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BioC 3.0: CHECK report for bigmemoryExtras on zin1

This page was generated on 2015-04-10 09:40:16 -0700 (Fri, 10 Apr 2015).

Package 84/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bigmemoryExtras 1.10.0
Peter M. Haverty
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/bigmemoryExtras
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED...
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: bigmemoryExtras
Version: 1.10.0
Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings bigmemoryExtras_1.10.0.tar.gz
StartedAt: 2015-04-09 21:55:42 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 21:56:14 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 32.5 seconds
RetCode: 0
Status:  OK 
CheckDir: bigmemoryExtras.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings bigmemoryExtras_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/bigmemoryExtras.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-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 ‘1.10.0’
* 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 ... [4s/4s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 ... NOTE
'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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [1s/1s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘prove.R’ [3s/3s]
  Comparing ‘prove.Rout’ to ‘prove.Rout.save’ ...10c10,15
< Attaching to on-disk data:/tmp/Rtmp2fVoSF/file76f310832659...
---
> 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...
12c17
< Attaching to on-disk data:/tmp/Rtmp2fVoSF/file76f310832659...
---
> Attaching to on-disk data:/tmp/Rtmpvp2xij/file6f6030905843...
14c19
< Attaching to on-disk data:/tmp/Rtmp2fVoSF/bigmat/ds...
---
> Attaching to on-disk data:/tmp/Rtmpvp2xij/bigmat/ds...
16c21
< Attaching to on-disk data:/tmp/Rtmp2fVoSF/bigmat/ds...
---
> Attaching to on-disk data:/tmp/Rtmpvp2xij/bigmat/ds...
33,38c38,42
<     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
<     as.data.frame, as.vector, cbind, colnames, do.call, duplicated,
<     eval, evalq, get, intersect, is.unsorted, 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, 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
48c52
< RUNIT TEST PROTOCOL -- Thu Apr  9 21:56:13 2015 
---
> RUNIT TEST PROTOCOL -- Fri Aug  9 09:52:34 2013 
 [3s/3s] OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: ‘GenomicRanges’
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

NOTE: There were 4 notes.
See
  ‘/home/biocbuild/bbs-3.0-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-class0.0680.0000.076
BigMatrix0.060.000.06
BigMatrixFactor-class0.060.000.06
BigMatrixFactor0.060.000.06
attachAssayDataElements0.0040.0000.000
updateAssayDataElementPaths0.0000.0000.001
updateBackingfiles000