Multiple platform build/check report for BioC 3.21 - CHECK results for TENxIO on palomino7

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"	4748
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"	4459
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4349
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*

CHECK results for TENxIO on palomino7

To the developers/maintainers of the TENxIO package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TENxIO.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: TENxIO

Version: 1.9.3

Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TENxIO.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings TENxIO_1.9.3.tar.gz

StartedAt: 2024-11-25 05:36:20 -0500 (Mon, 25 Nov 2024)

EndedAt: 2024-11-25 05:40:00 -0500 (Mon, 25 Nov 2024)

EllapsedTime: 220.3 seconds

RetCode: 0

Status: OK

CheckDir: TENxIO.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TENxIO.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings TENxIO_1.9.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/TENxIO.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'TENxIO/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TENxIO' version '1.9.3'
* 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 'TENxIO' 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 files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'tinytest.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

TENxIO.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL TENxIO
###
##############################################################################
##############################################################################


* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'TENxIO' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** 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 (TENxIO)

Tests output

TENxIO.Rcheck/tests/tinytest.Rout


R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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.

> if (requireNamespace("tinytest", quietly = TRUE))
+     tinytest::test_package("TENxIO")
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
Loading required package: generics

Attaching package: 'generics'

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

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, 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

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_TENxFile-class.R.........    1 tests [0;32mOK[0m 
test_TENxFile-class.R.........    1 tests [0;32mOK[0m 
test_TENxFile-class.R.........    1 tests [0;32mOK[0m 
test_TENxFile-class.R.........    2 tests [0;32mOK[0m 
test_TENxFile-class.R.........    2 tests [0;32mOK[0m 
test_TENxFile-class.R.........    3 tests [0;32mOK[0m 
test_TENxFile-class.R.........    3 tests [0;32mOK[0m 
test_TENxFile-class.R.........    3 tests [0;32mOK[0m 
test_TENxFile-class.R.........    3 tests [0;32mOK[0m 
test_TENxFile-class.R.........    4 tests [0;32mOK[0m 
test_TENxFile-class.R.........    5 tests [0;32mOK[0m 
test_TENxFile-class.R.........    6 tests [0;32mOK[0m 
test_TENxFile-class.R.........    6 tests [0;32mOK[0m 
test_TENxFile-class.R.........    6 tests [0;32mOK[0m 
test_TENxFile-class.R.........    6 tests [0;32mOK[0m 
test_TENxFile-class.R.........    6 tests [0;32mOK[0m 
test_TENxFile-class.R.........    7 tests [0;32mOK[0m 
test_TENxFile-class.R.........    7 tests [0;32mOK[0m 
test_TENxFile-class.R.........    7 tests [0;32mOK[0m 
test_TENxFile-class.R.........    9 tests [0;32mOK[0m [0;34m1.4s[0m

test_TENxFileList-class.R.....    0 tests    
test_TENxFileList-class.R.....    0 tests    
test_TENxFileList-class.R.....    1 tests [0;32mOK[0m 
test_TENxFileList-class.R.....    2 tests [0;32mOK[0m 
test_TENxFileList-class.R.....    3 tests [0;32mOK[0m 
test_TENxFileList-class.R.....    3 tests [0;32mOK[0m 
test_TENxFileList-class.R.....    4 tests [0;32mOK[0m 
test_TENxFileList-class.R.....    5 tests [0;32mOK[0m 
test_TENxFileList-class.R.....    6 tests [0;32mOK[0m 
test_TENxFileList-class.R.....    7 tests [0;32mOK[0m 
test_TENxFileList-class.R.....    8 tests [0;32mOK[0m 
test_TENxFileList-class.R.....    9 tests [0;32mOK[0m [0;34m1.6s[0m

test_TENxFragments-class.R....    0 tests    
test_TENxFragments-class.R....    1 tests [0;32mOK[0m 
test_TENxFragments-class.R....    1 tests [0;32mOK[0m 
test_TENxFragments-class.R....    2 tests [0;32mOK[0m 
test_TENxFragments-class.R....    3 tests [0;32mOK[0m 
test_TENxFragments-class.R....    4 tests [0;32mOK[0m 
test_TENxFragments-class.R....    4 tests [0;32mOK[0m 
test_TENxFragments-class.R....    5 tests [0;32mOK[0m 
test_TENxFragments-class.R....    6 tests [0;32mOK[0m 
test_TENxFragments-class.R....    7 tests [0;32mOK[0m [0;34m1.5s[0m

