BioC 2.12: CHECK report for bigmemoryExtras on pelham

Package: bigmemoryExtras

Version: 1.1.7

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch bigmemoryExtras_1.1.7.tar.gz

StartedAt: 2013-03-24 02:44:31 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 02:45:34 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 63.0 seconds

RetCode: 0

Status: OK

CheckDir: bigmemoryExtras.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/bigmemoryExtras.Rcheck'
* using R version 3.0.0 beta (2013-03-21 r62346)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'bigmemoryExtras/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'bigmemoryExtras' version '1.1.7'
* 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 ... [8s/8s] 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 for unstated 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 examples ... [3s/3s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'prove.R' [5s/5s]
  Comparing 'prove.Rout' to 'prove.Rout.save' ...3c3
< > require("bigmemoryExtras") || stop("unable to load bigmemoryExtras package")
---
> > require("BigMatrix") || stop("unable to load BigMatrix package")
5,6c5,6
< 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.
---
> bigmemory >= 4.0 is a major revision since 3.1.2; please see package
> biganalytics and http://www.bigmemory.org for more information.
9,23c9,16
< > bigmemoryExtras:::.test()
< Attaching to on-disk data:/private/tmp/Rtmppq1mwx/file17fd1a99a73a.desc.rds...
< 
< Attaching to on-disk data:/private/tmp/Rtmppq1mwx/file17fd21a16685.desc.rds...
< 
< Attaching to on-disk data:/private/tmp/Rtmppq1mwx/file17fd21a16685.desc.rds...
< 
< Attaching to on-disk data:/private/tmp/Rtmppq1mwx/file17fd21a16685.desc.rds...
< 
< Attaching to on-disk data:/private/tmp/Rtmppq1mwx/file17fd21a16685.desc.rds...
< 
< Attaching to on-disk data:/private/tmp/Rtmppq1mwx/bigmat/ds.desc.rds...
< 
< Attaching to on-disk data:/private/tmp/Rtmppq1mwx/bigmat/ds.desc.rds...
< 
---
> > BigMatrix:::.test()
> Attaching to on-disk data: /tmp/RtmpwTXGpU/file508557463e5e.desc.rds ...
> Note: no visible binding for global variable 'description' 
> Attaching to on-disk data: /tmp/RtmpwTXGpU/file50854899071f.desc.rds ...
> Attaching to on-disk data: /tmp/RtmpwTXGpU/file50854899071f.desc.rds ...
> Attaching to on-disk data: /tmp/RtmpwTXGpU/file50854899071f.desc.rds ...
> Attaching to on-disk data: /tmp/RtmpwTXGpU/file50854899071f.desc.rds ...
> Attaching to on-disk data: /tmp/RtmpwTXGpU/file50854899071f.desc.rds ...
27,33c20
< 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:stats':
---
> The following object(s) are masked from 'package:stats':
37c24
< The following objects are masked from 'package:base':
---
> The following object(s) are masked from 'package:base':
39,43c26,29
<     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
---
>     Filter, Find, Map, Position, Reduce, anyDuplicated, cbind,
>     colnames, duplicated, eval, get, intersect, lapply, mapply, mget,
>     order, paste, pmax, pmax.int, pmin, pmin.int, rbind, rep.int,
>     rownames, sapply, setdiff, table, tapply, union, unique
53c39
< RUNIT TEST PROTOCOL -- Sun Mar 24 02:45:29 2013 
---
> RUNIT TEST PROTOCOL -- Mon Sep 10 15:44:56 2012 
55c41
< Number of test functions: 11 
---
> Number of test functions: 10 
61,62c47,48
< bigmemoryExtras RUnit Tests - 11 test functions, 0 errors, 0 failures
< Number of test functions: 11 
---
> BigMatrix RUnit Tests - 10 test functions, 0 errors, 0 failures
> Number of test functions: 10 
65,67d50
< Warning message:
< In attach.resource(obj, ...) :
<   big.matrix object could only be opened read-only.
 [5s/5s] OK
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-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 'levels' from package 'base' in package 'bigmemoryExtras'
Creating a generic function for 'nlevels' from package 'base' in package 'bigmemoryExtras'
Note: no visible binding for '<<-' assignment to '.->.bm' 
Note: no visible binding for '<<-' assignment to '.->descpath' 
Note: no visible binding for '<<-' assignment to '.->.bm' 
Note: no visible binding for '<<-' assignment to '.->descpath' 
Note: no visible binding for '<<-' assignment to '.->levels' 
** help
*** installing help indices
** building package indices
** installing vignettes
   'bigmemoryExtras.Rnw' 
** testing if installed package can be loaded
* DONE (bigmemoryExtras)

name	user	system	elapsed
BigMatrix-class	0.181	0.018	0.201
BigMatrix	0.132	0.026	0.158
BigMatrixFactor-class	0.134	0.017	0.152
BigMatrixFactor	0.133	0.025	0.162
attachAssayDataElements	0.006	0.001	0.007
updateAssayDataElementPaths	0.006	0.001	0.008

Summary

Command output