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This page was generated on 2024-03-04 11:40:07 -0500 (Mon, 04 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4676
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4414
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4441
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4417
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 2187/2251HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
UMI4Cats 1.13.0  (landing page)
Mireia Ramos-Rodriguez
Snapshot Date: 2024-03-01 14:00:22 -0500 (Fri, 01 Mar 2024)
git_url: https://git.bioconductor.org/packages/UMI4Cats
git_branch: devel
git_last_commit: 686977e
git_last_commit_date: 2023-10-24 11:24:33 -0500 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    ERROR  

CHECK results for UMI4Cats on merida1


To the developers/maintainers of the UMI4Cats package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/UMI4Cats.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: UMI4Cats
Version: 1.13.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:UMI4Cats.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings UMI4Cats_1.13.0.tar.gz
StartedAt: 2024-03-02 12:11:51 -0500 (Sat, 02 Mar 2024)
EndedAt: 2024-03-02 12:25:13 -0500 (Sat, 02 Mar 2024)
EllapsedTime: 802.3 seconds
RetCode: 1
Status:   ERROR  
CheckDir: UMI4Cats.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:UMI4Cats.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings UMI4Cats_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/UMI4Cats.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘UMI4Cats/DESCRIPTION’ ... OK
* this is package ‘UMI4Cats’ version ‘1.13.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘UMI4Cats’ 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
UMI4C               8.207  0.180   9.710
plotUMI4C           7.111  0.101   8.688
callInteractions    5.884  0.262   7.236
UMI4C-methods       5.136  0.295   6.372
waldUMI4C           5.066  0.085   5.910
plotDifferential    4.982  0.126   5.948
plotDomainogram     4.496  0.177   5.362
getSignInteractions 4.386  0.139   5.286
fisherUMI4C         4.270  0.081   5.048
digestGenome        4.087  0.249   5.155
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
      FileForFormat
  
  > 
  > test_check("UMI4Cats")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 21 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-statsUMI4C.R:8:3'): Stats plot output is correct ─────────────
  length(stats_plot) not equal to 9.
  1/1 mismatches
  [1] 11 - 9 == 2
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 21 ]
  Error: Test failures
  Execution halted
* 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: 1 ERROR
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/UMI4Cats.Rcheck/00check.log’
for details.


Installation output

UMI4Cats.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL UMI4Cats
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘UMI4Cats’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (UMI4Cats)

Tests output

UMI4Cats.Rcheck/tests/testthat.Rout.fail


R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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(UMI4Cats)
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, table, tapply,
    union, 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
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


> library(BSgenome)
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

Loading required package: BiocIO
Loading required package: rtracklayer

Attaching package: 'rtracklayer'

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

    FileForFormat

> 
> test_check("UMI4Cats")
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 21 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-statsUMI4C.R:8:3'): Stats plot output is correct ─────────────
length(stats_plot) not equal to 9.
1/1 mismatches
[1] 11 - 9 == 2

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 21 ]
Error: Test failures
Execution halted

Example timings

UMI4Cats.Rcheck/UMI4Cats-Ex.timings

nameusersystemelapsed
UMI4C-methods5.1360.2956.372
UMI4C8.2070.1809.710
addGrouping2.8240.0473.344
alignmentUMI4C0.0010.0010.001
callInteractions5.8840.2627.236
combineUMI4C0.7420.0180.921
contactsUMI4C0.0040.0020.007
counterUMI4C0.0020.0010.004
createGeneAnnotation2.7250.1553.439
darken0.0010.0000.001
demultiplexFastq0.0000.0010.001
differentialNbinomWaldTestUMI4C0.0000.0020.002
digestGenome4.0870.2495.155
downloadUMI4CexampleData0.0000.0010.001
fisherUMI4C4.2700.0815.048
getSignInteractions4.3860.1395.286
getViewpointCoordinates1.2390.1001.560
makeWindowFragments0.7700.0230.935
pipe0.0080.0020.010
plotDifferential4.9820.1265.948
plotDomainogram4.4960.1775.362
plotGenes2.7790.0583.379
plotTrend1.3540.0511.682
plotUMI4C7.1110.1018.688
prepUMI4C0.0010.0010.001
splitUMI4C0.0010.0000.001
statsUMI4C1.6800.0232.153
theme0.2470.0060.323
themeXYblank0.2240.0060.261
themeXblank0.2870.0050.353
themeYblank0.2390.0040.279
waldUMI4C5.0660.0855.910