bigmemoryExtras 1.14.0
Peter M. Haverty
| Snapshot Date: 2015-11-09 16:24:09 -0800 (Mon, 09 Nov 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/bigmemoryExtras | | Last Changed Rev: 109589 / Revision: 110496 | | Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | ERROR | | |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | [ WARNINGS ] | OK |  |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | ERROR | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings bigmemoryExtras_1.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/bigmemoryExtras.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.14.0’
* 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 ... [5s/6s] 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)
annotatedDataFrameFrom,BigMatrix : .local: no visible global function
definition for ‘AnnotatedDataFrame’
* 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 ... [2s/2s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘prove.R’ [4s/4s]
Comparing ‘prove.Rout’ to ‘prove.Rout.save’ ...10c10,15
< Attaching to on-disk data:/tmp/Rtmp6NkFO9/file6f05218c97b4...
---
> 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/Rtmp6NkFO9/file6f05218c97b4...
---
> Attaching to on-disk data:/tmp/Rtmpvp2xij/file6f6030905843...
14c19
< Attaching to on-disk data:/tmp/Rtmp6NkFO9/bigmat/ds...
---
> Attaching to on-disk data:/tmp/Rtmpvp2xij/bigmat/ds...
16c21
< Attaching to on-disk data:/tmp/Rtmp6NkFO9/bigmat/ds...
---
> Attaching to on-disk data:/tmp/Rtmpvp2xij/bigmat/ds...
27c32
< The following objects are masked from 'package:stats':
---
> The following object is masked from 'package:stats':
29c34
< IQR, mad, xtabs
---
> xtabs
33,38c38,42
< anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,
< do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl,
< intersect, is.unsorted, lapply, lengths, Map, mapply, match, mget,
< order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
< rbind, Reduce, 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 -- Tue Nov 10 02:30:26 2015
---
> RUNIT TEST PROTOCOL -- Fri Aug 9 09:52:34 2013
[4s/4s] OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.2-bioc/meat/bigmemoryExtras.Rcheck/00check.log’
for details.