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CHECK report for pbcmc on merida2

This page was generated on 2018-10-17 08:56:28 -0400 (Wed, 17 Oct 2018).

Package 1068/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pbcmc 1.8.0
Cristobal Fresno
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/pbcmc
Branch: RELEASE_3_7
Last Commit: 0920caf
Last Changed Date: 2018-04-30 10:35:41 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  ERROR 
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  ERROR  OK 
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ ERROR ] OK 

Summary

Package: pbcmc
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:pbcmc.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings pbcmc_1.8.0.tar.gz
StartedAt: 2018-10-16 23:09:12 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 23:12:24 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 192.4 seconds
RetCode: 1
Status:  ERROR 
CheckDir: pbcmc.Rcheck
Warnings: NA

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:pbcmc.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings pbcmc_1.8.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/pbcmc.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pbcmc/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pbcmc’ version ‘1.8.0’
* 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 ‘pbcmc’ 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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: 1 ERROR
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/pbcmc.Rcheck/00check.log’
for details.


Installation output

pbcmc.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL pbcmc
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* 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
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in package ‘BiocGenerics’ for request: ‘unlist’ when loading ‘pbcmc’
* DONE (pbcmc)

Tests output

pbcmc.Rcheck/tests/runTests.Rout.fail


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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.

> BiocGenerics:::testPackage("pbcmc")
Package 'mclust' version 5.4.1
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: 2.129 0.082 2.24
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.
Timing stopped at: 1.885 0.181 2.09
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 -- Tue Oct 16 23:12:17 2018 
*********************************************** 
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/pbcmc-Ex.timings

nameusersystemelapsed
MolecularPermutationClassifierConstructor1.0810.0601.178
MolecularPermutationClassifierGenerics0.9450.5940.824
MolecularPermutationClassifierGetseters0.0790.0100.089
MolecularPermutationClassifierShow0.0510.0060.057
PAM50-class4.0210.6794.171
PAM50Classify0.0830.0070.091
PAM50Constructor1.0810.1321.229
PAM50Filtrate1.0320.0881.135
PAM50Permutate0.8310.5650.697
PAM50SubjectReport3.7790.2224.038
PAM50Subtype0.0790.0070.086