Helena L. Crowell
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/CATALYST |
| Branch: RELEASE_3_9 |
| Last Commit: e1bc86f |
| Last Changed Date: 2019-10-14 12:05:43 -0400 (Mon, 14 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 13:00:02 -0400 (Wed, 16 Oct 2019).
| Package 214/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CATALYST 1.8.7 Helena L. Crowell
| malbec2 | Linux (Ubuntu 18.04.2 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: 1.8.7 |
| 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_1.8.7.tar.gz |
| StartedAt: 2019-10-16 01:10:22 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 01:24:04 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 822.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CATALYST.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_1.8.7.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/CATALYST.Rcheck’ * using R version 3.6.1 (2019-07-05) * 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 ‘1.8.7’ * 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 ... NOTE plotClusterHeatmap,daFrame :: no visible binding for global variable ‘cluster_id’ Undefined global functions or variables: cluster_id * 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 runDR 33.780 2.758 36.625 plotClusterExprs 26.521 3.485 30.335 plotClusterHeatmap 20.407 3.076 23.509 plotYields 17.901 1.569 16.905 plotMahal 19.158 0.263 19.472 plotMedExprs 16.954 2.430 19.391 plotDiffHeatmap 14.798 3.774 14.597 applyCutoffs 17.177 0.368 17.547 outFCS 16.940 0.200 17.143 plotEvents 16.396 0.153 16.553 estCutoffs 15.500 0.648 15.317 outFrames 15.299 0.158 15.462 plotAbundances 12.792 2.525 15.318 assignPrelim 15.158 0.143 15.312 mergeClusters 12.202 2.296 14.551 dbFrame-methods 13.563 0.142 13.707 plotDR 10.813 2.518 13.339 extractClusters 9.936 2.425 12.362 normCytof 12.125 0.177 12.319 cluster 10.079 2.220 12.309 compCytof 11.693 0.347 12.056 plotCodes 9.262 2.693 11.961 adaptSpillmat 10.692 0.673 11.366 daFrame-methods 9.093 1.777 10.873 filter 8.693 2.136 10.853 plotSpillmat 10.143 0.431 10.575 computeSpillmat 9.951 0.376 10.330 plotExprs 7.027 0.348 7.375 * 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-3.9-bioc/meat/CATALYST.Rcheck/00check.log’ for details.
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 Creating a new generic function for ‘filter’ in package ‘CATALYST’ ** 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 3.6.1 (2019-07-05) -- "Action of the Toes"
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)
Attaching package: 'CATALYST'
The following object is masked from 'package:stats':
filter
>
> test_check("CATALYST")
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 86 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
40.295 2.650 43.274
CATALYST.Rcheck/CATALYST-Ex.timings
| name | user | system | elapsed | |
| adaptSpillmat | 10.692 | 0.673 | 11.366 | |
| applyCutoffs | 17.177 | 0.368 | 17.547 | |
| assignPrelim | 15.158 | 0.143 | 15.312 | |
| cluster | 10.079 | 2.220 | 12.309 | |
| compCytof | 11.693 | 0.347 | 12.056 | |
| computeSpillmat | 9.951 | 0.376 | 10.330 | |
| concatFCS | 0.069 | 0.011 | 0.080 | |
| daFrame-class | 0.672 | 0.011 | 0.683 | |
| daFrame-methods | 9.093 | 1.777 | 10.873 | |
| data | 0.014 | 0.012 | 0.026 | |
| dbFrame-methods | 13.563 | 0.142 | 13.707 | |
| estCutoffs | 15.500 | 0.648 | 15.317 | |
| extractClusters | 9.936 | 2.425 | 12.362 | |
| filter | 8.693 | 2.136 | 10.853 | |
| guessPanel | 0.033 | 0.015 | 0.048 | |
| launchGUI | 0 | 0 | 0 | |
| mergeClusters | 12.202 | 2.296 | 14.551 | |
| normCytof | 12.125 | 0.177 | 12.319 | |
| outFCS | 16.940 | 0.200 | 17.143 | |
| outFrames | 15.299 | 0.158 | 15.462 | |
| plotAbundances | 12.792 | 2.525 | 15.318 | |
| plotClusterExprs | 26.521 | 3.485 | 30.335 | |
| plotClusterHeatmap | 20.407 | 3.076 | 23.509 | |
| plotCodes | 9.262 | 2.693 | 11.961 | |
| plotCounts | 0.808 | 0.008 | 0.873 | |
| plotDR | 10.813 | 2.518 | 13.339 | |
| plotDiffHeatmap | 14.798 | 3.774 | 14.597 | |
| plotEvents | 16.396 | 0.153 | 16.553 | |
| plotExprHeatmap | 1.846 | 0.059 | 1.907 | |
| plotExprs | 7.027 | 0.348 | 7.375 | |
| plotMDS | 1.485 | 0.027 | 1.521 | |
| plotMahal | 19.158 | 0.263 | 19.472 | |
| plotMedExprs | 16.954 | 2.430 | 19.391 | |
| plotNRS | 1.542 | 0.017 | 1.560 | |
| plotSpillmat | 10.143 | 0.431 | 10.575 | |
| plotYields | 17.901 | 1.569 | 16.905 | |
| runDR | 33.780 | 2.758 | 36.625 | |