BioC 3.2: CHECK report for bigmemoryExtras on oaxaca

Package: bigmemoryExtras

Version: 1.14.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings bigmemoryExtras_1.14.2.tar.gz

StartedAt: 2016-04-22 22:05:33 -0700 (Fri, 22 Apr 2016)

EndedAt: 2016-04-22 22:06:16 -0700 (Fri, 22 Apr 2016)

EllapsedTime: 43.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: bigmemoryExtras.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings bigmemoryExtras_1.14.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/bigmemoryExtras.Rcheck’
* using R version 3.2.4 (2016-03-10)
* 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 ‘1.14.2’
* 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 ... [5s/6s] 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)

annotatedDataFrameFrom,BigMatrix : .local: no visible global function
  definition for ‘AnnotatedDataFrame’
* 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 ... [2s/2s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘prove.R’ [3s/4s]
  Comparing ‘prove.Rout’ to ‘prove.Rout.save’ ...3a4,7
> 
> bigmemory >= 4.0 is a major revision since 3.1.2; please see packages
> biganalytics and and bigtabulate and http://www.bigmemory.org for more information.
> 
6c10,15
< Attaching to on-disk data:/tmp/RtmpzLuYMc/filedc067cb3072d...
---
> Note: no visible binding for global variable '.xData' 
> Note: no visible binding for global variable 'object' 
> Note: no visible binding for global variable '.xData' 
> Note: no visible binding for global variable '.xData' 
> Note: no visible binding for global variable '.xData' 
> Attaching to on-disk data:/tmp/Rtmpvp2xij/file6f6030905843...
8c17
< Attaching to on-disk data:/tmp/RtmpzLuYMc/filedc067cb3072d...
---
> Attaching to on-disk data:/tmp/Rtmpvp2xij/file6f6030905843...
10c19
< Attaching to on-disk data:/tmp/RtmpzLuYMc/bigmat/ds...
---
> Attaching to on-disk data:/tmp/Rtmpvp2xij/bigmat/ds...
12c21
< Attaching to on-disk data:/tmp/RtmpzLuYMc/bigmat/ds...
---
> Attaching to on-disk data:/tmp/Rtmpvp2xij/bigmat/ds...
23c32
< The following objects are masked from 'package:stats':
---
> The following object is masked from 'package:stats':
25c34
<     IQR, mad, xtabs
---
>     xtabs
29,34c38,42
<     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
<     as.data.frame, as.vector, 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, unlist, unsplit
---
>     Filter, Find, Map, Position, Reduce, anyDuplicated, as.data.frame,
>     cbind, colnames, duplicated, eval, get, intersect, lapply, mapply,
>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
>     rbind, rep.int, rownames, sapply, setdiff, sort, table, tapply,
>     union, unique, unlist
44c52
< RUNIT TEST PROTOCOL -- Fri Apr 22 22:06:14 2016 
---
> RUNIT TEST PROTOCOL -- Fri Aug  9 09:52:34 2013 
 [4s/4s] OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/bigmemoryExtras.Rcheck/00check.log’
for details.

* 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	0.098	0.002	0.479
BigMatrix	0.069	0.001	0.071
BigMatrixFactor-class	0.065	0.001	0.067
BigMatrixFactor	0.069	0.002	0.070
attachAssayDataElements	0.000	0.000	0.001
updateAssayDataElementPaths	0.000	0.000	0.001
updateBackingfiles	0.001	0.000	0.001