Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2021-11-30 13:55:21 -0500 (Tue, 30 Nov 2021).

CHECK results for CATALYST on merida1

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 245/2068HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CATALYST 1.19.0  (landing page)
Helena L. Crowell
Snapshot Date: 2021-11-29 14:50:17 -0500 (Mon, 29 Nov 2021)
git_url: https://git.bioconductor.org/packages/CATALYST
git_branch: master
git_last_commit: 4988576
git_last_commit_date: 2021-10-26 12:34:36 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: CATALYST
Version: 1.19.0
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_1.19.0.tar.gz
StartedAt: 2021-11-30 01:25:16 -0500 (Tue, 30 Nov 2021)
EndedAt: 2021-11-30 01:43:07 -0500 (Tue, 30 Nov 2021)
EllapsedTime: 1070.5 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_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/CATALYST.Rcheck’
* using R Under development (unstable) (2021-11-01 r81125)
* 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 ‘1.19.0’
* 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 ... NOTE
Found the following non-portable file paths:
  CATALYST/vignettes/differential_cache/html/plotDiffHeatmap-filter-1_9a7f08528c92652faeef0e8673c7f2c5.RData
  CATALYST/vignettes/differential_cache/html/plotDiffHeatmap-filter-1_9a7f08528c92652faeef0e8673c7f2c5.rdb
  CATALYST/vignettes/differential_cache/html/plotDiffHeatmap-filter-1_9a7f08528c92652faeef0e8673c7f2c5.rdx
  CATALYST/vignettes/differential_cache/html/plotDiffHeatmap-filter-2_70aab5a5fe69b1a734f1bf2d75d315e4.RData
  CATALYST/vignettes/differential_cache/html/plotDiffHeatmap-filter-2_70aab5a5fe69b1a734f1bf2d75d315e4.rdb
  CATALYST/vignettes/differential_cache/html/plotDiffHeatmap-filter-2_70aab5a5fe69b1a734f1bf2d75d315e4.rdx
  CATALYST/vignettes/differential_cache/html/plotDiffHeatmap-pals_0e4a315b3005825016c90c7b0da453a4.RData
  CATALYST/vignettes/differential_cache/html/plotExprHeatmap-both_d58f7fde77a690e82ec4fde8a8e0f845.RData
  CATALYST/vignettes/differential_cache/html/plotExprHeatmap-cluster_a20f45393f12a73d0206ace3ef67ca27.RData
  CATALYST/vignettes/differential_cache/html/plotExprHeatmap-cluster_a20f45393f12a73d0206ace3ef67ca27.rdb
  CATALYST/vignettes/differential_cache/html/plotExprHeatmap-cluster_a20f45393f12a73d0206ace3ef67ca27.rdx
  CATALYST/vignettes/differential_cache/html/plotExprHeatmap-complete_8566e32f3311ce62c9dcd7130b5df772.RData
  CATALYST/vignettes/differential_cache/html/plotExprHeatmap-complete_8566e32f3311ce62c9dcd7130b5df772.rdb
  CATALYST/vignettes/differential_cache/html/plotExprHeatmap-complete_8566e32f3311ce62c9dcd7130b5df772.rdx
  CATALYST/vignettes/differential_cache/html/plotExprHeatmap-minimal_7b57ac5fa2aaad801b41b88bef43ac5e.RData
  CATALYST/vignettes/differential_cache/html/plotExprHeatmap-minimal_7b57ac5fa2aaad801b41b88bef43ac5e.rdb
  CATALYST/vignettes/differential_cache/html/plotExprHeatmap-minimal_7b57ac5fa2aaad801b41b88bef43ac5e.rdx
  CATALYST/vignettes/differential_cache/html/plotExprHeatmap-sample_dc0d4c182554c791cd9c0e693ff88800.RData
  CATALYST/vignettes/differential_cache/html/plotExprHeatmap-sample_dc0d4c182554c791cd9c0e693ff88800.rdb
  CATALYST/vignettes/differential_cache/html/plotExprHeatmap-sample_dc0d4c182554c791cd9c0e693ff88800.rdx
  CATALYST/vignettes/differential_cache/html/plotFreqHeatmap-complete_be26c943824e5d197058eeac25e17e9d.RData
  CATALYST/vignettes/differential_cache/html/plotFreqHeatmap-complete_be26c943824e5d197058eeac25e17e9d.rdb
  CATALYST/vignettes/differential_cache/html/plotFreqHeatmap-complete_be26c943824e5d197058eeac25e17e9d.rdx
  CATALYST/vignettes/differential_cache/html/plotFreqHeatmap-minimal_db01a593666e7d59c0c6b8c878dcb5e6.RData
  CATALYST/vignettes/differential_cache/html/plotFreqHeatmap-minimal_db01a593666e7d59c0c6b8c878dcb5e6.rdb
  CATALYST/vignettes/differential_cache/html/plotFreqHeatmap-minimal_db01a593666e7d59c0c6b8c878dcb5e6.rdx
  CATALYST/vignettes/differential_cache/html/plotMedExprs-custom_57130a71b2f09d862e31b29deba69b65.RData
  CATALYST/vignettes/differential_cache/html/plotMultiHeatmap-custom_8366c25bc20317be97f0b863d71d08ee.RData
  CATALYST/vignettes/differential_cache/html/plotMultiHeatmap-custom_8366c25bc20317be97f0b863d71d08ee.rdb
  CATALYST/vignettes/differential_cache/html/plotMultiHeatmap-custom_8366c25bc20317be97f0b863d71d08ee.rdx

