Back to Multiple platform build/check report for BioC 3.8
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

CHECK report for CATALYST on merida1

This page was generated on 2019-04-16 12:00:35 -0400 (Tue, 16 Apr 2019).

Package 204/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CATALYST 1.6.7
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)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

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

Command output

##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################


* 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.



Installation output

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)

Tests output

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 

Example timings

CATALYST.Rcheck/CATALYST-Ex.timings

nameusersystemelapsed
adaptSpillmat8.8770.4289.360
applyCutoffs13.459 0.08013.642
assignPrelim12.057 0.14012.279
cluster6.4790.8867.396
compCytof7.5690.1687.775
computeSpillmat7.0490.0867.191
concatFCS0.1080.0500.158
daFrame-class0.5780.0050.588
daFrame-methods6.2310.9777.245
data0.0090.0050.014
dbFrame-methods12.330 0.12512.623
estCutoffs11.652 1.44811.543
extractClusters4.7110.8635.608
filter5.0770.9896.098
guessPanel0.0210.0050.025
launchGUI000
mergeClusters6.1871.0437.248
normCytof6.3190.0856.412
outFCS10.213 0.08510.338
outFrames11.749 0.11912.024
plotAbundances 9.823 1.32411.272
plotClusterExprs20.496 1.61922.316
plotClusterHeatmap21.627 1.86123.723
plotCodes7.5811.3439.024
plotCounts0.7760.0060.788
plotDR8.1721.3539.617
plotDiffHeatmap13.901 4.45314.173
plotEvents13.575 0.06413.807
plotExprHeatmap2.1190.0462.176
plotExprs5.2850.1295.467
plotMDS1.1270.0161.156
plotMahal16.853 0.09817.173
plotMedExprs17.511 1.33919.178
plotNRS1.3590.0181.400
plotSpillmat8.8770.2269.426
plotYields15.299 2.60814.437
runDR23.809 1.91526.135