Back to Multiple platform build/check report for BioC 3.19:   simplified   long
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

This page was generated on 2024-05-20 11:38:30 -0400 (Mon, 20 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4751
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4485
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4515
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 2080/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
standR 1.8.0  (landing page)
Ning Liu
Snapshot Date: 2024-05-19 14:00:13 -0400 (Sun, 19 May 2024)
git_url: https://git.bioconductor.org/packages/standR
git_branch: RELEASE_3_19
git_last_commit: 897a04b
git_last_commit_date: 2024-04-30 11:41:38 -0400 (Tue, 30 Apr 2024)
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
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for standR on lconway


To the developers/maintainers of the standR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/standR.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: standR
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:standR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings standR_1.8.0.tar.gz
StartedAt: 2024-05-20 00:19:46 -0400 (Mon, 20 May 2024)
EndedAt: 2024-05-20 00:26:14 -0400 (Mon, 20 May 2024)
EllapsedTime: 387.9 seconds
RetCode: 0
Status:   OK  
CheckDir: standR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:standR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings standR_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/standR.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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 ‘standR/DESCRIPTION’ ... OK
* this is package ‘standR’ version ‘1.8.0’
* 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 ‘standR’ 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 code 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
prepareSpatialDecon 11.999  2.343  13.199
readGeoMx            8.404  1.096   9.826
findBestK            6.742  0.287   7.090
* 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

standR.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘standR’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for ‘drawPCA’ with signature ‘"DGEList"’: no definition for class “DGEList”
in method for ‘drawPCA’ with signature ‘"SpatialExperiment"’: no definition for class “SpatialExperiment”
in method for ‘plotDR’ with signature ‘"SpatialExperiment","ANY"’: no definition for class “SpatialExperiment”
in method for ‘plotMDS’ with signature ‘"DGEList","ANY","ANY","ANY"’: no definition for class “DGEList”
in method for ‘plotMDS’ with signature ‘"SpatialExperiment"’: no definition for class “SpatialExperiment”
in method for ‘plotRLExpr’ with signature ‘"DGEList","ANY"’: no definition for class “DGEList”
** 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 (standR)

Tests output

standR.Rcheck/tests/testthat.Rout


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
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(standR)
> 
> test_check("standR")
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, 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

New names:
* `cv` -> `cv...1`
* `cv` -> `cv...2`
* `cv` -> `cv...3`
* `cv` -> `cv...4`
* `cv` -> `cv...5`
* `cv` -> `cv...6`
* `cv` -> `cv...7`
New names:
* `cv` -> `cv...1`
* `cv` -> `cv...2`
* `cv` -> `cv...3`
* `cv` -> `cv...4`
* `cv` -> `cv...5`
* `cv` -> `cv...6`
* `cv` -> `cv...7`
Rows: 18504 Columns: 232
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr   (1): TargetName
dbl (231): disease3_scan | 001 | PanCK, disease3_scan | 001 | neg, disease3_...

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 231 Columns: 25
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr  (8): SlideName, ScanName, SegmentLabel, SegmentDisplayName, Sample_ID, ...
dbl (17): ROILabel, AOISurfaceArea, AOINucleiCount, ROICoordinateX, ROICoord...

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 18504 Columns: 232
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr   (1): TargetName
dbl (231): disease3_scan | 001 | PanCK, disease3_scan | 001 | neg, disease3_...

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 18504 Columns: 232
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr   (1): TargetName
dbl (231): disease3_scan | 001 | PanCK, disease3_scan | 001 | neg, disease3_...

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 231 Columns: 25
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr  (8): SlideName, ScanName, SegmentLabel, SegmentDisplayName, Sample_ID, ...
dbl (17): ROILabel, AOISurfaceArea, AOINucleiCount, ROICoordinateX, ROICoord...

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Loading required namespace: scater
Loading required package: scuttle
Loading required package: ggplot2

Attaching package: 'scater'

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

    plotMDS

Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr

Attaching package: 'AnnotationHub'

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

    cache

see ?standR and browseVignettes('standR') for documentation
loading from cache
see ?standR and browseVignettes('standR') for documentation
loading from cache
Rows: 18504 Columns: 232
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr   (1): TargetName
dbl (231): disease3_scan | 001 | PanCK, disease3_scan | 001 | neg, disease3_...

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 231 Columns: 25
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr  (8): SlideName, ScanName, SegmentLabel, SegmentDisplayName, Sample_ID, ...
dbl (17): ROILabel, AOISurfaceArea, AOINucleiCount, ROICoordinateX, ROICoord...

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 104 ]
> 
> proc.time()
   user  system elapsed 
 73.998   7.482 115.379 

Example timings

standR.Rcheck/standR-Ex.timings

nameusersystemelapsed
addPerROIQC1.7880.0811.894
computeClusterEvalStats2.4090.1122.541
dkd_spe_subset0.0550.0050.061
drawPCA0.3850.0420.432
findBestK6.7420.2877.090
findNCGs1.0050.1071.121
geomxBatchCorrection2.0170.1352.174
geomxNorm1.3620.0961.472
plotClusterEvalStats2.5660.0482.630
plotDR0.6790.0300.716
plotGeneQC1.4170.0191.446
plotMDS0.8200.0600.889
plotPCAbiplot0.4030.0050.413
plotPairPCA1.0520.0261.084
plotRLExpr1.6550.0231.690
plotROIQC1.1580.0361.201
plotSampleInfo0.8950.0180.920
plotScreePCA0.3120.0090.327
prepareSpatialDecon11.999 2.34313.199
readGeoMx8.4041.0969.826
readGeoMxFromDGE0.7110.0141.272
spe2dge0.9460.0441.257