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 12:12:37 -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: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:CATALYST.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings CATALYST_1.10.3.tar.gz |
| StartedAt: 2020-04-15 04:45:13 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 04:57:07 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 713.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CATALYST.Rcheck |
| Warnings: 0 |
##############################################################################
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### Running command:
###
### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:CATALYST.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings CATALYST_1.10.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/CATALYST.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.10.3’
* 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
plotYields 33.868 0.120 19.806
plotClusterHeatmap 32.064 0.136 22.964
plotDiffHeatmap 24.792 0.092 15.915
plotDR 24.356 0.020 23.578
plotClusterExprs 23.580 0.072 23.406
plotMedExprs 21.320 0.016 17.602
plotMahal 15.516 0.000 15.772
mergeClusters 13.968 0.056 9.145
estCutoffs 12.896 0.016 11.826
outFCS 12.268 0.000 12.335
applyCutoffs 12.100 0.008 12.135
plotEvents 12.036 0.004 12.253
assignPrelim 10.940 0.004 11.040
normCytof 10.916 0.024 11.007
dbFrame-methods 9.852 0.004 10.413
outFrames 9.756 0.004 9.895
SCE-utils 8.460 0.144 8.680
plotSpillmat 8.200 0.016 8.300
plotAbundances 8.196 0.012 8.217
plotExprs 8.196 0.004 8.325
cluster 7.856 0.004 7.992
adaptSpillmat 7.404 0.024 7.446
compCytof 7.296 0.016 7.396
plotCodes 7.148 0.004 7.304
filterSCE 6.976 0.008 7.215
extractClusters 6.888 0.000 6.951
computeSpillmat 6.644 0.004 6.813
runDR 5.412 0.000 5.445
* 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: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL CATALYST ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.10-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 ** 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-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)
>
> test_check("CATALYST")
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 228 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
96.780 0.808 70.334
CATALYST.Rcheck/CATALYST-Ex.timings
| name | user | system | elapsed | |
| SCE-utils | 8.460 | 0.144 | 8.680 | |
| adaptSpillmat | 7.404 | 0.024 | 7.446 | |
| applyCutoffs | 12.100 | 0.008 | 12.135 | |
| assignPrelim | 10.940 | 0.004 | 11.040 | |
| cluster | 7.856 | 0.004 | 7.992 | |
| compCytof | 7.296 | 0.016 | 7.396 | |
| computeSpillmat | 6.644 | 0.004 | 6.813 | |
| concatFCS | 0.072 | 0.000 | 0.073 | |
| data | 0.008 | 0.000 | 0.007 | |
| dbFrame-methods | 9.852 | 0.004 | 10.413 | |
| estCutoffs | 12.896 | 0.016 | 11.826 | |
| extractClusters | 6.888 | 0.000 | 6.951 | |
| filterSCE | 6.976 | 0.008 | 7.215 | |
| guessPanel | 0.032 | 0.000 | 0.031 | |
| launchGUI | 0 | 0 | 0 | |
| mergeClusters | 13.968 | 0.056 | 9.145 | |
| normCytof | 10.916 | 0.024 | 11.007 | |
| outFCS | 12.268 | 0.000 | 12.335 | |
| outFrames | 9.756 | 0.004 | 9.895 | |
| plotAbundances | 8.196 | 0.012 | 8.217 | |
| plotClusterExprs | 23.580 | 0.072 | 23.406 | |
| plotClusterHeatmap | 32.064 | 0.136 | 22.964 | |
| plotCodes | 7.148 | 0.004 | 7.304 | |
| plotCounts | 0.764 | 0.004 | 0.777 | |
| plotDR | 24.356 | 0.020 | 23.578 | |
| plotDiffHeatmap | 24.792 | 0.092 | 15.915 | |
| plotEvents | 12.036 | 0.004 | 12.253 | |
| plotExprHeatmap | 2.224 | 0.000 | 1.880 | |
| plotExprs | 8.196 | 0.004 | 8.325 | |
| plotMDS | 1.132 | 0.004 | 1.137 | |
| plotMahal | 15.516 | 0.000 | 15.772 | |
| plotMedExprs | 21.320 | 0.016 | 17.602 | |
| plotNRS | 2.012 | 0.000 | 2.081 | |
| plotSpillmat | 8.200 | 0.016 | 8.300 | |
| plotYields | 33.868 | 0.120 | 19.806 | |
| prepData | 0.444 | 0.000 | 0.451 | |
| runDR | 5.412 | 0.000 | 5.445 | |