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* 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
plotPbExprs      21.874  1.221  23.119
plotDiffHeatmap  21.951  1.079  23.074
plotMultiHeatmap 22.236  0.640  22.915
sce2fcs          20.263  0.918  21.236
plotDR           17.960  0.721  18.708
plotExprHeatmap  15.821  0.714  16.564
plotClusterExprs 12.445  0.530  12.991
SCE-accessors    11.740  1.216  13.003
plotCodes        12.103  0.812  12.942
mergeClusters    12.135  0.687  12.836
pbMDS            12.017  0.761  12.794
plotAbundances   11.874  0.515  12.408
plotFreqHeatmap  11.138  1.061  12.217
clrDR            10.600  0.702  11.319
plotMahal        10.324  0.119  10.456
extractClusters   9.292  0.700  10.006
filterSCE         8.821  0.580   9.411
cluster           8.756  0.412   9.187
compCytof         8.622  0.184   8.820
estCutoffs        8.091  0.080   8.186
plotYields        8.000  0.108   8.123
plotScatter       7.770  0.143   7.923
plotSpillmat      7.814  0.098   7.923
computeSpillmat   7.695  0.165   7.872
adaptSpillmat     7.474  0.157   7.649
plotExprs         7.153  0.053   7.214
runDR             6.447  0.078   6.528
applyCutoffs      6.208  0.093   6.309
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.15-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/4.2/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 Under development (unstable) (2021-11-01 r81125) -- "Unsuffered Consequences"
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 
304.727   9.119 314.302 

Example timings

CATALYST.Rcheck/CATALYST-Ex.timings

nameusersystemelapsed
SCE-accessors11.740 1.21613.003
adaptSpillmat7.4740.1577.649
applyCutoffs6.2080.0936.309
assignPrelim3.8930.0203.918
clrDR10.600 0.70211.319
cluster8.7560.4129.187
compCytof8.6220.1848.820
computeSpillmat7.6950.1657.872
data0.0110.0150.027
estCutoffs8.0910.0808.186
extractClusters 9.292 0.70010.006
filterSCE8.8210.5809.411
guessPanel0.0510.0040.056
mergeClusters12.135 0.68712.836
normCytof4.4370.0804.525
pbMDS12.017 0.76112.794
plotAbundances11.874 0.51512.408
plotClusterExprs12.445 0.53012.991
plotCodes12.103 0.81212.942
plotCounts1.9000.0231.928
plotDR17.960 0.72118.708
plotDiffHeatmap21.951 1.07923.074
plotEvents4.2150.0304.252
plotExprHeatmap15.821 0.71416.564
plotExprs7.1530.0537.214
plotFreqHeatmap11.138 1.06112.217
plotMahal10.324 0.11910.456
plotMultiHeatmap22.236 0.64022.915
plotNRS2.2770.0102.289
plotPbExprs21.874 1.22123.119
plotScatter7.7700.1437.923
plotSpillmat7.8140.0987.923
plotYields8.0000.1088.123
prepData3.3030.0213.328
runDR6.4470.0786.528
sce2fcs20.263 0.91821.236