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CHECK report for MCbiclust on malbec2

This page was generated on 2019-04-09 11:47:23 -0400 (Tue, 09 Apr 2019).

Package 920/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MCbiclust 1.7.1
Robert Bentham
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/MCbiclust
Branch: master
Last Commit: 8759508
Last Changed Date: 2019-01-04 13:37:39 -0400 (Fri, 04 Jan 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  OK  OK 

Summary

Package: MCbiclust
Version: 1.7.1
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:MCbiclust.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings MCbiclust_1.7.1.tar.gz
StartedAt: 2019-04-09 01:45:21 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 01:51:10 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 349.1 seconds
RetCode: 1
Status:  ERROR 
CheckDir: MCbiclust.Rcheck
Warnings: NA

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:MCbiclust.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings MCbiclust_1.7.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/MCbiclust.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 ‘MCbiclust/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MCbiclust’ version ‘1.7.1’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MCbiclust’ 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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
SilhouetteClustGroups 34.937  0.384  35.730
CVPlot                18.919  0.100  19.022
PointScoreCalc        15.635  0.427  16.497
CVEval                11.214  0.230  11.935
ThresholdBic           8.775  0.623   9.835
PC1VecFun              9.144  0.210   9.806
SampleSort             7.919  0.208   8.552
GOEnrichmentAnalysis   6.826  0.036   6.914
* 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:
  [7]  -29 -  -35 ==   6
  [8]  -59 -  -29 == -30
  [9] -221 - -235 ==  14
  ...
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 18 SKIPPED: 0 FAILED: 5
  1. Failure: Basic functioning remains constant (@test-constant.R#75) 
  2. Failure: Basic functioning remains constant (@test-constant.R#76) 
  3. Failure: Basic functioning remains constant (@test-constant.R#77) 
  4. Failure: Basic functioning remains constant (@test-constant.R#78) 
  5. Failure: Basic functioning remains constant (@test-constant.R#81) 
  
  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
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/MCbiclust.Rcheck/00check.log’
for details.


Installation output

MCbiclust.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL MCbiclust
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘MCbiclust’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** 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 (MCbiclust)

Tests output

MCbiclust.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.

> Sys.setenv("R_TESTS" = "")
> 
> library(testthat)
> library(MCbiclust)


> 
> test_check("MCbiclust")
── 1. Failure: Basic functioning remains constant (@test-constant.R#75)  ───────
`CCLE.seed` has changed from known value recorded in 'ccle_seed.rds'.
10/10 mismatches (average diff: 105)
[1]  91 - 146 ==  -55
[2] 214 - 302 ==  -88
[3]  12 - 255 == -243
[4]  78 - 327 == -249
[5] 105 -  51 ==   54
[6] 255 - 388 == -133
[7] 261 - 289 ==  -28
[8] 266 - 383 == -117
[9] 316 - 373 ==  -57
...

── 2. Failure: Basic functioning remains constant (@test-constant.R#76)  ───────
`CCLE.sort` has changed from known value recorded in 'ccle_sort.rds'.
10/11 mismatches (average diff: 105)
[1]  91 - 146 ==  -55
[2] 214 - 302 ==  -88
[3]  12 - 255 == -243
[4]  78 - 327 == -249
[5] 105 -  51 ==   54
[6] 255 - 388 == -133
[7] 261 - 289 ==  -28
[8] 266 - 383 == -117
[9] 316 - 373 ==  -57
...

── 3. Failure: Basic functioning remains constant (@test-constant.R#77)  ───────
`CCLE.cor.vec` has changed from known value recorded in 'ccle_cv.rds'.
1000/1000 mismatches (average diff: 0.285)
[1] 0.683 -  0.1608 ==  0.522121
[2] 0.544 -  0.2842 ==  0.260153
[3] 0.375 - -0.5455 ==  0.920613
[4] 0.380 -  0.6360 == -0.256235
[5] 0.497 -  0.4965 ==  0.000234
[6] 0.503 -  0.0108 ==  0.492579
[7] 0.676 -  0.5043 ==  0.171809
[8] 0.267 -  0.6904 == -0.423668
[9] 0.691 -  0.8556 == -0.164747
...

── 4. Failure: Basic functioning remains constant (@test-constant.R#78)  ───────
`CCLE.bic` has changed from known value recorded in 'ccle_bic.rds'.
Component 1: 360 element mismatches

── 5. Failure: Basic functioning remains constant (@test-constant.R#81)  ───────
`CCLE.ps` has changed from known value recorded in 'ccle_ps.rds'.
493/500 mismatches (average diff: 28.2)
[1]  -89 -  -77 == -12
[2]  157 -  101 ==  56
[3]   57 -  139 == -82
[4]  121 -  155 == -34
[5]  -93 -  -91 ==  -2
[6]   95 -   57 ==  38
[7]  -29 -  -35 ==   6
[8]  -59 -  -29 == -30
[9] -221 - -235 ==  14
...

══ testthat results  ═══════════════════════════════════════════════════════════
OK: 18 SKIPPED: 0 FAILED: 5
1. Failure: Basic functioning remains constant (@test-constant.R#75) 
2. Failure: Basic functioning remains constant (@test-constant.R#76) 
3. Failure: Basic functioning remains constant (@test-constant.R#77) 
4. Failure: Basic functioning remains constant (@test-constant.R#78) 
5. Failure: Basic functioning remains constant (@test-constant.R#81) 

Error: testthat unit tests failed
Execution halted

Example timings

MCbiclust.Rcheck/MCbiclust-Ex.timings

nameusersystemelapsed
CVEval11.214 0.23011.935
CVPlot18.919 0.10019.022
CorScoreCalc2.4140.0482.462
FindSeed3.2500.0433.304
GOEnrichmentAnalysis6.8260.0366.914
HclustGenesHiCor3.8140.0483.867
PC1VecFun9.1440.2109.806
PointScoreCalc15.635 0.42716.497
SampleSort7.9190.2088.552
SilhouetteClustGroups34.937 0.38435.730
ThresholdBic8.7750.6239.835