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CHECK report for pbcmc on tokay1

This page was generated on 2019-04-13 11:26:39 -0400 (Sat, 13 Apr 2019).

Package 1131/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pbcmc 1.10.1
Cristobal Fresno
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/pbcmc
Branch: RELEASE_3_8
Last Commit: bb53ec7
Last Changed Date: 2018-11-30 11:38:31 -0400 (Fri, 30 Nov 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  ERROR 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ ERROR ] OK 
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  ERROR  OK 

Summary

Package: pbcmc
Version: 1.10.1
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pbcmc.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings pbcmc_1.10.1.tar.gz
StartedAt: 2019-04-13 04:25:48 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 04:33:14 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 445.4 seconds
RetCode: 1
Status:  ERROR  
CheckDir: pbcmc.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pbcmc.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings pbcmc_1.10.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/pbcmc.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'pbcmc/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'pbcmc' version '1.10.1'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 'pbcmc' can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'pbcmc' is deprecated and will be removed from Bioconductor
See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/pbcmc.Rcheck/00install.out' for details.
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                                       user system elapsed
PAM50-class                            2.21   0.16   15.42
MolecularPermutationClassifierGenerics 0.20   0.01   21.73
PAM50Permutate                         0.08   0.06   28.09
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                                       user system elapsed
PAM50-class                            3.08   0.10   16.20
MolecularPermutationClassifierGenerics 0.35   0.04   28.11
PAM50Permutate                         0.20   0.00   23.50
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 ERROR
Running the tests in 'tests/runTests.R' failed.
Last 13 lines of output:
  FAILURE in test_subjectReport: Error in checkEquals(names(report), c("data", "layout", "plot"), msg = "subjectReport names check: OK.") : 
    Lengths (9, 3) differ (string compare on first 3)
  2 string mismatches
  subjectReport names check: OK.
  
  Test files with failing tests
  
     test_pbcmc.R 
       test_databaseReport 
       test_subjectReport 
  
  
  Error in BiocGenerics:::testPackage("pbcmc") : 
    unit tests failed for package pbcmc
  Execution halted
** running tests for arch 'x64' ...
  Running 'runTests.R'
 ERROR
Running the tests in 'tests/runTests.R' failed.
Last 13 lines of output:
  FAILURE in test_subjectReport: Error in checkEquals(names(report), c("data", "layout", "plot"), msg = "subjectReport names check: OK.") : 
    Lengths (9, 3) differ (string compare on first 3)
  2 string mismatches
  subjectReport names check: OK.
  
  Test files with failing tests
  
     test_pbcmc.R 
       test_databaseReport 
       test_subjectReport 
  
  
  Error in BiocGenerics:::testPackage("pbcmc") : 
    unit tests failed for package pbcmc
  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, 1 WARNING
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/pbcmc.Rcheck/00check.log'
for details.


Installation output

pbcmc.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/pbcmc_1.10.1.tar.gz && rm -rf pbcmc.buildbin-libdir && mkdir pbcmc.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=pbcmc.buildbin-libdir pbcmc_1.10.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL pbcmc_1.10.1.zip && rm pbcmc_1.10.1.tar.gz pbcmc_1.10.1.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  555k  100  555k    0     0  11.3M      0 --:--:-- --:--:-- --:--:-- 12.3M

install for i386

* installing *source* package 'pbcmc' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
No methods found in package 'BiocGenerics' for request: 'unlist' when loading 'pbcmc'
** help
*** installing help indices
  converting help for package 'pbcmc'
    finding HTML links ... done
    MolecularPermutationClassifier-class    html  
    MolecularPermutationClassifierConstructor
                                            html  
    MolecularPermutationClassifierGenerics
                                            html  
    MolecularPermutationClassifierGetseters
                                            html  
    MolecularPermutationClassifierShow      html  
    PAM50-class                             html  
    PAM50Classify                           html  
    PAM50Constructor                        html  
    finding level-2 HTML links ... done

    PAM50Filtrate                           html  
    PAM50Permutate                          html  
    PAM50SubjectReport                      html  
    PAM50Subtype                            html  
    pbcmcData                               html  
    pbcmcPackage                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in package 'BiocGenerics' for request: 'unlist' when loading 'pbcmc'
Warning: Package 'pbcmc' is deprecated and will be removed from Bioconductor
  version 3.9
In R CMD INSTALL

install for x64

* installing *source* package 'pbcmc' ...
** testing if installed package can be loaded
No methods found in package 'BiocGenerics' for request: 'unlist' when loading 'pbcmc'
Warning: Package 'pbcmc' is deprecated and will be removed from Bioconductor
  version 3.9
* MD5 sums
packaged installation of 'pbcmc' as pbcmc_1.10.1.zip
* DONE (pbcmc)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'pbcmc' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

pbcmc.Rcheck/tests_i386/runTests.Rout.fail


R version 3.5.3 (2019-03-11) -- "Great Truth"
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.

> BiocGenerics:::testPackage("pbcmc")
Package 'mclust' version 5.4.3
Type 'citation("mclust")' for citing this R package in publications.