test_TENxH5-class.R...........    0 tests    
test_TENxH5-class.R...........    0 tests    
test_TENxH5-class.R...........    1 tests [0;32mOK[0m 
test_TENxH5-class.R...........    2 tests [0;32mOK[0m 
test_TENxH5-class.R...........    2 tests [0;32mOK[0m 
test_TENxH5-class.R...........    3 tests [0;32mOK[0m 
test_TENxH5-class.R...........    4 tests [0;32mOK[0m 
test_TENxH5-class.R...........    4 tests [0;32mOK[0m preview <= 12 rowRanges: pbmc_granulocyte_ff_bc_ex.h5 

test_TENxH5-class.R...........    4 tests [0;32mOK[0m 
test_TENxH5-class.R...........    5 tests [0;32mOK[0m 
test_TENxH5-class.R...........    6 tests [0;32mOK[0m 
test_TENxH5-class.R...........    7 tests [0;32mOK[0m 
test_TENxH5-class.R...........    8 tests [0;32mOK[0m 
test_TENxH5-class.R...........    9 tests [0;32mOK[0m [0;34m1.8s[0m

test_TENxMTX-class.R..........    0 tests    
test_TENxMTX-class.R..........    0 tests    
test_TENxMTX-class.R..........    1 tests [0;32mOK[0m 
test_TENxMTX-class.R..........    2 tests [0;32mOK[0m 
test_TENxMTX-class.R..........    3 tests [0;32mOK[0m 
test_TENxMTX-class.R..........    3 tests [0;32mOK[0m 
test_TENxMTX-class.R..........    4 tests [0;32mOK[0m 
test_TENxMTX-class.R..........    5 tests [0;32mOK[0m 
test_TENxMTX-class.R..........    6 tests [0;32mOK[0m [0;36m38ms[0m

test_TENxPeaks-class.R........    0 tests    
test_TENxPeaks-class.R........    0 tests    
test_TENxPeaks-class.R........    1 tests [0;32mOK[0m 
test_TENxPeaks-class.R........    2 tests [0;32mOK[0m 
test_TENxPeaks-class.R........    2 tests [0;32mOK[0m 
test_TENxPeaks-class.R........    3 tests [0;32mOK[0m 
test_TENxPeaks-class.R........    4 tests [0;32mOK[0m 
test_TENxPeaks-class.R........    5 tests [0;32mOK[0m 
test_TENxPeaks-class.R........    5 tests [0;32mOK[0m 
test_TENxPeaks-class.R........    6 tests [0;32mOK[0m 
test_TENxPeaks-class.R........    7 tests [0;32mOK[0m 
test_TENxPeaks-class.R........    8 tests [0;32mOK[0m 
test_TENxPeaks-class.R........    9 tests [0;32mOK[0m 
test_TENxPeaks-class.R........   10 tests [0;32mOK[0m 
test_TENxPeaks-class.R........   11 tests [0;32mOK[0m 
test_TENxPeaks-class.R........   12 tests [0;32mOK[0m 
test_TENxPeaks-class.R........   13 tests [0;32mOK[0m 
test_TENxPeaks-class.R........   14 tests [0;32mOK[0m [0;34m0.3s[0m
All ok, 54 results (6.7s)
Warning messages:
1: In rhdf5::h5read(file, name = paste0(group, ranges), index = list(1L),  :
  Object 'matrix/features/interval' does not exist in this HDF5 file.
2: In TENxFragments(fr, extension = "tsv.gz") :
  Using default 'yieldSize' parameter
> 
> proc.time()
   user  system elapsed 
  13.17    0.92   15.07

Example timings

TENxIO.Rcheck/TENxIO-Ex.timings

name	user	system	elapsed
TENxFile	0	0	0
TENxFileList	1.93	0.16	3.44
TENxFragments	1.53	0.09	1.63
TENxH5	2.59	0.14	2.83
TENxMTX	0.02	0.00	0.01
TENxPeaks	1.66	0.16	1.80