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CHECK report for CATALYST on celaya2

This page was generated on 2019-04-09 13:18:10 -0400 (Tue, 09 Apr 2019).

Package 211/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CATALYST 1.7.7
Helena L. Crowell
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/CATALYST
Branch: master
Last Commit: 3376967
Last Changed Date: 2019-03-26 08:04:22 -0400 (Tue, 26 Mar 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  ERROR 
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  ERROR  OK 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ ERROR ] OK 
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  ERROR  OK 

Summary

Package: CATALYST
Version: 1.7.7
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_1.7.7.tar.gz
StartedAt: 2019-04-09 00:25:08 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 00:38:14 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 786.6 seconds
RetCode: 1
Status:  ERROR 
CheckDir: CATALYST.Rcheck
Warnings: NA

Command output

##############################################################################
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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_1.7.7.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/CATALYST.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.7.7’
* 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 ... NOTE
plotClusterHeatmap,daFrame : <anonymous>: 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              32.263  2.724  35.005
plotClusterExprs   24.107  3.533  27.650
plotMedExprs       20.058  2.523  22.624
plotClusterHeatmap 19.842  2.648  22.499
plotYields         18.103  1.890  17.021
plotMahal          18.331  0.207  18.590
plotDiffHeatmap    13.790  4.332  15.090
plotEvents         16.203  0.221  16.427
estCutoffs         15.515  0.799  15.205
outFrames          15.256  0.154  15.587
applyCutoffs       14.848  0.285  15.164
outFCS             14.879  0.202  15.082
plotAbundances     12.045  2.595  14.644
assignPrelim       13.744  0.117  13.873
dbFrame-methods    13.051  0.164  13.215
mergeClusters      10.695  2.408  13.106
plotDR              9.643  2.476  12.121
extractClusters     9.444  2.121  11.565
cluster             9.136  2.070  11.208
adaptSpillmat      10.242  0.949  11.193
plotCodes           8.914  2.201  11.115
compCytof          10.620  0.365  10.990
plotSpillmat       10.130  0.485  10.970
normCytof          10.395  0.213  10.615
filter              8.005  2.025  10.030
computeSpillmat     9.345  0.406   9.754
daFrame-methods     7.436  1.760   9.196
plotExprs           6.857  0.276   7.134
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
         invokeRestart("muffleWarning")
     })
  5: eval_bare(get_expr(quo), get_env(quo))
  6: runDR(y, "PCA", i, use_dimred = "MDS")
  7: runDR(y, "PCA", i, use_dimred = "MDS")
  8: .local(x, ...)
  9: fun(y, exprs_values = "exprs", feature_set = cols_to_use, ...)
  10: fun(y, exprs_values = "exprs", feature_set = cols_to_use, ...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 85 SKIPPED: 0 FAILED: 1
  1. Error: throw warning when 'use_dimred' is supplied to PCA (@test_runDR.R#43) 
  
  Error: testthat unit tests failed
  Execution halted
* 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 ERROR, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/CATALYST.Rcheck/00check.log’
for details.

Installation output

CATALYST.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CATALYST
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/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)

Tests output

CATALYST.Rcheck/tests/testthat.Rout.fail


R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
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")
── 1. Error: throw warning when 'use_dimred' is supplied to PCA (@test_runDR.R#4
unused argument (use_dimred = "MDS")
1: expect_warning(runDR(y, "PCA", i, use_dimred = "MDS")) at testthat/test_runDR.R:43
2: quasi_capture(enquo(object), capture_warnings, label = label)
3: capture(act$val <- eval_bare(get_expr(quo), get_env(quo)))
4: withCallingHandlers(code, warning = function(condition) {
       out$push(condition)
       invokeRestart("muffleWarning")
   })
5: eval_bare(get_expr(quo), get_env(quo))
6: runDR(y, "PCA", i, use_dimred = "MDS")
7: runDR(y, "PCA", i, use_dimred = "MDS")
8: .local(x, ...)
9: fun(y, exprs_values = "exprs", feature_set = cols_to_use, ...)
10: fun(y, exprs_values = "exprs", feature_set = cols_to_use, ...)

══ testthat results  ═══════════════════════════════════════════════════════════
OK: 85 SKIPPED: 0 FAILED: 1
1. Error: throw warning when 'use_dimred' is supplied to PCA (@test_runDR.R#43) 

Error: testthat unit tests failed
Execution halted

Example timings

CATALYST.Rcheck/CATALYST-Ex.timings

nameusersystemelapsed
adaptSpillmat10.242 0.94911.193
applyCutoffs14.848 0.28515.164
assignPrelim13.744 0.11713.873
cluster 9.136 2.07011.208
compCytof10.620 0.36510.990
computeSpillmat9.3450.4069.754
concatFCS0.0520.0060.057
daFrame-class0.6160.0110.627
daFrame-methods7.4361.7609.196
data0.0130.0100.024
dbFrame-methods13.051 0.16413.215
estCutoffs15.515 0.79915.205
extractClusters 9.444 2.12111.565
filter 8.005 2.02510.030
guessPanel0.0350.0150.051
launchGUI0.0000.0000.001
mergeClusters10.695 2.40813.106
normCytof10.395 0.21310.615
outFCS14.879 0.20215.082
outFrames15.256 0.15415.587
plotAbundances12.045 2.59514.644
plotClusterExprs24.107 3.53327.650
plotClusterHeatmap19.842 2.64822.499
plotCodes 8.914 2.20111.115
plotCounts0.8540.0080.862
plotDR 9.643 2.47612.121
plotDiffHeatmap13.790 4.33215.090
plotEvents16.203 0.22116.427
plotExprHeatmap1.6450.0471.692
plotExprs6.8570.2767.134
plotMDS1.3580.0211.385
plotMahal18.331 0.20718.590
plotMedExprs20.058 2.52322.624
plotNRS1.6040.0221.653
plotSpillmat10.130 0.48510.970
plotYields18.103 1.89017.021
runDR32.263 2.72435.005