Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-10-15 15:06:04 -0400 (Fri, 15 Oct 2021).

CHECK results for ExperimentSubset on tokay2

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: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 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: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ExperimentSubset.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ExperimentSubset_1.2.0.tar.gz
StartedAt: 2021-10-14 23:00:08 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 23:08:28 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 500.6 seconds
RetCode: 0
Status:   OK  
CheckDir: ExperimentSubset.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ExperimentSubset.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ExperimentSubset_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/ExperimentSubset.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 ... OK
* checking for portable file names ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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: OK


Installation output

ExperimentSubset.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/ExperimentSubset_1.2.0.tar.gz && rm -rf ExperimentSubset.buildbin-libdir && mkdir ExperimentSubset.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ExperimentSubset.buildbin-libdir ExperimentSubset_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL ExperimentSubset_1.2.0.zip && rm ExperimentSubset_1.2.0.tar.gz ExperimentSubset_1.2.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 56186  100 56186    0     0   253k      0 --:--:-- --:--:-- --:--:--  255k

install for i386

* 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
  converting help for package 'ExperimentSubset'
    finding HTML links ... done
    AssaySubset-class                       html  
    AssaySubset                             html  
    ExperimentSubset                        html  
    SubsetRangedSummarizedExperiment-class
                                            html  
    SubsetSingleCellExperiment-class        html  
    SubsetSpatialExperiment-class           html  
    SubsetSummarizedExperiment-class        html  
    SubsetTreeSummarizedExperiment-class    html  
    createSubset                            html  
    getSubsetAssay                          html  
    reducedDimNames-set                     html  
    reducedDimNames                         html  
    reducedDims-set-ANY-method              html  
    reducedDims-set                         html  
    setSubsetAssay                          html  
    subsetAssayCount                        html  
    subsetAssayNames                        html  
    subsetColData                           html  
    subsetColLinks                          html  
    subsetColnames                          html  
    subsetCount                             html  
    subsetDim                               html  
    subsetNames                             html  
    subsetParent                            html  
    subsetRowData                           html  
    subsetRowLinks                          html  
    subsetRownames                          html  
    subsetSpatialCoords                     html  
    subsetSpatialData                       html  
    subsetSummary                           html  
** 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

install for x64

* installing *source* package 'ExperimentSubset' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ExperimentSubset' as ExperimentSubset_1.2.0.zip
* DONE (ExperimentSubset)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'ExperimentSubset' successfully unpacked and MD5 sums checked

Tests output

ExperimentSubset.Rcheck/tests_i386/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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

Attaching package: 'IRanges'

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

    windows

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 
  84.85    6.20   93.25 

ExperimentSubset.Rcheck/tests_x64/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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

Attaching package: 'IRanges'

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

    windows

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 
  97.45    5.14  104.37 

Example timings

ExperimentSubset.Rcheck/examples_i386/ExperimentSubset-Ex.timings

nameusersystemelapsed
ExperimentSubset1.030.171.21
createSubset1.230.221.45
getSubsetAssay0.590.000.59
reducedDimNames-set2.140.112.25
reducedDimNames0.930.081.00
reducedDims-set0.950.010.97
setSubsetAssay1.260.131.39
subsetAssayCount1.190.011.21
subsetAssayNames0.500.030.53
subsetColData0.460.020.47
subsetColnames0.390.060.45
subsetCount0.420.020.44
subsetDim0.400.030.43
subsetNames0.430.030.46
subsetParent0.530.000.53
subsetRowData0.450.020.47
subsetRownames0.440.010.45
subsetSummary0.590.020.61

ExperimentSubset.Rcheck/examples_x64/ExperimentSubset-Ex.timings

nameusersystemelapsed
ExperimentSubset1.060.051.11
createSubset2.110.002.11
getSubsetAssay0.500.040.54
reducedDimNames-set2.440.072.50
reducedDimNames1.080.041.13
reducedDims-set1.070.031.11
setSubsetAssay2.140.022.15
subsetAssayCount0.610.030.64
subsetAssayNames0.570.030.60
subsetColData0.450.000.45
subsetColnames0.440.030.47
subsetCount0.470.000.47
subsetDim0.420.020.44
subsetNames0.420.030.45
subsetParent0.540.000.53
subsetRowData0.480.000.48
subsetRownames0.440.000.44
subsetSummary0.650.000.65