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This page was generated on 2021-12-01 17:18:13 -0500 (Wed, 01 Dec 2021).

CHECK results for CATALYST on machv2

To the developers/maintainers of the CATALYST package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 249/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CATALYST 1.18.0  (landing page)
Helena L. Crowell
Snapshot Date: 2021-11-30 04:15:05 -0500 (Tue, 30 Nov 2021)
git_url: https://git.bioconductor.org/packages/CATALYST
git_branch: RELEASE_3_14
git_last_commit: aa3b9c4
git_last_commit_date: 2021-10-26 12:34:36 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: CATALYST
Version: 1.18.0
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_1.18.0.tar.gz
StartedAt: 2021-11-30 14:33:03 -0500 (Tue, 30 Nov 2021)
EndedAt: 2021-11-30 14:50:26 -0500 (Tue, 30 Nov 2021)
EllapsedTime: 1043.2 seconds
RetCode: 0
Status:   OK  
CheckDir: CATALYST.Rcheck
Warnings: 0

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_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/CATALYST.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CATALYST/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CATALYST’ version ‘1.18.0’
* 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 ... 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 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 22.822  1.006  23.869
sce2fcs          20.415  0.858  21.355
plotPbExprs      20.527  0.657  21.200
plotDiffHeatmap  19.843  0.788  20.659
plotDR           17.753  0.724  18.494
plotExprHeatmap  15.040  0.586  15.638
plotCodes        11.067  0.916  12.002
plotClusterExprs 11.510  0.379  11.898
pbMDS            11.251  0.534  11.802
plotFreqHeatmap  10.595  0.735  11.345
SCE-accessors     9.715  0.982  10.704
compCytof        10.411  0.251  10.675
clrDR             9.948  0.602  10.622
mergeClusters     9.504  0.518  10.034
filterSCE         9.470  0.437   9.915
plotMahal         9.826  0.078   9.916
cluster           9.104  0.609   9.721
plotAbundances    9.295  0.402   9.703
plotSpillmat      8.660  0.155   8.823
extractClusters   8.044  0.673   8.730
computeSpillmat   8.533  0.167   8.706
adaptSpillmat     8.285  0.192   8.482
estCutoffs        8.164  0.085   8.261
plotYields        7.717  0.113   7.833
plotScatter       7.723  0.099   7.831
applyCutoffs      7.434  0.091   7.530
runDR             6.253  0.124   6.381
plotExprs         5.832  0.070   5.907
normCytof         5.498  0.069   5.575
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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: OK


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/4.1/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


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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, 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
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 0 | WARN 21 | SKIP 0 | PASS 742 ]
> 
> proc.time()
   user  system elapsed 
333.712   9.017 343.063 

Example timings

CATALYST.Rcheck/CATALYST-Ex.timings

nameusersystemelapsed
SCE-accessors 9.715 0.98210.704
adaptSpillmat8.2850.1928.482
applyCutoffs7.4340.0917.530
assignPrelim3.7740.0233.800
clrDR 9.948 0.60210.622
cluster9.1040.6099.721
compCytof10.411 0.25110.675
computeSpillmat8.5330.1678.706
data0.0120.0180.031
estCutoffs8.1640.0858.261
extractClusters8.0440.6738.730
filterSCE9.4700.4379.915
guessPanel0.0510.0070.056
mergeClusters 9.504 0.51810.034
normCytof5.4980.0695.575
pbMDS11.251 0.53411.802
plotAbundances9.2950.4029.703
plotClusterExprs11.510 0.37911.898
plotCodes11.067 0.91612.002
plotCounts1.8620.0111.877
plotDR17.753 0.72418.494
plotDiffHeatmap19.843 0.78820.659
plotEvents4.1420.0204.165
plotExprHeatmap15.040 0.58615.638
plotExprs5.8320.0705.907
plotFreqHeatmap10.595 0.73511.345
plotMahal9.8260.0789.916
plotMultiHeatmap22.822 1.00623.869
plotNRS2.3740.0102.385
plotPbExprs20.527 0.65721.200
plotScatter7.7230.0997.831
plotSpillmat8.6600.1558.823
plotYields7.7170.1137.833
prepData3.3750.0203.398
runDR6.2530.1246.381
sce2fcs20.415 0.85821.355