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This page was generated on 2023-01-02 09:00:54 -0500 (Mon, 02 Jan 2023).

HostnameOSArch (*)R versionInstalled pkgs
palomino5Windows Server 2022 Datacenterx64R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" 4165
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CHECK results for TENxIO on palomino5


To the developers/maintainers of the TENxIO package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 2012/2158HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TENxIO 1.1.0  (landing page)
Marcel Ramos
Snapshot Date: 2022-12-28 11:00:06 -0500 (Wed, 28 Dec 2022)
git_url: https://git.bioconductor.org/packages/TENxIO
git_branch: master
git_last_commit: 4b38b34
git_last_commit_date: 2022-11-01 11:27:43 -0500 (Tue, 01 Nov 2022)
palomino5Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  

Summary

Package: TENxIO
Version: 1.1.0
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TENxIO.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings TENxIO_1.1.0.tar.gz
StartedAt: 2022-12-29 04:08:10 -0500 (Thu, 29 Dec 2022)
EndedAt: 2022-12-29 04:11:12 -0500 (Thu, 29 Dec 2022)
EllapsedTime: 181.8 seconds
RetCode: 0
Status:   OK  
CheckDir: TENxIO.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TENxIO.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings TENxIO_1.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/TENxIO.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server 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 '1.1.0'
* 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 '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 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
Examples with CPU (user + system) or elapsed time > 5s
         user system elapsed
TENxFile 9.03   2.14   32.91
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'tinytest.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

TENxIO.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL TENxIO
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.17-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) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
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.

> 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

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, 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_TENxFile-class.R.........    1 tests OK 
test_TENxFile-class.R.........    1 tests OK 
test_TENxFile-class.R.........    1 tests OK 
test_TENxFile-class.R.........    2 tests OK 
test_TENxFile-class.R.........    2 tests OK 
test_TENxFile-class.R.........    3 tests OK 
test_TENxFile-class.R.........    3 tests OK 
test_TENxFile-class.R.........    3 tests OK 
test_TENxFile-class.R.........    3 tests OK 
test_TENxFile-class.R.........    4 tests OK 
test_TENxFile-class.R.........    5 tests OK 
test_TENxFile-class.R.........    6 tests OK 
test_TENxFile-class.R.........    6 tests OK 
test_TENxFile-class.R.........    6 tests OK 
test_TENxFile-class.R.........    6 tests OK 
test_TENxFile-class.R.........    6 tests OK 
test_TENxFile-class.R.........    7 tests OK 
test_TENxFile-class.R.........    7 tests OK 
test_TENxFile-class.R.........    7 tests OK 
test_TENxFile-class.R.........    8 tests OK 
test_TENxFile-class.R.........    9 tests OK 3.1s

test_TENxFileList-class.R.....    0 tests    
test_TENxFileList-class.R.....    0 tests    
test_TENxFileList-class.R.....    1 tests OK 
test_TENxFileList-class.R.....    2 tests OK 
test_TENxFileList-class.R.....    3 tests OK 
test_TENxFileList-class.R.....    3 tests OK 
test_TENxFileList-class.R.....    4 tests OK 
test_TENxFileList-class.R.....    5 tests OK 
test_TENxFileList-class.R.....    6 tests OK 
test_TENxFileList-class.R.....    7 tests OK 
test_TENxFileList-class.R.....    8 tests OK 1.3s

test_TENxFragments-class.R....    0 tests    
test_TENxFragments-class.R....    1 tests OK 
test_TENxFragments-class.R....    1 tests OK 
test_TENxFragments-class.R....    2 tests OK 
test_TENxFragments-class.R....    3 tests OK 
test_TENxFragments-class.R....    4 tests OK 
test_TENxFragments-class.R....    4 tests OK 
test_TENxFragments-class.R....    5 tests OK 
test_TENxFragments-class.R....    6 tests OK 
test_TENxFragments-class.R....    7 tests OK 2.9s

test_TENxH5-class.R...........    0 tests    
test_TENxH5-class.R...........    0 tests    
test_TENxH5-class.R...........    1 tests OK 
test_TENxH5-class.R...........    2 tests OK 
test_TENxH5-class.R...........    2 tests OK 
test_TENxH5-class.R...........    3 tests OK 
test_TENxH5-class.R...........    4 tests OK 
test_TENxH5-class.R...........    4 tests OK 
test_TENxH5-class.R...........    4 tests OK 
test_TENxH5-class.R...........    5 tests OK 
test_TENxH5-class.R...........    6 tests OK 
test_TENxH5-class.R...........    7 tests OK 
test_TENxH5-class.R...........    8 tests OK 
test_TENxH5-class.R...........    9 tests OK 1.3s

test_TENxMTX-class.R..........    0 tests    
test_TENxMTX-class.R..........    0 tests    
test_TENxMTX-class.R..........    1 tests OK 
test_TENxMTX-class.R..........    2 tests OK 
test_TENxMTX-class.R..........    3 tests OK 
test_TENxMTX-class.R..........    3 tests OK 
test_TENxMTX-class.R..........    4 tests OK 
test_TENxMTX-class.R..........    5 tests OK 
test_TENxMTX-class.R..........    6 tests OK 23ms

test_TENxPeaks-class.R........    0 tests    
test_TENxPeaks-class.R........    0 tests    
test_TENxPeaks-class.R........    1 tests OK 
test_TENxPeaks-class.R........    2 tests OK 
test_TENxPeaks-class.R........    2 tests OK 
test_TENxPeaks-class.R........    3 tests OK 
test_TENxPeaks-class.R........    4 tests OK 
test_TENxPeaks-class.R........    5 tests OK 
test_TENxPeaks-class.R........    5 tests OK 
test_TENxPeaks-class.R........    6 tests OK 
test_TENxPeaks-class.R........    7 tests OK 
test_TENxPeaks-class.R........    8 tests OK 
test_TENxPeaks-class.R........    9 tests OK 
test_TENxPeaks-class.R........   10 tests OK 
test_TENxPeaks-class.R........   11 tests OK 
test_TENxPeaks-class.R........   12 tests OK 
test_TENxPeaks-class.R........   13 tests OK 
test_TENxPeaks-class.R........   14 tests OK 0.4s
All ok, 53 results (8.9s)
Warning message:
In TENxFragments(fr, extension = "tsv.gz") :
  Using default 'yieldSize' parameter
> 
> proc.time()
   user  system elapsed 
  10.45    1.96   14.92

Example timings

TENxIO.Rcheck/TENxIO-Ex.timings

nameusersystemelapsed
TENxFile 9.03 2.1432.91
TENxFileList0.610.013.17
TENxFragments1.400.071.48
TENxH51.160.111.27
TENxMTX0.010.010.03
TENxPeaks1.490.141.65