Helena L. Crowell
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/CATALYST |
| Branch: RELEASE_3_7 |
| Last Commit: 668abb2 |
| Last Changed Date: 2018-05-18 10:28:54 -0400 (Fri, 18 May 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:58:05 -0400 (Wed, 17 Oct 2018).
| Package 191/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CATALYST 1.4.2 Helena L. Crowell
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: CATALYST |
| Version: 1.4.2 |
| 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_1.4.2.tar.gz |
| StartedAt: 2018-10-16 20:16:40 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 20:25:13 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 513.0 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_1.4.2.tar.gz
###
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##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/CATALYST.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.4.2’
* 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 ... NOTE
plotDiffHeatmap,matrix-SummarizedExperiment: no visible binding for
global variable ‘cluster_id’
plotDiffHeatmap,matrix-SummarizedExperiment: no visible binding for
global variable ‘sample_id’
Undefined global functions or variables:
cluster_id sample_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
plotDiffHeatmap 18.106 1.492 19.774
plotMedExprs 17.541 1.513 19.254
plotMahal 16.367 0.128 16.668
plotClusterHeatmap 14.532 1.306 15.917
plotSNE 13.252 1.794 15.219
plotYields 13.661 0.119 13.996
plotEvents 13.224 0.068 13.467
applyCutoffs 13.019 0.087 13.189
assignPrelim 11.654 0.044 11.766
plotCodes 9.128 1.281 10.502
adaptSpillmat 8.860 0.303 9.210
estCutoffs 8.787 0.086 8.897
outFCS 8.471 0.080 8.550
outFrames 8.421 0.124 8.544
dbFrame-methods 8.436 0.058 8.504
plotSpillmat 8.181 0.181 8.546
plotAbundances 7.020 1.260 8.313
compCytof 8.074 0.133 8.274
computeSpillmat 7.433 0.138 7.611
cluster 6.657 0.894 7.607
mergeClusters 6.135 1.117 7.293
daFrame-methods 6.415 0.746 7.215
normCytof 6.513 0.099 6.623
plotExprs 6.061 0.133 6.233
extractClusters 5.011 1.037 6.081
tSNE 5.227 0.021 5.312
* 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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.7-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 ** 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 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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)
>
> test_check("CATALYST")
══ testthat results ═══════════════════════════════════════════════════════════
OK: 45 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
21.233 1.007 22.666
CATALYST.Rcheck/CATALYST-Ex.timings
| name | user | system | elapsed | |
| adaptSpillmat | 8.860 | 0.303 | 9.210 | |
| applyCutoffs | 13.019 | 0.087 | 13.189 | |
| assignPrelim | 11.654 | 0.044 | 11.766 | |
| cluster | 6.657 | 0.894 | 7.607 | |
| compCytof | 8.074 | 0.133 | 8.274 | |
| computeSpillmat | 7.433 | 0.138 | 7.611 | |
| concatFCS | 0.058 | 0.003 | 0.064 | |
| daFrame-methods | 6.415 | 0.746 | 7.215 | |
| data | 0.012 | 0.006 | 0.018 | |
| dbFrame-methods | 8.436 | 0.058 | 8.504 | |
| estCutoffs | 8.787 | 0.086 | 8.897 | |
| extractClusters | 5.011 | 1.037 | 6.081 | |
| guessPanel | 0.020 | 0.004 | 0.024 | |
| launchGUI | 0.000 | 0.000 | 0.001 | |
| mergeClusters | 6.135 | 1.117 | 7.293 | |
| normCytof | 6.513 | 0.099 | 6.623 | |
| outFCS | 8.471 | 0.080 | 8.550 | |
| outFrames | 8.421 | 0.124 | 8.544 | |
| plotAbundances | 7.020 | 1.260 | 8.313 | |
| plotClusterHeatmap | 14.532 | 1.306 | 15.917 | |
| plotCodes | 9.128 | 1.281 | 10.502 | |
| plotCounts | 0.714 | 0.005 | 0.728 | |
| plotDiffHeatmap | 18.106 | 1.492 | 19.774 | |
| plotEvents | 13.224 | 0.068 | 13.467 | |
| plotExprHeatmap | 1.632 | 0.012 | 1.655 | |
| plotExprs | 6.061 | 0.133 | 6.233 | |
| plotMDS | 0.890 | 0.007 | 0.902 | |
| plotMahal | 16.367 | 0.128 | 16.668 | |
| plotMedExprs | 17.541 | 1.513 | 19.254 | |
| plotNRS | 1.304 | 0.016 | 1.341 | |
| plotSNE | 13.252 | 1.794 | 15.219 | |
| plotSpillmat | 8.181 | 0.181 | 8.546 | |
| plotYields | 13.661 | 0.119 | 13.996 | |
| tSNE | 5.227 | 0.021 | 5.312 | |