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CHECK report for MCbiclust on tokay2

This page was generated on 2019-04-09 12:29:09 -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: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MCbiclust.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings MCbiclust_1.7.1.tar.gz
StartedAt: 2019-04-09 04:01:21 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 04:14:11 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 770.1 seconds
RetCode: 1
Status:  ERROR  
CheckDir: MCbiclust.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MCbiclust.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings MCbiclust_1.7.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/MCbiclust.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
SilhouetteClustGroups 59.25   3.60   63.22
CVPlot                27.72   1.59   29.33
SampleSort            17.14   1.22   18.70
PointScoreCalc        15.22   1.48   17.01
CVEval                14.28   1.57   16.28
PC1VecFun             11.95   1.67   14.05
ThresholdBic          11.53   1.23   13.07
GOEnrichmentAnalysis   7.59   0.35    7.93
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
SilhouetteClustGroups 52.99   5.39   58.78
CVPlot                30.16   1.67   31.86
PointScoreCalc        21.31   1.61   23.31
SampleSort            16.34   1.91   18.69
PC1VecFun             16.55   1.50   18.61
ThresholdBic          15.09   1.85   17.39
CVEval                13.33   1.71   15.34
GOEnrichmentAnalysis   8.01   0.56    8.58
FindSeed               5.08   0.59    5.67
CorScoreCalc           4.71   0.58    5.29
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  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
** running tests for arch 'x64' ...
  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: 2 ERRORs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/MCbiclust.Rcheck/00check.log'
for details.

Installation output

MCbiclust.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/MCbiclust_1.7.1.tar.gz && rm -rf MCbiclust.buildbin-libdir && mkdir MCbiclust.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MCbiclust.buildbin-libdir MCbiclust_1.7.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL MCbiclust_1.7.1.zip && rm MCbiclust_1.7.1.tar.gz MCbiclust_1.7.1.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 2543k  100 2543k    0     0  8224k      0 --:--:-- --:--:-- --:--:-- 8393k

install for i386

* installing *source* package 'MCbiclust' ...
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MCbiclust'
    finding HTML links ... done
    CCLE_samples                            html  
    CCLE_small                              html  
    CVEval                                  html  
    CVPlot                                  html  
    CorScoreCalc                            html  
    FindSeed                                html  
    GOEnrichmentAnalysis                    html  
    HclustGenesHiCor                        html  
    MCbiclust                               html  
    Mitochondrial_genes                     html  
    PC1VecFun                               html  
    PointScoreCalc                          html  
    SampleSort                              html  
    SilhouetteClustGroups                   html  
    ThresholdBic                            html  
** 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

install for x64

* installing *source* package 'MCbiclust' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MCbiclust' as MCbiclust_1.7.1.zip
* DONE (MCbiclust)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'MCbiclust' successfully unpacked and MD5 sums checked

Tests output

MCbiclust.Rcheck/tests_i386/testthat.Rout.fail


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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/tests_x64/testthat.Rout.fail


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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/examples_i386/MCbiclust-Ex.timings

nameusersystemelapsed
CVEval14.28 1.5716.28
CVPlot27.72 1.5929.33
CorScoreCalc3.540.423.97
FindSeed3.410.503.91
GOEnrichmentAnalysis7.590.357.93
HclustGenesHiCor2.990.373.36
PC1VecFun11.95 1.6714.05
PointScoreCalc15.22 1.4817.01
SampleSort17.14 1.2218.70
SilhouetteClustGroups59.25 3.6063.22
ThresholdBic11.53 1.2313.07

MCbiclust.Rcheck/examples_x64/MCbiclust-Ex.timings

nameusersystemelapsed
CVEval13.33 1.7115.34
CVPlot30.16 1.6731.86
CorScoreCalc4.710.585.29
FindSeed5.080.595.67
GOEnrichmentAnalysis8.010.568.58
HclustGenesHiCor3.470.534.00
PC1VecFun16.55 1.5018.61
PointScoreCalc21.31 1.6123.31
SampleSort16.34 1.9118.69
SilhouetteClustGroups52.99 5.3958.78
ThresholdBic15.09 1.8517.39