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 12:10:54 -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: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:CATALYST.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings CATALYST_1.8.7.tar.gz |
| StartedAt: 2019-10-16 00:18:39 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 00:27:48 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 548.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CATALYST.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:CATALYST.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings CATALYST_1.8.7.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/CATALYST.Rcheck’ * using R version 3.6.1 (2019-07-05) * 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 ‘1.8.7’ * 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 30.157 0.012 30.203 plotYields 25.783 0.077 13.661 plotClusterExprs 20.448 0.100 20.549 plotDiffHeatmap 18.344 0.040 9.933 plotClusterHeatmap 14.639 0.044 14.687 plotMedExprs 12.928 0.020 12.964 plotMahal 12.633 0.000 12.825 estCutoffs 11.258 0.028 10.331 outFrames 11.012 0.000 11.016 outFCS 10.540 0.004 10.562 dbFrame-methods 10.305 0.008 10.330 applyCutoffs 10.246 0.012 10.399 plotEvents 9.687 0.004 9.693 plotAbundances 9.433 0.016 9.448 assignPrelim 7.861 0.064 8.031 plotDR 7.047 0.505 7.573 adaptSpillmat 7.360 0.063 7.561 mergeClusters 7.108 0.008 7.117 plotSpillmat 6.740 0.012 6.752 extractClusters 6.695 0.008 7.073 normCytof 6.433 0.004 6.437 computeSpillmat 6.367 0.012 6.383 filter 6.254 0.004 6.268 compCytof 6.186 0.028 6.331 plotExprs 6.185 0.016 6.204 plotCodes 5.862 0.008 5.886 daFrame-methods 5.770 0.004 5.817 * 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 ‘/home/biocbuild/bbs-3.9-bioc/meat/CATALYST.Rcheck/00check.log’ for details.
CATALYST.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL CATALYST ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-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 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-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)
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
29.467 1.093 30.609
CATALYST.Rcheck/CATALYST-Ex.timings
| name | user | system | elapsed | |
| adaptSpillmat | 7.360 | 0.063 | 7.561 | |
| applyCutoffs | 10.246 | 0.012 | 10.399 | |
| assignPrelim | 7.861 | 0.064 | 8.031 | |
| cluster | 3.904 | 0.028 | 3.932 | |
| compCytof | 6.186 | 0.028 | 6.331 | |
| computeSpillmat | 6.367 | 0.012 | 6.383 | |
| concatFCS | 0.074 | 0.000 | 0.074 | |
| daFrame-class | 0.550 | 0.008 | 0.558 | |
| daFrame-methods | 5.770 | 0.004 | 5.817 | |
| data | 0.007 | 0.000 | 0.007 | |
| dbFrame-methods | 10.305 | 0.008 | 10.330 | |
| estCutoffs | 11.258 | 0.028 | 10.331 | |
| extractClusters | 6.695 | 0.008 | 7.073 | |
| filter | 6.254 | 0.004 | 6.268 | |
| guessPanel | 0.017 | 0.004 | 0.021 | |
| launchGUI | 0 | 0 | 0 | |
| mergeClusters | 7.108 | 0.008 | 7.117 | |
| normCytof | 6.433 | 0.004 | 6.437 | |
| outFCS | 10.540 | 0.004 | 10.562 | |
| outFrames | 11.012 | 0.000 | 11.016 | |
| plotAbundances | 9.433 | 0.016 | 9.448 | |
| plotClusterExprs | 20.448 | 0.100 | 20.549 | |
| plotClusterHeatmap | 14.639 | 0.044 | 14.687 | |
| plotCodes | 5.862 | 0.008 | 5.886 | |
| plotCounts | 0.810 | 0.000 | 0.811 | |
| plotDR | 7.047 | 0.505 | 7.573 | |
| plotDiffHeatmap | 18.344 | 0.040 | 9.933 | |
| plotEvents | 9.687 | 0.004 | 9.693 | |
| plotExprHeatmap | 1.507 | 0.000 | 1.509 | |
| plotExprs | 6.185 | 0.016 | 6.204 | |
| plotMDS | 1.185 | 0.008 | 1.194 | |
| plotMahal | 12.633 | 0.000 | 12.825 | |
| plotMedExprs | 12.928 | 0.020 | 12.964 | |
| plotNRS | 1.278 | 0.004 | 1.283 | |
| plotSpillmat | 6.740 | 0.012 | 6.752 | |
| plotYields | 25.783 | 0.077 | 13.661 | |
| runDR | 30.157 | 0.012 | 30.203 | |