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from 'package:limma':

    plotMA

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

No methods found in package 'BiocGenerics' for request: 'unlist' when loading 'pbcmc'
Loading required namespace: breastCancerNKI
Timing stopped at: 1.67 0.34 2.01
Error in checkEquals(names(report), c("data", "layout", "plot"), msg = "subjectReport names check: OK.") : 
  Lengths (9, 3) differ (string compare on first 3)
2 string mismatches
subjectReport names check: OK.
In addition: Warning message:
Package 'pbcmc' is deprecated and will be removed from Bioconductor
  version 3.9 
No methods found in package 'BiocGenerics' for request: 'unlist' when loading 'pbcmc'
No methods found in package 'BiocGenerics' for request: 'unlist' when loading 'pbcmc'
No methods found in package 'BiocGenerics' for request: 'unlist' when loading 'pbcmc'
No methods found in package 'BiocGenerics' for request: 'unlist' when loading 'pbcmc'
Timing stopped at: 1.41 0.05 1.46
Error in checkEquals(names(report), c("data", "layout", "plot"), msg = "subjectReport names check: OK.") : 
  Lengths (9, 3) differ (string compare on first 3)
2 string mismatches
subjectReport names check: OK.


RUNIT TEST PROTOCOL -- Sat Apr 13 04:32:27 2019 
*********************************************** 
Number of test functions: 14 
Number of errors: 0 
Number of failures: 2 

 
1 Test Suite : 
pbcmc RUnit Tests - 14 test functions, 0 errors, 2 failures
FAILURE in test_databaseReport: Error in checkEquals(names(report), c("data", "layout", "plot"), msg = "subjectReport names check: OK.") : 
  Lengths (9, 3) differ (string compare on first 3)
2 string mismatches
subjectReport names check: OK.
FAILURE in test_subjectReport: Error in checkEquals(names(report), c("data", "layout", "plot"), msg = "subjectReport names check: OK.") : 
  Lengths (9, 3) differ (string compare on first 3)
2 string mismatches
subjectReport names check: OK.

Test files with failing tests

   test_pbcmc.R 
     test_databaseReport 
     test_subjectReport 


Error in BiocGenerics:::testPackage("pbcmc") : 
  unit tests failed for package pbcmc
Execution halted

pbcmc.Rcheck/tests_x64/runTests.Rout.fail


R version 3.5.3 (2019-03-11) -- "Great Truth"
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.

> BiocGenerics:::testPackage("pbcmc")
Package 'mclust' version 5.4.3
Type 'citation("mclust")' for citing this R package in publications.

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from 'package:limma':

    plotMA

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

No methods found in package 'BiocGenerics' for request: 'unlist' when loading 'pbcmc'
Loading required namespace: breastCancerNKI
Timing stopped at: 1.36 0.03 1.39
Error in checkEquals(names(report), c("data", "layout", "plot"), msg = "subjectReport names check: OK.") : 
  Lengths (9, 3) differ (string compare on first 3)
2 string mismatches
subjectReport names check: OK.
In addition: Warning message:
Package 'pbcmc' is deprecated and will be removed from Bioconductor
  version 3.9 
No methods found in package 'BiocGenerics' for request: 'unlist' when loading 'pbcmc'
No methods found in package 'BiocGenerics' for request: 'unlist' when loading 'pbcmc'
No methods found in package 'BiocGenerics' for request: 'unlist' when loading 'pbcmc'
No methods found in package 'BiocGenerics' for request: 'unlist' when loading 'pbcmc'
Timing stopped at: 1.15 0.03 1.19
Error in checkEquals(names(report), c("data", "layout", "plot"), msg = "subjectReport names check: OK.") : 
  Lengths (9, 3) differ (string compare on first 3)
2 string mismatches
subjectReport names check: OK.


RUNIT TEST PROTOCOL -- Sat Apr 13 04:33:09 2019 
*********************************************** 
Number of test functions: 14 
Number of errors: 0 
Number of failures: 2 

 
1 Test Suite : 
pbcmc RUnit Tests - 14 test functions, 0 errors, 2 failures
FAILURE in test_databaseReport: Error in checkEquals(names(report), c("data", "layout", "plot"), msg = "subjectReport names check: OK.") : 
  Lengths (9, 3) differ (string compare on first 3)
2 string mismatches
subjectReport names check: OK.
FAILURE in test_subjectReport: Error in checkEquals(names(report), c("data", "layout", "plot"), msg = "subjectReport names check: OK.") : 
  Lengths (9, 3) differ (string compare on first 3)
2 string mismatches
subjectReport names check: OK.

Test files with failing tests

   test_pbcmc.R 
     test_databaseReport 
     test_subjectReport 


Error in BiocGenerics:::testPackage("pbcmc") : 
  unit tests failed for package pbcmc
Execution halted

Example timings

pbcmc.Rcheck/examples_i386/pbcmc-Ex.timings

nameusersystemelapsed
MolecularPermutationClassifierConstructor0.920.030.96
MolecularPermutationClassifierGenerics 0.20 0.0121.73
MolecularPermutationClassifierGetseters0.060.000.06
MolecularPermutationClassifierShow0.050.020.06
PAM50-class 2.21 0.1615.42
PAM50Classify0.070.010.08
PAM50Constructor0.890.020.91
PAM50Filtrate0.870.080.95
PAM50Permutate 0.08 0.0628.09
PAM50SubjectReport1.840.141.99
PAM50Subtype0.080.000.08

pbcmc.Rcheck/examples_x64/pbcmc-Ex.timings

nameusersystemelapsed
MolecularPermutationClassifierConstructor1.380.071.44
MolecularPermutationClassifierGenerics 0.35 0.0428.11
MolecularPermutationClassifierGetseters0.060.020.07
MolecularPermutationClassifierShow0.030.020.05
PAM50-class 3.08 0.1016.20
PAM50Classify0.060.000.06
PAM50Constructor1.140.101.24
PAM50Filtrate1.250.081.33
PAM50Permutate 0.2 0.023.5
PAM50SubjectReport2.570.042.60
PAM50Subtype0.040.020.07