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This page was generated on 2024-03-27 11:37:26 -0400 (Wed, 27 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4667
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4403
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4426
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 273/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CATALYST 1.26.0  (landing page)
Helena L. Crowell
Snapshot Date: 2024-03-25 14:05:07 -0400 (Mon, 25 Mar 2024)
git_url: https://git.bioconductor.org/packages/CATALYST
git_branch: RELEASE_3_18
git_last_commit: 98fffcb
git_last_commit_date: 2023-10-24 10:56:46 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino4Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for CATALYST on merida1


To the developers/maintainers of the CATALYST package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CATALYST.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: CATALYST
Version: 1.26.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CATALYST.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CATALYST_1.26.0.tar.gz
StartedAt: 2024-03-26 00:08:53 -0400 (Tue, 26 Mar 2024)
EndedAt: 2024-03-26 00:31:07 -0400 (Tue, 26 Mar 2024)
EllapsedTime: 1333.6 seconds
RetCode: 1
Status:   ERROR  
CheckDir: CATALYST.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CATALYST.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CATALYST_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/CATALYST.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-apple-darwin20 (64-bit)
* 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 ‘CATALYST/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CATALYST’ version ‘1.26.0’
* 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 ‘CATALYST’ 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 ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.cluster_cols’
* 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 LazyData ... 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
plotMultiHeatmap 29.837  0.828  33.098
plotPbExprs      28.022  0.806  30.454
plotDiffHeatmap  26.700  0.846  29.902
sce2fcs          22.720  0.892  24.764
plotDR           20.812  0.836  23.158
plotExprHeatmap  20.274  0.859  21.850
mergeClusters    14.486  0.815  16.412
pbMDS            14.163  0.758  15.536
plotClusterExprs 13.848  0.847  15.158
plotAbundances   13.392  0.889  14.812
plotCodes        13.565  0.686  14.846
plotFreqHeatmap  12.782  0.826  14.199
SCE-accessors    12.206  0.956  14.056
clrDR            12.375  0.725  14.005
plotMahal        12.740  0.168  13.453
compCytof        11.241  0.379  12.821
cluster          10.517  0.734  12.197
filterSCE        10.449  0.680  11.701
extractClusters  10.259  0.738  11.469
estCutoffs       10.729  0.189  11.719
plotSpillmat     10.416  0.208  11.083
plotScatter       9.643  0.173  10.291
plotYields        9.418  0.194  10.311
computeSpillmat   9.275  0.335  11.026
adaptSpillmat     8.699  0.299  10.094
applyCutoffs      7.775  0.181   8.511
plotExprs         7.787  0.081   8.215
runDR             6.440  0.064   6.834
normCytof         5.341  0.082   5.671
plotEvents        5.152  0.048   5.425
prepData          4.768  0.075   5.043
* 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:
  The following objects are masked from 'package:matrixStats':
  
      anyMissing, rowMedians
  
  > 
  > test_check("CATALYST")
  [ FAIL 1 | WARN 3 | SKIP 0 | PASS 740 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_plotScatter.R:39:5'): plotScatter() - color_by ───────────────
  p$guides$colour inherits from `'NULL'` not `'character'`.
  
  [ FAIL 1 | WARN 3 | SKIP 0 | PASS 740 ]
  Error: Test failures
  Execution halted
* 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 ERROR, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.18-bioc/meat/CATALYST.Rcheck/00check.log’
for details.


Installation output

CATALYST.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘CATALYST’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (CATALYST)

Tests output

CATALYST.Rcheck/tests/testthat.Rout.fail


R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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(CATALYST)
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 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

> 
> test_check("CATALYST")
[ FAIL 1 | WARN 3 | SKIP 0 | PASS 740 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_plotScatter.R:39:5'): plotScatter() - color_by ───────────────
p$guides$colour inherits from `'NULL'` not `'character'`.

[ FAIL 1 | WARN 3 | SKIP 0 | PASS 740 ]
Error: Test failures
Execution halted

Example timings

CATALYST.Rcheck/CATALYST-Ex.timings

nameusersystemelapsed
SCE-accessors12.206 0.95614.056
adaptSpillmat 8.699 0.29910.094
applyCutoffs7.7750.1818.511
assignPrelim4.5850.0864.872
clrDR12.375 0.72514.005
cluster10.517 0.73412.197
compCytof11.241 0.37912.821
computeSpillmat 9.275 0.33511.026
data0.0150.0300.048
estCutoffs10.729 0.18911.719
extractClusters10.259 0.73811.469
filterSCE10.449 0.68011.701
guessPanel0.0460.0100.056
mergeClusters14.486 0.81516.412
normCytof5.3410.0825.671
pbMDS14.163 0.75815.536
plotAbundances13.392 0.88914.812
plotClusterExprs13.848 0.84715.158
plotCodes13.565 0.68614.846
plotCounts2.2570.0192.399
plotDR20.812 0.83623.158
plotDiffHeatmap26.700 0.84629.902
plotEvents5.1520.0485.425
plotExprHeatmap20.274 0.85921.850
plotExprs7.7870.0818.215
plotFreqHeatmap12.782 0.82614.199
plotMahal12.740 0.16813.453
plotMultiHeatmap29.837 0.82833.098
plotNRS2.9930.0213.055
plotPbExprs28.022 0.80630.454
plotScatter 9.643 0.17310.291
plotSpillmat10.416 0.20811.083
plotYields 9.418 0.19410.311
prepData4.7680.0755.043
runDR6.4400.0646.834
sce2fcs22.720 0.89224.764