Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-09-22 15:05:43 -0400 (Wed, 22 Sep 2021).

CHECK results for ExperimentSubset on machv2

To the developers/maintainers of the ExperimentSubset package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 608/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ExperimentSubset 1.2.0  (landing page)
Irzam Sarfraz
Snapshot Date: 2021-09-21 04:50:12 -0400 (Tue, 21 Sep 2021)
git_url: https://git.bioconductor.org/packages/ExperimentSubset
git_branch: RELEASE_3_13
git_last_commit: f9c08bb
git_last_commit_date: 2021-05-19 12:56:45 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ExperimentSubset
Version: 1.2.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ExperimentSubset.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ExperimentSubset_1.2.0.tar.gz
StartedAt: 2021-09-21 19:00:49 -0400 (Tue, 21 Sep 2021)
EndedAt: 2021-09-21 19:07:21 -0400 (Tue, 21 Sep 2021)
EllapsedTime: 391.7 seconds
RetCode: 0
Status:   OK  
CheckDir: ExperimentSubset.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ExperimentSubset.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ExperimentSubset_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/ExperimentSubset.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ExperimentSubset/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ExperimentSubset’ version ‘1.2.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* 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
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/ExperimentSubset.Rcheck/00check.log’
for details.



Installation output

ExperimentSubset.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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(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
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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

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: 64102 8 
metadata(1): ''
assays(1): counts
rownames(64102): ENSG00000000003 ENSG00000000005 ... LRG_98 LRG_99
rowData names(0):
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 
110.833   4.919 117.686 

Example timings

ExperimentSubset.Rcheck/ExperimentSubset-Ex.timings

nameusersystemelapsed
ExperimentSubset1.3470.0831.431
createSubset1.6650.0401.705
getSubsetAssay0.6800.0120.692
reducedDimNames-set2.9030.0692.976
reducedDimNames1.3430.0181.367
reducedDims-set1.3210.0141.336
setSubsetAssay1.8940.0171.913
subsetAssayCount1.4420.0101.455
subsetAssayNames0.6260.0100.636
subsetColData0.6420.0290.671
subsetColnames0.6330.0370.671
subsetCount0.6140.0040.619
subsetDim0.5940.0050.599
subsetNames0.5210.0040.525
subsetParent0.6030.0080.611
subsetRowData0.5170.0080.525
subsetRownames0.5040.0080.511
subsetSummary0.7110.0070.718