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BioC 3.3: CHECK report for bigmemoryExtras on oaxaca

This page was generated on 2016-10-13 12:58:39 -0700 (Thu, 13 Oct 2016).

Package 97/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bigmemoryExtras 1.18.1
Peter M. Haverty
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/bigmemoryExtras
Last Changed Rev: 117513 / Revision: 122332
Last Changed Date: 2016-05-15 13:18:19 -0700 (Sun, 15 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED...
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: bigmemoryExtras
Version: 1.18.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings bigmemoryExtras_1.18.1.tar.gz
StartedAt: 2016-10-12 23:34:27 -0700 (Wed, 12 Oct 2016)
EndedAt: 2016-10-12 23:34:57 -0700 (Wed, 12 Oct 2016)
EllapsedTime: 30.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: bigmemoryExtras.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings bigmemoryExtras_1.18.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.3-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 ‘1.18.1’
* 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’
  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/Rtmp2ILGZj/file1231c48e0ba90...
---
> 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/Rtmp2ILGZj/file1231c48e0ba90...
---
> Attaching to on-disk data:/tmp/Rtmpvp2xij/file6f6030905843...
10c19
< Attaching to on-disk data:/tmp/Rtmp2ILGZj/bigmat/ds...
---
> Attaching to on-disk data:/tmp/Rtmpvp2xij/bigmat/ds...
12c21
< Attaching to on-disk data:/tmp/Rtmp2ILGZj/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
29,31c38,39
<     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,
---
>     Filter, Find, Map, Position, Reduce, anyDuplicated, as.data.frame,
>     cbind, colnames, duplicated, eval, get, intersect, lapply, mapply,
33,34c41,42
<     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
<     unique, unsplit
---
>     rbind, rep.int, rownames, sapply, setdiff, sort, table, tapply,
>     union, unique, unlist
44c52
< RUNIT TEST PROTOCOL -- Wed Oct 12 23:34:55 2016 
---
> RUNIT TEST PROTOCOL -- Fri Aug  9 09:52:34 2013 
 OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.3-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 ‘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)

bigmemoryExtras.Rcheck/bigmemoryExtras-Ex.timings:

nameusersystemelapsed
BigMatrix-class0.0640.0031.446
BigMatrix0.0550.0020.194
BigMatrixFactor-class0.0490.0010.059
BigMatrixFactor0.0530.0020.057
updateBackingfiles000