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This page was generated on 2024-07-19 17:39 -0400 (Fri, 19 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4742
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4484
merida1macOS 12.7.5 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4513
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4462
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 692/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ExperimentSubset 1.14.0  (landing page)
Irzam Sarfraz
Snapshot Date: 2024-07-17 14:00 -0400 (Wed, 17 Jul 2024)
git_url: https://git.bioconductor.org/packages/ExperimentSubset
git_branch: RELEASE_3_19
git_last_commit: 1d4782f
git_last_commit_date: 2024-04-30 11:28:17 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for ExperimentSubset on merida1

To the developers/maintainers of the ExperimentSubset package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ExperimentSubset.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: ExperimentSubset
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ExperimentSubset.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ExperimentSubset_1.14.0.tar.gz
StartedAt: 2024-07-18 05:06:58 -0400 (Thu, 18 Jul 2024)
EndedAt: 2024-07-18 05:18:54 -0400 (Thu, 18 Jul 2024)
EllapsedTime: 715.5 seconds
RetCode: 0
Status:   OK  
CheckDir: ExperimentSubset.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ExperimentSubset.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ExperimentSubset_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/ExperimentSubset.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 12.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ExperimentSubset/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ExperimentSubset’ version ‘1.14.0’
* 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 ‘ExperimentSubset’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
reducedDimNames-set 5.073  0.257   8.226
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/ExperimentSubset.Rcheck/00check.log’
for details.


Installation output

ExperimentSubset.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘ExperimentSubset’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning in makePrototypeFromClassDef(properties, ClassDef, immediate, where) :
  in constructing the prototype for class “SubsetSummarizedExperiment”, slots in prototype and not in class: listData, elementType
Warning in makePrototypeFromClassDef(properties, ClassDef, immediate, where) :
  in constructing the prototype for class “SubsetRangedSummarizedExperiment”, slots in prototype and not in class: listData, elementType
Warning in makePrototypeFromClassDef(properties, ClassDef, immediate, where) :
  in constructing the prototype for class “SubsetSingleCellExperiment”, slots in prototype and not in class: listData, elementType
Warning in makePrototypeFromClassDef(properties, ClassDef, immediate, where) :
  in constructing the prototype for class “SubsetTreeSummarizedExperiment”, slots in prototype and not in class: listData, elementType
Warning in makePrototypeFromClassDef(properties, ClassDef, immediate, where) :
  in constructing the prototype for class “SubsetSpatialExperiment”, slots in prototype and not in class: listData, elementType
** 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 (ExperimentSubset)

Tests output

ExperimentSubset.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
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(ExperimentSubset)
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: SingleCellExperiment
Loading required package: SpatialExperiment
Loading required package: TreeSummarizedExperiment
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit


Attaching package: 'ExperimentSubset'

The following objects are masked from 'package:SingleCellExperiment':

    reducedDimNames, reducedDimNames<-, reducedDims<-

> 
> test_check("ExperimentSubset")
class: SubsetSummarizedExperiment 
dim: 2000 2000 
metadata(0):
assays(2): counts logcounts
rownames(2000): C12orf73 RNU6-1256P ... FOXF1 PRR3
rowData names(0):
colnames(2000): CTGCTGTCAGGGTATG CAGTCCTTCGGTTAAC ... GATGCTATCAGCAACT
  ATTTCTGGTGATGATA
colData names(0):
subsets(1): s1
subsetAssays(1): s1Main assay(s):
 counts logcounts assay2 

Subset(s):
  Name      Dim Parent Assays
1   s1 10, 2000 counts  newS1
Main assay(s):
 counts 

Subset(s):
NULL
class: SubsetRangedSummarizedExperiment 
dim: 63677 8 
metadata(1): ''
assays(1): counts
rownames(63677): ENSG00000000003 ENSG00000000005 ... ENSG00000273492
  ENSG00000273493
rowData names(10): gene_id gene_name ... seq_coord_system symbol
colnames(8): SRR1039508 SRR1039509 ... SRR1039520 SRR1039521
colData names(9): SampleName cell ... Sample BioSample
subsets(1): s2
subsetAssays(1): s2Main assay(s):
 counts assay2 

Subset(s):
  Name   Dim Parent Assays
1   s2 15, 8 counts  newS2
Main assay(s):
 counts logcounts 

Subset(s):
     Name    Dim Parent        Assays
1 subset1 10, 10 counts scaledSubset1
class: SubsetSingleCellExperiment 
dim: 2000 2000 
metadata(0):
assays(2): counts logcounts
rownames(2000): C12orf73 RNU6-1256P ... FOXF1 PRR3
rowData names(1): gene
colnames(2000): CTGCTGTCAGGGTATG CAGTCCTTCGGTTAAC ... GATGCTATCAGCAACT
  ATTTCTGGTGATGATA
colData names(11): nGene nUMI ... ident doublet_true_labels
reducedDimNames(0):
mainExpName: NULL
altExpNames(0):
subsets(1): subset1
subsetAssays(2): subset1 scaledSubset1[ FAIL 0 | WARN 0 | SKIP 0 | PASS 127 ]
> 
> proc.time()
   user  system elapsed 
124.861  11.119 179.360 

Example timings

ExperimentSubset.Rcheck/ExperimentSubset-Ex.timings

nameusersystemelapsed
ExperimentSubset1.4610.0512.351
createSubset1.1250.0632.175
getSubsetAssay0.7610.1081.610
reducedDimNames-set5.0730.2578.226
reducedDimNames1.5160.0662.762
reducedDims-set1.4930.0542.453
setSubsetAssay1.1420.0241.458
subsetAssayCount0.7990.0171.019
subsetAssayNames0.8200.0401.094
subsetColData0.6010.0100.771
subsetColnames0.6220.0110.809
subsetCount0.6050.0080.788
subsetDim0.6500.0180.847
subsetNames0.5920.0110.755
subsetParent0.7680.0090.965
subsetRowData0.6540.0190.814
subsetRownames0.6070.0090.782
subsetSummary0.9200.0151.149