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BioC 3.5: CHECK report for MultiDataSet on oaxaca

This page was generated on 2017-03-04 16:52:21 -0500 (Sat, 04 Mar 2017).

Package 837/1339HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MultiDataSet 1.3.2
Carlos Ruiz-Arenas
Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MultiDataSet
Last Changed Rev: 126272 / Revision: 127142
Last Changed Date: 2017-01-27 11:07:07 -0500 (Fri, 27 Jan 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  ERROR 
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  ERROR  OK 
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  ERROR  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ ERROR ] OK 

Summary

Package: MultiDataSet
Version: 1.3.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MultiDataSet_1.3.2.tar.gz
StartedAt: 2017-03-04 06:15:00 -0800 (Sat, 04 Mar 2017)
EndedAt: 2017-03-04 06:20:21 -0800 (Sat, 04 Mar 2017)
EllapsedTime: 320.6 seconds
RetCode: 1
Status:  ERROR 
CheckDir: MultiDataSet.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MultiDataSet_1.3.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/MultiDataSet.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MultiDataSet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MultiDataSet’ version ‘1.3.2’
* 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 ‘MultiDataSet’ 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘MultiDataSet-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getMs
> ### Title: Transforms beta values to M-values
> ### Aliases: getMs
> 
> ### ** Examples
> 
> if (require(minfiData)){
+ set <- prepareMethylationSet(MsetEx[1:100, ], pData(MsetEx))
+ mvalues <- getMs(set)
+ head(mvalues)
+ }
Loading required package: minfiData
Loading required package: minfi
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: DelayedArray
Loading required package: matrixStats
matrixStats v0.51.0 (2016-10-08) successfully loaded. See ?matrixStats for help.

Attaching package: ‘matrixStats’

The following object is masked from ‘package:MultiDataSet’:

    rowRanges

The following objects are masked from ‘package:Biobase’:

    anyMissing, rowMedians


Attaching package: ‘DelayedArray’

The following objects are masked from ‘package:matrixStats’:

    colMaxs, rowMaxs

The following object is masked from ‘package:base’:

    apply


Attaching package: ‘SummarizedExperiment’

The following object is masked from ‘package:matrixStats’:

    rowRanges

Loading required package: Biostrings
Loading required package: XVector

Attaching package: ‘Biostrings’

The following object is masked from ‘package:DelayedArray’:

    type

Loading required package: bumphunter
Loading required package: foreach
Loading required package: iterators
Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22
Loading required package: IlluminaHumanMethylation450kmanifest
Loading required package: IlluminaHumanMethylation450kanno.ilmn12.hg19
Error in methylationSet(betas = matrix, phenotypes = phenotypes, annotationDataFrame = annotation,  : 
  phenotypes must be a data.frame or an AnnotatedDataFrame.
Calls: prepareMethylationSet -> methylationSet
Execution halted
* 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:
         value) 
     standardGeneric("fData<-"), generic = structure("fData<-", package = "Biobase"), package = "Biobase", group = list(), valueClass = character(0), signature = c("object", 
     "value"), default = `\001NULL\001`, skeleton = (function (object, value) 
     stop("invalid call in method dispatch to 'fData<-' (no default method)", domain = NA))(object, 
         value), class = structure("standardGeneric", package = "methods")), <environment>)
  3: stop(gettextf("unable to find an inherited method for function %s for signature %s", 
         sQuote(fdef@generic), sQuote(cnames)), domain = NA)
  
  testthat results ================================================================
  OK: 122 SKIPPED: 0 FAILED: 2
  1. Error: Add other objects (@test_00createSet.R#6) 
  2. Error: MultiSet (@test_01addeSet.R#80) 
  
  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
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/MultiDataSet.Rcheck/00check.log’
for details.

testthat.Rout.fail:


R Under development (unstable) (2017-02-15 r72177) -- "Unsuffered Consequences"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.4.0 (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.

> library(testthat)
> library(MultiDataSet)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

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 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, cbind, colMeans, colSums, colnames, 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")'.

Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
> 
> test_check("MultiDataSet")
Loading required package: minfi
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: DelayedArray
Loading required package: matrixStats
matrixStats v0.51.0 (2016-10-08) successfully loaded. See ?matrixStats for help.

Attaching package: 'matrixStats'

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

    rowRanges

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

    anyMissing, rowMedians


Attaching package: 'DelayedArray'

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

    colMaxs, rowMaxs

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

    apply


Attaching package: 'SummarizedExperiment'

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

    rowRanges

Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    type

Loading required package: bumphunter
Loading required package: foreach
Loading required package: iterators
Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22
Loading required package: IlluminaHumanMethylation450kmanifest
Loading required package: IlluminaHumanMethylation450kanno.ilmn12.hg19
1. Error: Add other objects (@test_00createSet.R#6) ----------------------------
unable to find an inherited method for function 'phenoData' for signature '"MethylSet"'
1: expect_match(class(prepareMethylationSet(matrix = MsetEx)), "MethylationSet") at testthat/test_00createSet.R:6
2: stopifnot(is.character(object))
3: prepareMethylationSet(matrix = MsetEx)
4: phenoData(matrix)
5: (function (classes, fdef, mtable) 
   {
       methods <- .findInheritedMethods(classes, fdef, mtable)
       if (length(methods) == 1L) 
           return(methods[[1L]])
       else if (length(methods) == 0L) {
           cnames <- paste0("\"", vapply(classes, as.character, ""), "\"", collapse = ", ")
           stop(gettextf("unable to find an inherited method for function %s for signature %s", 
               sQuote(fdef@generic), sQuote(cnames)), domain = NA)
       }
       else stop("Internal error in finding inherited methods; didn't return a unique method", 
           domain = NA)
   })(list(structure("MethylSet", package = "minfi")), structure(function (object) 
   standardGeneric("phenoData"), generic = structure("phenoData", package = "Biobase"), package = "Biobase", group = list(), valueClass = character(0), signature = "object", default = `\001NULL\001`, skeleton = (function (object) 
   stop("invalid call in method dispatch to 'phenoData' (no default method)", domain = NA))(object), class = structure("standardGeneric", package = "methods")), 
       <environment>)
6: stop(gettextf("unable to find an inherited method for function %s for signature %s", 
       sQuote(fdef@generic), sQuote(cnames)), domain = NA)

