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CHECK report for CATALYST on malbec2

This page was generated on 2019-04-09 11:47:54 -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: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:CATALYST.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings CATALYST_1.7.7.tar.gz
StartedAt: 2019-04-08 23:13:59 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-08 23:23:03 -0400 (Mon, 08 Apr 2019)
EllapsedTime: 543.8 seconds
RetCode: 1
Status:  ERROR 
CheckDir: CATALYST.Rcheck
Warnings: NA

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:CATALYST.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings CATALYST_1.7.7.tar.gz
###
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##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/CATALYST.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (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              30.261  0.052  30.421
plotYields         24.365  0.084  12.581
plotDiffHeatmap    17.861  0.119  12.415
plotClusterExprs   17.195  0.068  17.277
plotMedExprs       12.016  0.012  12.032
applyCutoffs       11.738  0.000  11.739
plotClusterHeatmap 11.702  0.012  11.714
plotMahal          11.335  0.000  11.352
dbFrame-methods    11.218  0.008  11.229
outFCS             10.440  0.004  10.445
estCutoffs         10.138  0.032   9.230
plotAbundances      9.717  0.024   9.747
assignPrelim        9.521  0.004   9.540
normCytof           9.342  0.024   9.371
plotEvents          9.235  0.008   9.253
outFrames           8.589  0.000   8.591
compCytof           8.244  0.000   8.246
daFrame-methods     7.811  0.011   7.838
mergeClusters       7.760  0.004   7.809
plotDR              6.631  0.372   7.006
computeSpillmat     6.632  0.004   6.637
plotSpillmat        6.509  0.005   6.513
cluster             6.413  0.004   6.419
extractClusters     6.189  0.008   6.200
plotCodes           6.165  0.008   6.174
adaptSpillmat       5.680  0.124   5.804
filter              5.769  0.012   5.783
* 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/CATALYST.Rcheck/00check.log’
for details.


Installation output

CATALYST.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL CATALYST
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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-pc-linux-gnu (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
adaptSpillmat5.6800.1245.804
applyCutoffs11.738 0.00011.739
assignPrelim9.5210.0049.540
cluster6.4130.0046.419
compCytof8.2440.0008.246
computeSpillmat6.6320.0046.637
concatFCS0.070.000.07
daFrame-class0.6620.0000.662
daFrame-methods7.8110.0117.838
data0.0090.0000.009
dbFrame-methods11.218 0.00811.229
estCutoffs10.138 0.032 9.230
extractClusters6.1890.0086.200
filter5.7690.0125.783
guessPanel0.0270.0000.026
launchGUI000
mergeClusters7.7600.0047.809
normCytof9.3420.0249.371
outFCS10.440 0.00410.445
outFrames8.5890.0008.591
plotAbundances9.7170.0249.747
plotClusterExprs17.195 0.06817.277
plotClusterHeatmap11.702 0.01211.714
plotCodes6.1650.0086.174
plotCounts0.560.000.56
plotDR6.6310.3727.006
plotDiffHeatmap17.861 0.11912.415
plotEvents9.2350.0089.253
plotExprHeatmap1.3920.0001.392
plotExprs4.8410.0084.849
plotMDS0.7330.0000.735
plotMahal11.335 0.00011.352
plotMedExprs12.016 0.01212.032
plotNRS0.9390.0000.938
plotSpillmat6.5090.0056.513
plotYields24.365 0.08412.581
runDR30.261 0.05230.421