Helena L. Crowell
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/CATALYST |
| Branch: RELEASE_3_8 |
| Last Commit: 88805f2 |
| Last Changed Date: 2019-03-21 07:35:25 -0400 (Thu, 21 Mar 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 12:00:35 -0400 (Tue, 16 Apr 2019).
| Package 204/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CATALYST 1.6.7 Helena L. Crowell
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: CATALYST |
| Version: 1.6.7 |
| 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_1.6.7.tar.gz |
| StartedAt: 2019-04-15 22:46:59 -0400 (Mon, 15 Apr 2019) |
| EndedAt: 2019-04-15 22:57:14 -0400 (Mon, 15 Apr 2019) |
| EllapsedTime: 615.3 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_1.6.7.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/CATALYST.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.6.7’
* 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 ... NOTE
Found the following hidden files and directories:
.travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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
runDR 23.809 1.915 26.135
plotClusterHeatmap 21.627 1.861 23.723
plotClusterExprs 20.496 1.619 22.316
plotMedExprs 17.511 1.339 19.178
plotDiffHeatmap 13.901 4.453 14.173
plotYields 15.299 2.608 14.437
plotMahal 16.853 0.098 17.173
plotEvents 13.575 0.064 13.807
applyCutoffs 13.459 0.080 13.642
estCutoffs 11.652 1.448 11.543
dbFrame-methods 12.330 0.125 12.623
assignPrelim 12.057 0.140 12.279
outFrames 11.749 0.119 12.024
plotAbundances 9.823 1.324 11.272
outFCS 10.213 0.085 10.338
plotDR 8.172 1.353 9.617
adaptSpillmat 8.877 0.428 9.360
plotSpillmat 8.877 0.226 9.426
plotCodes 7.581 1.343 9.024
compCytof 7.569 0.168 7.775
cluster 6.479 0.886 7.396
mergeClusters 6.187 1.043 7.248
daFrame-methods 6.231 0.977 7.245
computeSpillmat 7.049 0.086 7.191
normCytof 6.319 0.085 6.412
filter 5.077 0.989 6.098
extractClusters 4.711 0.863 5.608
plotExprs 5.285 0.129 5.467
* 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-3.8-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/3.5/Resources/library’ * installing *source* package ‘CATALYST’ ... ** 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 * DONE (CATALYST)
CATALYST.Rcheck/tests/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
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 FAILED: 0
>
> proc.time()
user system elapsed
32.322 1.022 33.785
CATALYST.Rcheck/CATALYST-Ex.timings
| name | user | system | elapsed | |
| adaptSpillmat | 8.877 | 0.428 | 9.360 | |
| applyCutoffs | 13.459 | 0.080 | 13.642 | |
| assignPrelim | 12.057 | 0.140 | 12.279 | |
| cluster | 6.479 | 0.886 | 7.396 | |
| compCytof | 7.569 | 0.168 | 7.775 | |
| computeSpillmat | 7.049 | 0.086 | 7.191 | |
| concatFCS | 0.108 | 0.050 | 0.158 | |
| daFrame-class | 0.578 | 0.005 | 0.588 | |
| daFrame-methods | 6.231 | 0.977 | 7.245 | |
| data | 0.009 | 0.005 | 0.014 | |
| dbFrame-methods | 12.330 | 0.125 | 12.623 | |
| estCutoffs | 11.652 | 1.448 | 11.543 | |
| extractClusters | 4.711 | 0.863 | 5.608 | |
| filter | 5.077 | 0.989 | 6.098 | |
| guessPanel | 0.021 | 0.005 | 0.025 | |
| launchGUI | 0 | 0 | 0 | |
| mergeClusters | 6.187 | 1.043 | 7.248 | |
| normCytof | 6.319 | 0.085 | 6.412 | |
| outFCS | 10.213 | 0.085 | 10.338 | |
| outFrames | 11.749 | 0.119 | 12.024 | |
| plotAbundances | 9.823 | 1.324 | 11.272 | |
| plotClusterExprs | 20.496 | 1.619 | 22.316 | |
| plotClusterHeatmap | 21.627 | 1.861 | 23.723 | |
| plotCodes | 7.581 | 1.343 | 9.024 | |
| plotCounts | 0.776 | 0.006 | 0.788 | |
| plotDR | 8.172 | 1.353 | 9.617 | |
| plotDiffHeatmap | 13.901 | 4.453 | 14.173 | |
| plotEvents | 13.575 | 0.064 | 13.807 | |
| plotExprHeatmap | 2.119 | 0.046 | 2.176 | |
| plotExprs | 5.285 | 0.129 | 5.467 | |
| plotMDS | 1.127 | 0.016 | 1.156 | |
| plotMahal | 16.853 | 0.098 | 17.173 | |
| plotMedExprs | 17.511 | 1.339 | 19.178 | |
| plotNRS | 1.359 | 0.018 | 1.400 | |
| plotSpillmat | 8.877 | 0.226 | 9.426 | |
| plotYields | 15.299 | 2.608 | 14.437 | |
| runDR | 23.809 | 1.915 | 26.135 | |