Multiple platform build/check report for BioC 3.14 - CHECK results for SingleCellExperiment on tokay2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4137
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: SingleCellExperiment

Version: 1.16.0

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SingleCellExperiment.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings SingleCellExperiment_1.16.0.tar.gz

StartedAt: 2022-04-13 03:02:48 -0400 (Wed, 13 Apr 2022)

EndedAt: 2022-04-13 03:10:22 -0400 (Wed, 13 Apr 2022)

EllapsedTime: 454.3 seconds

RetCode: 0

Status: OK

CheckDir: SingleCellExperiment.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SingleCellExperiment.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings SingleCellExperiment_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/SingleCellExperiment.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SingleCellExperiment/DESCRIPTION' ... OK
* this is package 'SingleCellExperiment' version '1.16.0'
* 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 'SingleCellExperiment' 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 ... NOTE
Unexported objects imported by ':::' calls:
  'BiocGenerics:::replaceSlots' 'S4Vectors:::disableValidity'
  'SummarizedExperiment:::.SummarizedExperiment.charbound'
  See the note in ?`:::` about the use of this operator.
* 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/SingleCellExperiment.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/SingleCellExperiment_1.16.0.tar.gz && rm -rf SingleCellExperiment.buildbin-libdir && mkdir SingleCellExperiment.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SingleCellExperiment.buildbin-libdir SingleCellExperiment_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL SingleCellExperiment_1.16.0.zip && rm SingleCellExperiment_1.16.0.tar.gz SingleCellExperiment_1.16.0.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 84683  100 84683    0     0   540k      0 --:--:-- --:--:-- --:--:--  544k

install for i386

* installing *source* package 'SingleCellExperiment' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'SingleCellExperiment'
    finding HTML links ... done
    LEM-combine                             html  
    LEM-getset                              html  
    LEM-misc                                html  
    LEM-subset                              html  
    LinearEmbeddingMatrix                   html  
    SingleCellExperiment                    html  
    finding level-2 HTML links ... done

    altExps                                 html  
    applySCE                                html  
    assays                                  html  
    colLabels                               html  
    colPairs                                html  
    combine                                 html  
    defunct                                 html  
    internals                               html  
    miscellaneous                           html  
    reduced.dim.matrix                      html  
    reducedDims                             html  
    rowPairs                                html  
    rowSubset                               html  
    simplifyToSCE                           html  
    sizeFactors                             html  
    splitAltExps                            html  
    swapAltExp                              html  
    unsplitAltExps                          html  
    updateObject                            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 'SingleCellExperiment' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SingleCellExperiment' as SingleCellExperiment_1.16.0.zip
* DONE (SingleCellExperiment)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'SingleCellExperiment' successfully unpacked and MD5 sums checked


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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(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, 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

> test_check("SingleCellExperiment")
class: SingleCellExperiment 
dim: 200 100 
metadata(0):
assays(2): counts logcounts
rownames: NULL
rowData names(0):
colnames: NULL
colData names(1): sizeFactor
reducedDimNames(2): PCA TSNE
mainExpName: NULL
altExpNames(2): Spike Protein
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 753 ]

[ FAIL 0 | WARN 6 | SKIP 0 | PASS 753 ]
> 
> proc.time()
   user  system elapsed 
 109.25    1.09  110.32


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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(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, 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

> test_check("SingleCellExperiment")
class: SingleCellExperiment 
dim: 200 100 
metadata(0):
assays(2): counts logcounts
rownames: NULL
rowData names(0):
colnames: NULL
colData names(1): sizeFactor
reducedDimNames(2): PCA TSNE
mainExpName: NULL
altExpNames(2): Spike Protein
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 753 ]

[ FAIL 0 | WARN 6 | SKIP 0 | PASS 753 ]
> 
> proc.time()
   user  system elapsed 
 117.92    0.67  118.64

name	user	system	elapsed
LEM-combine	0.06	0.07	0.12
LEM-getset	0.16	0.06	0.22
LEM-misc	0.03	0.00	0.03
LEM-subset	0.04	0.03	0.08
LinearEmbeddingMatrix	0.02	0.00	0.01
SingleCellExperiment	0.80	0.13	0.93
altExps	1.17	0.07	1.25
applySCE	1.94	0.00	1.93
assays	0.54	0.00	0.55
colLabels	0.41	0.00	0.41
colPairs	1.02	0.00	1.01
combine	2.42	0.03	2.46
internals	0.42	0.00	0.42
miscellaneous	0.83	0.00	0.83
reduced.dim.matrix	0	0	0
reducedDims	0.81	0.02	0.82
rowPairs	0.95	0.00	0.96
rowSubset	0.47	0.00	0.47
simplifyToSCE	1.91	0.02	1.92
sizeFactors	0.53	0.00	0.53
splitAltExps	1	0	1
swapAltExp	1.81	0.01	1.83
unsplitAltExps	1.42	0.00	1.42

name	user	system	elapsed
LEM-combine	0.64	0.00	0.64
LEM-getset	0.08	0.05	0.12
LEM-misc	0	0	0
LEM-subset	0.03	0.01	0.05
LinearEmbeddingMatrix	0	0	0
SingleCellExperiment	0.80	0.05	0.84
altExps	1.08	0.02	1.09
applySCE	2.14	0.01	2.16
assays	0.63	0.00	0.63
colLabels	0.48	0.00	0.48
colPairs	1.11	0.00	1.11
combine	2.78	0.00	2.78
internals	0.44	0.00	0.44
miscellaneous	0.84	0.00	0.84
reduced.dim.matrix	0	0	0
reducedDims	0.92	0.00	0.92
rowPairs	0.98	0.00	0.98
rowSubset	0.47	0.00	0.47
simplifyToSCE	1.81	0.00	1.82
sizeFactors	0.54	0.00	0.53
splitAltExps	0.98	0.00	0.98
swapAltExp	1.88	0.00	1.88
unsplitAltExps	1.5	0.0	1.5

CHECK results for SingleCellExperiment on tokay2

Summary

Command output

Installation output

Tests output

Example timings