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BioC 2.12: CHECK report for bigmemoryExtras on petty

This page was generated on 2013-10-09 09:40:15 -0700 (Wed, 09 Oct 2013).

Package 68/671HostnameOS / ArchBUILDCHECKBUILD BIN
bigmemoryExtras 1.2.0
Peter M. Haverty
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/bigmemoryExtras
Last Changed Rev: 75263 / Revision: 81334
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 N O T   S U P P O R T E D
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: bigmemoryExtras
Version: 1.2.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch bigmemoryExtras_1.2.0.tar.gz
StartedAt: 2013-10-08 21:41:55 -0700 (Tue, 08 Oct 2013)
EndedAt: 2013-10-08 21:43:11 -0700 (Tue, 08 Oct 2013)
EllapsedTime: 76.3 seconds
RetCode: 0
Status:  OK 
CheckDir: bigmemoryExtras.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/bigmemoryExtras.Rcheck'
* using R version 3.0.1 (2013-05-16)
* 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 '1.2.0'
* 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 ... 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 ... [9s/9s] 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 sizes of PDF files under 'inst/doc' ... 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' [6s/6s]
  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/Rtmplyshhi/file7f9d50d50631.desc.rds...
< 
< Attaching to on-disk data:/private/tmp/Rtmplyshhi/file7f9d2c39d415.desc.rds...
< 
< Attaching to on-disk data:/private/tmp/Rtmplyshhi/file7f9d2c39d415.desc.rds...
< 
< Attaching to on-disk data:/private/tmp/Rtmplyshhi/file7f9d2c39d415.desc.rds...
< 
< Attaching to on-disk data:/private/tmp/Rtmplyshhi/file7f9d2c39d415.desc.rds...
< 
< Attaching to on-disk data:/private/tmp/Rtmplyshhi/bigmat/ds.desc.rds...
< 
< Attaching to on-disk data:/private/tmp/Rtmplyshhi/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 -- Tue Oct  8 21:43:03 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.
 [6s/7s] 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.

bigmemoryExtras.Rcheck/00install.out:

* 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'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (bigmemoryExtras)

bigmemoryExtras.Rcheck/bigmemoryExtras-Ex.timings:

nameusersystemelapsed
BigMatrix-class0.1820.0170.202
BigMatrix0.1520.0260.178
BigMatrixFactor-class0.1590.0150.175
BigMatrixFactor0.1440.0240.168
attachAssayDataElements0.0070.0000.007
updateAssayDataElementPaths0.0070.0000.007