2. Error: MultiSet (@test_01addeSet.R#80) --------------------------------------
unable to find an inherited method for function 'fData<-' for signature '"RatioSet", "data.frame"'
1: `fData<-`(`*tmp*`, value = structure(list(chromosome = c("chrY", "chrY"), position = c(9363356L, 
   21239348L), strand = c("-", "-"), Forward_Sequence = c("TATCTCTGTCTGGCGAGGAGGCAACGCACAACTGTGGTGGTTTTTGGAGTGGGTGGACCC[CG]GCCAAGACGGCCTGGGCTGACCAGAGACGGGAGGCAGAAAAAGTGGGCAGGTGGTTGCAG", 
   "CCATTGGCCCGCCCCAGTTGGCCGCAGGGACTGAGCAAGTTATGCGGTCGGGAAGACGTG[CG]TTAAAGGGCTGAAGGGGAGGGACGGAACTGACAGTCTCTGTGACAGCTCTGAGGTGGGAG"
   ), SourceSeq = c("CGGGGTCCACCCACTCCAAAAACCACCACAGTTGTGCGTTGCCTCCTCGC", "CGCACGTCTTCCCGACCGCATAACTTGCTCAGTCCCTGCGGCCAACTGGG"
   ), Random_Loci = c("", ""), Methyl27_Loci = c("", ""), genes = c("TSPY4;FAM197Y2", 
   "TTTY14"), UCSC_RefGene_Accession = c("NM_001164471;NR_001553", "NR_001543"), group = c("Body;TSS1500", 
   "TSS200"), Phantom = c("", ""), DMR = c("", ""), Enhancer = c("", ""), HMM_Island = c("Y:9973136-9976273", 
   "Y:19697854-19699393"), Regulatory_Feature_Name = c("", ""), Regulatory_Feature_Group = c("", 
   ""), DHS = c("", "")), .Names = c("chromosome", "position", "strand", "Forward_Sequence", 
   "SourceSeq", "Random_Loci", "Methyl27_Loci", "genes", "UCSC_RefGene_Accession", "group", 
   "Phantom", "DMR", "Enhancer", "HMM_Island", "Regulatory_Feature_Name", "Regulatory_Feature_Group", 
   "DHS"), row.names = c("cg00050873", "cg00212031"), class = "data.frame")) at testthat/test_01addeSet.R:80
2: (function (classes, fdef, mtable) 
   {
       methods <- .findInheritedMethods(classes, fdef, mtable)
       if (length(methods) == 1L) 
           return(methods[[1L]])
       else if (length(methods) == 0L) {
           cnames <- paste0("\"", vapply(classes, as.character, ""), "\"", collapse = ", ")
           stop(gettextf("unable to find an inherited method for function %s for signature %s", 
               sQuote(fdef@generic), sQuote(cnames)), domain = NA)
       }
       else stop("Internal error in finding inherited methods; didn't return a unique method", 
           domain = NA)
   })(list(structure("RatioSet", package = "minfi"), "data.frame"), structure(function (object, 
       value) 
   standardGeneric("fData<-"), generic = structure("fData<-", package = "Biobase"), package = "Biobase", group = list(), valueClass = character(0), signature = c("object", 
   "value"), default = `\001NULL\001`, skeleton = (function (object, value) 
   stop("invalid call in method dispatch to 'fData<-' (no default method)", domain = NA))(object, 
       value), class = structure("standardGeneric", package = "methods")), <environment>)
3: stop(gettextf("unable to find an inherited method for function %s for signature %s", 
       sQuote(fdef@generic), sQuote(cnames)), domain = NA)

testthat results ================================================================
OK: 122 SKIPPED: 0 FAILED: 2
1. Error: Add other objects (@test_00createSet.R#6) 
2. Error: MultiSet (@test_01addeSet.R#80) 

Error: testthat unit tests failed
Execution halted

MultiDataSet.Rcheck/00install.out:

* installing *source* package ‘MultiDataSet’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MultiDataSet)

MultiDataSet.Rcheck/MultiDataSet-Ex.timings:

nameusersystemelapsed
MethylationSet-class0.0020.0000.002
MultiDataSet-class0.0030.0010.003
add_eset0.2480.0230.271
add_genexp0.6300.0040.634
add_methy10.804 1.05314.636
add_rnaseq-methods0.1100.0140.124
add_rse0.3880.0200.409
add_se0.1250.0010.126
add_snps0.0570.0010.058
checkProbes-methods2.7250.0092.735
checkSamples-methods2.4730.0182.493
chrNumToChar0.0010.0000.001
commonIds0.1410.0000.141
commonSamples0.2400.0000.241