| Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-04-09 13:17:40 -0400 (Tue, 09 Apr 2019).
| Package 920/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| MCbiclust 1.7.1 Robert Bentham
| 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 |
| Package: MCbiclust |
| Version: 1.7.1 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MCbiclust.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MCbiclust_1.7.1.tar.gz |
| StartedAt: 2019-04-09 03:17:43 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 03:27:04 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 560.8 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: MCbiclust.Rcheck |
| Warnings: NA |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MCbiclust.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MCbiclust_1.7.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/MCbiclust.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 ‘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 56.443 3.305 60.458
CVPlot 37.202 2.340 39.667
PointScoreCalc 22.411 2.759 25.879
CVEval 16.059 1.189 18.046
ThresholdBic 14.971 1.443 17.083
SampleSort 13.875 1.321 15.854
PC1VecFun 13.736 1.290 15.824
GOEnrichmentAnalysis 10.340 0.562 10.966
HclustGenesHiCor 5.541 0.627 6.206
* 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
‘/Users/biocbuild/bbs-3.9-bioc/meat/MCbiclust.Rcheck/00check.log’
for details.
MCbiclust.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL MCbiclust ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/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)
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-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.
> 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
MCbiclust.Rcheck/MCbiclust-Ex.timings
| name | user | system | elapsed | |
| CVEval | 16.059 | 1.189 | 18.046 | |
| CVPlot | 37.202 | 2.340 | 39.667 | |
| CorScoreCalc | 3.876 | 0.616 | 4.491 | |
| FindSeed | 4.141 | 0.469 | 4.610 | |
| GOEnrichmentAnalysis | 10.340 | 0.562 | 10.966 | |
| HclustGenesHiCor | 5.541 | 0.627 | 6.206 | |
| PC1VecFun | 13.736 | 1.290 | 15.824 | |
| PointScoreCalc | 22.411 | 2.759 | 25.879 | |
| SampleSort | 13.875 | 1.321 | 15.854 | |
| SilhouetteClustGroups | 56.443 | 3.305 | 60.458 | |
| ThresholdBic | 14.971 | 1.443 | 17.083 | |