Helena L. Crowell
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/CATALYST |
| Branch: RELEASE_3_10 |
| Last Commit: d2e724c |
| Last Changed Date: 2020-04-02 07:29:58 -0400 (Thu, 02 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:45:16 -0400 (Wed, 15 Apr 2020).
| Package 228/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CATALYST 1.10.3 Helena L. Crowell
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: CATALYST |
| Version: 1.10.3 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CATALYST.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CATALYST_1.10.3.tar.gz |
| StartedAt: 2020-04-15 00:57:34 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 01:08:58 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 683.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CATALYST.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CATALYST.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CATALYST_1.10.3.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/CATALYST.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.10.3’
* 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 data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotClusterHeatmap 25.885 9.764 21.293
plotDR 23.286 1.161 23.527
plotClusterExprs 21.184 2.334 22.218
plotMedExprs 17.957 2.447 17.226
plotYields 14.271 2.680 13.205
plotDiffHeatmap 13.144 3.525 11.757
plotMahal 15.847 0.082 16.130
mergeClusters 10.211 4.201 9.592
outFrames 13.871 0.102 14.214
plotEvents 12.586 0.067 12.746
outFCS 12.439 0.085 12.645
applyCutoffs 11.302 0.177 11.554
estCutoffs 9.888 1.204 9.914
plotAbundances 9.166 0.787 10.038
plotSpillmat 9.234 0.346 9.898
assignPrelim 8.918 0.111 9.075
normCytof 8.467 0.099 8.605
dbFrame-methods 8.449 0.100 8.575
SCE-utils 7.619 0.916 8.565
plotCodes 6.740 1.062 7.863
filterSCE 5.813 0.867 6.711
extractClusters 5.557 1.032 6.623
cluster 5.642 0.899 6.563
compCytof 6.332 0.163 6.519
plotExprs 6.247 0.149 6.452
adaptSpillmat 5.839 0.170 6.019
computeSpillmat 5.382 0.162 5.557
runDR 5.055 0.095 5.179
* 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
CATALYST.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CATALYST ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/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)
CATALYST.Rcheck/tests/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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)
>
> test_check("CATALYST")
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 228 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
64.196 12.235 57.564
CATALYST.Rcheck/CATALYST-Ex.timings
| name | user | system | elapsed | |
| SCE-utils | 7.619 | 0.916 | 8.565 | |
| adaptSpillmat | 5.839 | 0.170 | 6.019 | |
| applyCutoffs | 11.302 | 0.177 | 11.554 | |
| assignPrelim | 8.918 | 0.111 | 9.075 | |
| cluster | 5.642 | 0.899 | 6.563 | |
| compCytof | 6.332 | 0.163 | 6.519 | |
| computeSpillmat | 5.382 | 0.162 | 5.557 | |
| concatFCS | 0.048 | 0.003 | 0.052 | |
| data | 0.006 | 0.004 | 0.010 | |
| dbFrame-methods | 8.449 | 0.100 | 8.575 | |
| estCutoffs | 9.888 | 1.204 | 9.914 | |
| extractClusters | 5.557 | 1.032 | 6.623 | |
| filterSCE | 5.813 | 0.867 | 6.711 | |
| guessPanel | 0.025 | 0.007 | 0.033 | |
| launchGUI | 0 | 0 | 0 | |
| mergeClusters | 10.211 | 4.201 | 9.592 | |
| normCytof | 8.467 | 0.099 | 8.605 | |
| outFCS | 12.439 | 0.085 | 12.645 | |
| outFrames | 13.871 | 0.102 | 14.214 | |
| plotAbundances | 9.166 | 0.787 | 10.038 | |
| plotClusterExprs | 21.184 | 2.334 | 22.218 | |
| plotClusterHeatmap | 25.885 | 9.764 | 21.293 | |
| plotCodes | 6.740 | 1.062 | 7.863 | |
| plotCounts | 0.750 | 0.004 | 0.760 | |
| plotDR | 23.286 | 1.161 | 23.527 | |
| plotDiffHeatmap | 13.144 | 3.525 | 11.757 | |
| plotEvents | 12.586 | 0.067 | 12.746 | |
| plotExprHeatmap | 3.591 | 0.669 | 2.614 | |
| plotExprs | 6.247 | 0.149 | 6.452 | |
| plotMDS | 1.099 | 0.013 | 1.125 | |
| plotMahal | 15.847 | 0.082 | 16.130 | |
| plotMedExprs | 17.957 | 2.447 | 17.226 | |
| plotNRS | 1.940 | 0.018 | 2.108 | |
| plotSpillmat | 9.234 | 0.346 | 9.898 | |
| plotYields | 14.271 | 2.680 | 13.205 | |
| prepData | 0.465 | 0.011 | 0.477 | |
| runDR | 5.055 | 0.095 | 5.179 | |