Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-24 13:04:53 -0500 (Mon, 24 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
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 CATALYST on nebbiolo2


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 1.18.1  (landing page)
Helena L. Crowell
Snapshot Date: 2022-01-23 01:55:04 -0500 (Sun, 23 Jan 2022)
git_url: https://git.bioconductor.org/packages/CATALYST
git_branch: RELEASE_3_14
git_last_commit: efeedac
git_last_commit_date: 2022-01-14 07:43:56 -0500 (Fri, 14 Jan 2022)
nebbiolo2Linux (Ubuntu 20.04.4 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: 1.18.1
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:CATALYST.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings CATALYST_1.18.1.tar.gz
StartedAt: 2022-01-23 06:49:16 -0500 (Sun, 23 Jan 2022)
EndedAt: 2022-01-23 06:59:44 -0500 (Sun, 23 Jan 2022)
EllapsedTime: 627.7 seconds
RetCode: 0
Status:   OK  
CheckDir: CATALYST.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:CATALYST.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings CATALYST_1.18.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/CATALYST.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-pc-linux-gnu (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 ‘1.18.1’
* 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
plotDR           12.280  0.268  12.542
sce2fcs          12.290  0.087  12.378
plotMultiHeatmap 12.153  0.089  12.175
plotPbExprs      12.070  0.147  12.167
plotDiffHeatmap  11.194  0.176  11.355
plotExprHeatmap   9.438  0.156   9.561
plotAbundances    7.236  0.184   7.420
plotClusterExprs  7.225  0.188   7.398
pbMDS             7.041  0.224   7.232
plotFreqHeatmap   6.811  0.132   6.943
mergeClusters     6.341  0.192   6.522
plotCodes         6.300  0.099   6.398
SCE-accessors     6.048  0.292   6.340
runDR             6.057  0.137   6.186
clrDR             5.722  0.068   5.791
compCytof         5.293  0.068   5.361
extractClusters   5.231  0.060   5.291
plotMahal         5.129  0.032   5.161
* 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:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL CATALYST
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/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-pc-linux-gnu (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 ]

[ FAIL 0 | WARN 21 | SKIP 0 | PASS 742 ]
> 
> proc.time()
   user  system elapsed 
202.669   2.855 204.993 

Example timings

CATALYST.Rcheck/CATALYST-Ex.timings

nameusersystemelapsed
SCE-accessors6.0480.2926.340
adaptSpillmat4.2870.0924.380
applyCutoffs3.7100.0643.774
assignPrelim1.7440.0121.757
clrDR5.7220.0685.791
cluster4.9010.0404.941
compCytof5.2930.0685.361
computeSpillmat4.1290.0444.174
data0.0060.0000.006
estCutoffs4.4250.0564.481
extractClusters5.2310.0605.291
filterSCE4.8370.0484.884
guessPanel0.0310.0000.031
mergeClusters6.3410.1926.522
normCytof2.6310.0642.695
pbMDS7.0410.2247.232
plotAbundances7.2360.1847.420
plotClusterExprs7.2250.1887.398
plotCodes6.3000.0996.398
plotCounts1.0510.0081.059
plotDR12.280 0.26812.542
plotDiffHeatmap11.194 0.17611.355
plotEvents2.0420.0162.058
plotExprHeatmap9.4380.1569.561
plotExprs3.6290.0683.698
plotFreqHeatmap6.8110.1326.943
plotMahal5.1290.0325.161
plotMultiHeatmap12.153 0.08912.175
plotNRS1.3130.0001.314
plotPbExprs12.070 0.14712.167
plotScatter4.4380.0324.469
plotSpillmat4.7600.0444.804
plotYields4.2900.0484.337
prepData2.1380.0042.143
runDR6.0570.1376.186
sce2fcs12.290 0.08712.378