BioC 3.4: CHECK report for bigmemoryExtras on morelia

Package: bigmemoryExtras

Version: 1.19.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings bigmemoryExtras_1.19.2.tar.gz

StartedAt: 2016-09-20 03:36:42 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 03:37:02 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 20.5 seconds

RetCode: 1

Status:  ERROR

CheckDir: bigmemoryExtras.Rcheck

Warnings: NA

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings bigmemoryExtras_1.19.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/bigmemoryExtras.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘bigmemoryExtras/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘bigmemoryExtras’ version ‘1.19.2’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘bigmemoryExtras’ can be installed ... OK
* checking installed package size ... OK
* checking package 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 loading without being on the library search path ... OK
* checking dependencies in R code ... WARNING
'::' or ':::' import not declared from: ‘biganalytics’
'library' or 'require' call not declared from: ‘biganalytics’
'library' or 'require' call to ‘biganalytics’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported object imported by a ':::' call: ‘BiocGenerics:::testPackage’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Found the following possibly unsafe calls:
File ‘bigmemoryExtras/R/collections.R’:
  unlockBinding(item, x)
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘prove.R’
 ERROR
Running the tests in ‘tests/prove.R’ failed.
Last 13 lines of output:
  ERROR in test_use_in_eset: Error in .validate_assayDataElementReplace(obj, value) : 
    object and replacement value have different dimensions
  
  Test files with failing tests
  
     test_eset.R 
       test_use_in_eset 
  
  
  Error in BiocGenerics:::testPackage("bigmemoryExtras") : 
    unit tests failed for package bigmemoryExtras
  Calls: <Anonymous> -> <Anonymous>
  Execution halted
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/bigmemoryExtras.Rcheck/00check.log’
for details.

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 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.

> require("bigmemoryExtras") || stop("unable to load bigmemoryExtras package")
Loading required package: bigmemoryExtras
Loading required package: bigmemory
Loading required package: bigmemory.sri
[1] TRUE
> bigmemoryExtras:::.test()
Attaching to on-disk data:/tmp/RtmphhO4AQ/fileaf9454fe13ba...

Attaching to on-disk data:/tmp/RtmphhO4AQ/fileaf9454fe13ba...

Attaching to on-disk data:/tmp/RtmphhO4AQ/bigmat/ds...

Attaching to on-disk data:/tmp/RtmphhO4AQ/bigmat/ds...

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, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, 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, 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")'.

Timing stopped at: 0.046 0 0.046 
Error in .validate_assayDataElementReplace(obj, value) : 
  object and replacement value have different dimensions
In addition: Warning message:
In attach.resource(obj, ...) :
  big.matrix object could only be opened read-only.


RUNIT TEST PROTOCOL -- Tue Sep 20 03:37:01 2016 
*********************************************** 
Number of test functions: 15 
Number of errors: 1 
Number of failures: 0 

 
1 Test Suite : 
bigmemoryExtras RUnit Tests - 15 test functions, 1 error, 0 failures
ERROR in test_use_in_eset: Error in .validate_assayDataElementReplace(obj, value) : 
  object and replacement value have different dimensions

Test files with failing tests

   test_eset.R 
     test_use_in_eset 


Error in BiocGenerics:::testPackage("bigmemoryExtras") : 
  unit tests failed for package bigmemoryExtras
Calls: <Anonymous> -> <Anonymous>
Execution halted

* installing *source* package ‘bigmemoryExtras’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for ‘apply’ from package ‘base’ in package ‘bigmemoryExtras’
Creating a generic function for ‘levels’ from package ‘base’ in package ‘bigmemoryExtras’
Creating a generic function for ‘nlevels’ from package ‘base’ in package ‘bigmemoryExtras’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (bigmemoryExtras)

name	user	system	elapsed
BigMatrix-class	0.046	0.002	0.098
BigMatrix	0.035	0.001	0.036
BigMatrixFactor-class	0.035	0.001	0.036
BigMatrixFactor	0.036	0.001	0.037
updateBackingfiles	0.001	0.000	0.000