Helena L. Crowell
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/CATALYST |
| Branch: master |
| Last Commit: 8898843 |
| Last Changed Date: 2019-10-29 13:42:18 -0500 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:47:47 -0500 (Thu, 16 Jan 2020).
| Package 227/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CATALYST 1.11.0 Helena L. Crowell
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: CATALYST |
| Version: 1.11.0 |
| 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_1.11.0.tar.gz |
| StartedAt: 2020-01-16 02:31:27 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 02:48:14 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 1007.4 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_1.11.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/CATALYST.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.11.0’
* 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 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 33.044 11.411 34.823
plotClusterHeatmap 34.368 6.166 30.899
plotClusterExprs 30.057 3.355 33.034
plotMedExprs 21.098 3.464 22.789
plotYields 21.546 0.820 19.965
plotMahal 21.753 0.276 22.320
plotDiffHeatmap 16.123 3.892 17.442
plotEvents 18.840 0.214 19.188
estCutoffs 18.288 0.535 18.504
mergeClusters 14.803 3.360 15.966
outFCS 17.227 0.163 17.411
applyCutoffs 17.088 0.237 17.329
outFrames 16.189 0.137 16.328
assignPrelim 16.023 0.131 16.156
dbFrame-methods 15.680 0.088 15.827
plotAbundances 13.821 1.933 15.759
SCE-utils 11.876 2.222 14.130
adaptSpillmat 12.994 0.439 13.446
normCytof 13.000 0.160 13.523
plotSpillmat 11.593 0.567 12.242
compCytof 11.289 0.316 11.629
cluster 9.661 1.858 11.835
filterSCE 9.401 1.850 11.252
plotCodes 9.085 2.135 11.221
extractClusters 9.179 1.981 11.161
computeSpillmat 10.726 0.315 11.090
plotExprs 7.054 0.355 7.412
runDR 6.822 0.189 7.108
* 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/4.0/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 Warning: replacing previous import ‘ncdfFlow::filter’ by ‘dplyr::filter’ when loading ‘CytoML’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import ‘ncdfFlow::filter’ by ‘dplyr::filter’ when loading ‘CytoML’ ** testing if installed package can be loaded from final location Warning: replacing previous import ‘ncdfFlow::filter’ by ‘dplyr::filter’ when loading ‘CytoML’ ** testing if installed package keeps a record of temporary installation path * DONE (CATALYST)
CATALYST.Rcheck/tests/testthat.Rout
R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 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)
Warning message:
replacing previous import 'ncdfFlow::filter' by 'dplyr::filter' when loading 'CytoML'
>
> test_check("CATALYST")
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 222 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
85.572 11.042 89.289
CATALYST.Rcheck/CATALYST-Ex.timings
| name | user | system | elapsed | |
| SCE-utils | 11.876 | 2.222 | 14.130 | |
| adaptSpillmat | 12.994 | 0.439 | 13.446 | |
| applyCutoffs | 17.088 | 0.237 | 17.329 | |
| assignPrelim | 16.023 | 0.131 | 16.156 | |
| cluster | 9.661 | 1.858 | 11.835 | |
| compCytof | 11.289 | 0.316 | 11.629 | |
| computeSpillmat | 10.726 | 0.315 | 11.090 | |
| concatFCS | 0.073 | 0.008 | 0.080 | |
| data | 0.013 | 0.012 | 0.024 | |
| dbFrame-methods | 15.680 | 0.088 | 15.827 | |
| estCutoffs | 18.288 | 0.535 | 18.504 | |
| extractClusters | 9.179 | 1.981 | 11.161 | |
| filterSCE | 9.401 | 1.850 | 11.252 | |
| guessPanel | 0.034 | 0.016 | 0.050 | |
| launchGUI | 0 | 0 | 0 | |
| mergeClusters | 14.803 | 3.360 | 15.966 | |
| normCytof | 13.000 | 0.160 | 13.523 | |
| outFCS | 17.227 | 0.163 | 17.411 | |
| outFrames | 16.189 | 0.137 | 16.328 | |
| plotAbundances | 13.821 | 1.933 | 15.759 | |
| plotClusterExprs | 30.057 | 3.355 | 33.034 | |
| plotClusterHeatmap | 34.368 | 6.166 | 30.899 | |
| plotCodes | 9.085 | 2.135 | 11.221 | |
| plotCounts | 0.984 | 0.010 | 0.993 | |
| plotDR | 33.044 | 11.411 | 34.823 | |
| plotDiffHeatmap | 16.123 | 3.892 | 17.442 | |
| plotEvents | 18.840 | 0.214 | 19.188 | |
| plotExprHeatmap | 3.527 | 0.193 | 2.570 | |
| plotExprs | 7.054 | 0.355 | 7.412 | |
| plotMDS | 1.318 | 0.026 | 1.348 | |
| plotMahal | 21.753 | 0.276 | 22.320 | |
| plotMedExprs | 21.098 | 3.464 | 22.789 | |
| plotNRS | 2.441 | 0.022 | 2.465 | |
| plotSpillmat | 11.593 | 0.567 | 12.242 | |
| plotYields | 21.546 | 0.820 | 19.965 | |
| prepData | 0.674 | 0.011 | 0.684 | |
| runDR | 6.822 | 0.189 | 7.108 | |