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BioC 3.5: CHECK report for bigmemoryExtras on malbec2

This page was generated on 2017-10-18 14:14:51 -0400 (Wed, 18 Oct 2017).

Package 109/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bigmemoryExtras 1.22.0
Peter M. Haverty
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/bigmemoryExtras
Branch: RELEASE_3_5
Last Commit: 9767ef7
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64 ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED...
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: bigmemoryExtras
Version: 1.22.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings bigmemoryExtras_1.22.0.tar.gz
StartedAt: 2017-10-17 21:31:01 -0400 (Tue, 17 Oct 2017)
EndedAt: 2017-10-17 21:31:26 -0400 (Tue, 17 Oct 2017)
EllapsedTime: 24.4 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: bigmemoryExtras.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings bigmemoryExtras_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/bigmemoryExtras.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (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 ‘1.22.0’
* 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 ... 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 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’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘bigmemoryExtras.Rmd’
* 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.
> 
6c10,36
< Attaching to on-disk data:/tmp/RtmpbJr30m/file318b2575fb0a...
---
> 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...
> 
> Attaching to on-disk data:/tmp/Rtmpvp2xij/file6f6030905843...
> 
> Attaching to on-disk data:/tmp/Rtmpvp2xij/bigmat/ds...
> 
> Attaching to on-disk data:/tmp/Rtmpvp2xij/bigmat/ds...
> 
> 
> 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 object is masked from 'package:stats':
> 
>     xtabs
> 
> The following objects are masked from 'package:base':
8c38,42
< Attaching to on-disk data:/tmp/RtmpbJr30m/file318b2575fb0a...
---
>     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
10c44
< Attaching to on-disk data:/tmp/RtmpbJr30m/bigmat/ds...
---
> Welcome to Bioconductor
12c46,48
< Attaching to on-disk data:/tmp/RtmpbJr30m/bigmat/ds...
---
>     Vignettes contain introductory material; view with
>     'browseVignettes()'. To cite Bioconductor, see
>     'citation("Biobase")', and for packages 'citation("pkgname")'.
16c52
< RUNIT TEST PROTOCOL -- Tue Oct 17 21:31:23 2017 
---
> RUNIT TEST PROTOCOL -- Fri Aug  9 09:52:34 2013 
18c54
< Number of test functions: 14 
---
> Number of test functions: 15 
24,25c60,61
< bigmemoryExtras RUnit Tests - 14 test functions, 0 errors, 0 failures
< Number of test functions: 14 
---
> bigmemoryExtras RUnit Tests - 15 test functions, 0 errors, 0 failures
> Number of test functions: 15 
 OK
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.5-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 ‘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-class0.2720.0000.289
BigMatrix0.1880.0000.187
BigMatrixFactor-class0.0760.0000.074
BigMatrixFactor0.0480.0000.051
updateBackingfiles000