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CHECK report for CATALYST on merida2

This page was generated on 2019-04-09 13:34:54 -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: 2019-04-08 23:40:56 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-08 23:50:48 -0400 (Mon, 08 Apr 2019)
EllapsedTime: 592.1 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) (2018-11-27 r75683)
* 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              21.908  1.464  23.521
plotClusterExprs   19.215  1.668  21.034
plotClusterHeatmap 15.787  1.466  17.427
plotMedExprs       15.424  1.451  17.064
plotYields         14.623  0.990  14.409
plotDiffHeatmap    11.924  3.608  11.758
plotMahal          14.664  0.081  14.891
plotEvents         12.045  0.074  12.224
applyCutoffs       11.704  0.112  11.876
plotAbundances     10.312  1.216  11.626
outFCS             11.233  0.217  11.552
outFrames          11.257  0.123  11.495
assignPrelim       10.763  0.204  11.104
estCutoffs          9.661  1.282   9.229
plotCodes           7.882  1.539   9.524
adaptSpillmat       8.275  0.481   8.818
plotDR              7.289  1.348   8.726
plotSpillmat        7.834  0.176   8.119
mergeClusters       6.906  0.987   7.938
dbFrame-methods     7.656  0.073   7.739
cluster             6.320  0.855   7.236
normCytof           6.858  0.224   7.123
filter              5.589  1.147   6.758
compCytof           6.440  0.251   6.753
computeSpillmat     5.992  0.165   6.183
daFrame-methods     4.695  1.016   5.731
extractClusters     4.521  1.156   5.686
plotExprs           5.297  0.142   5.478
* 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’ ...
** 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.fail


R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
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)

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
adaptSpillmat8.2750.4818.818
applyCutoffs11.704 0.11211.876
assignPrelim10.763 0.20411.104
cluster6.3200.8557.236
compCytof6.4400.2516.753
computeSpillmat5.9920.1656.183
concatFCS0.0440.0020.046
daFrame-class0.4580.0150.474
daFrame-methods4.6951.0165.731
data0.0070.0040.011
dbFrame-methods7.6560.0737.739
estCutoffs9.6611.2829.229
extractClusters4.5211.1565.686
filter5.5891.1476.758
guessPanel0.0200.0050.026
launchGUI000
mergeClusters6.9060.9877.938
normCytof6.8580.2247.123
outFCS11.233 0.21711.552
outFrames11.257 0.12311.495
plotAbundances10.312 1.21611.626
plotClusterExprs19.215 1.66821.034
plotClusterHeatmap15.787 1.46617.427
plotCodes7.8821.5399.524
plotCounts0.6770.0030.686
plotDR7.2891.3488.726
plotDiffHeatmap11.924 3.60811.758
plotEvents12.045 0.07412.224
plotExprHeatmap1.2930.0221.327
plotExprs5.2970.1425.478
plotMDS1.1210.0121.149
plotMahal14.664 0.08114.891
plotMedExprs15.424 1.45117.064
plotNRS1.3420.0111.378
plotSpillmat7.8340.1768.119
plotYields14.623 0.99014.409
runDR21.908 1.46423.521