics.com/samples/spatial-exp/2.0.0/Visium_Mouse_Olfactory_Bulb/Visium_Mouse_Olfactory_Bulb_spatial.tar.gz'
Content type 'application/x-tar' length 7806681 bytes (7.4 MB)
==================================================
downloaded 7.4 MB

see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
[ FAIL 0 | WARN 0 | SKIP 17 | PASS 577 ]

══ Skipped tests (17) ══════════════════════════════════════════════════════════
• On CRAN (17): 'test-bivariate.R:129:5', 'test-bivariate.R:150:5',
  'test-gstat.R:187:5', 'test-plot.R:334:5', 'test-plot.R:380:5',
  'test-plot.R:417:5', 'test-plot.R:435:5', 'test-plot.R:449:5',
  'test-plot.R:493:5', 'test-plot.R:571:5', 'test-plot.R:604:5',
  'test-plot.R:626:5', 'test-plot.R:786:5', 'test-plot.R:821:5',
  'test-plot.R:832:5', 'test-plot.R:873:5', 'test-plot.R:894:5'

[ FAIL 0 | WARN 0 | SKIP 17 | PASS 577 ]
Deleting unused snapshots:
• bivariate/plot-cross-variograms-no-np.svg
• bivariate/plot-cross-variograms-with-anisotropy.svg
• gstat/multiple-samples-multiple-features.svg
• gstat/multiple-samples-one-feature.svg
• gstat/plot-np.svg
• plot/both-positive-and-negative.svg
• plot/change-the-number-of-columns.svg
• plot/cluster-by-gene-instead.svg
• plot/coldata-freqpoly-multiple-variables.svg
• plot/coldata-histogram-multiple-variables.svg
• plot/correlograms-for-multispati-pcs-one-component.svg
• plot/elbowplot-more-pcs-than-available.svg
• plot/elbowplot-with-10-of-the-20-pcs.svg
• plot/facetting-by-sample.svg
• plot/illegal-symbol-freqpoly.svg
• plot/illegal-symbol.svg
• plot/moran-plot-don-t-plot-influential.svg
• plot/multiple-samples.svg
• plot/multiple-variables-color-by.svg
• plot/multiple-variables-facetting.svg
• plot/multiple-variables-fill-by.svg
• plot/not-facetting-multispati-elbow-negative-only.svg
• plot/one-variable-color-by.svg
• plot/one-variable-facetting.svg
• plot/one-variable-fill-by.svg
• plot/plotcorrelogram-categorical-color-by.svg
• plot/plotcorrelogram-coldata-i.svg
• plot/plotcorrelogram-continuous-color-by.svg
• plot/plotcorrelogram-one-gene-c.svg
• plot/plotcorrelogram-one-gene-corr.svg
• plot/plotcorrelogram-specify-gene-and-coldata-i.svg
• plot/plotdimloadings-not-balanced.svg
• plot/with-subset-freqpoly.svg
• plot/with-subset.svg
> 
> proc.time()
   user  system elapsed 
217.847  10.047 241.724 

Example timings

Voyager.Rcheck/Voyager-Ex.timings

nameusersystemelapsed
ElbowPlot13.237 1.58723.407
SFEMethod0.0030.0010.004
calculateBivariate23.368 0.85727.481
calculateMultivariate68.471 1.59774.368
calculateUnivariate7.3950.3868.051
clusterCorrelograms3.9060.2344.315
clusterMoranPlot4.1670.2474.717
clusterVariograms16.744 0.40317.537
colFeatureData3.6120.2644.116
getDivergeRange0.0000.0000.001
getParams3.8920.2694.330
listSFEMethods0.0020.0000.003
listw2sparse3.0240.2153.405
moranBounds3.1350.2253.532
moranPlot9.0270.3449.612
multi_listw2sparse0.0000.0000.001
multispati_rsp3.6800.2104.086
plotCellBin2D8.0110.4398.637
plotColDataFreqpoly5.0920.2365.560
plotColDataHistogram6.5030.3036.987
plotColGraph4.7670.2155.246
plotCorrelogram5.5360.2085.935
plotCrossVariogram6.1790.2476.602
plotCrossVariogramMap6.3840.2646.853
plotDimLoadings3.5240.1873.879
plotGeometry10.298 0.44511.088
plotLocalResult6.5780.2357.023
plotMoranMC3.3250.1793.668
plotSpatialFeature5.5020.2165.920
plotVariogram8.4750.2178.879
plotVariogramMap5.0430.2015.452
spatialReducedDim3.6550.1774.009