bigmemoryExtras 1.17.3
Peter M. Haverty
| Snapshot Date: 2016-04-20 17:20:35 -0700 (Wed, 20 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bigmemoryExtras | | Last Changed Rev: 116063 / Revision: 116626 | | Last Changed Date: 2016-04-09 22:41:51 -0700 (Sat, 09 Apr 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | WARNINGS | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED... |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ WARNINGS ] | 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_1.17.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/bigmemoryExtras.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* 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 ‘1.17.3’
* 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 ... [3s/3s] 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 ... [1s/1s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘prove.R’ [3s/3s]
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/Rtmpv84AXg/filea06711a8ada7...
---
> 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/Rtmpv84AXg/filea06711a8ada7...
---
> Attaching to on-disk data:/tmp/Rtmpvp2xij/file6f6030905843...
10c19
< Attaching to on-disk data:/tmp/Rtmpv84AXg/bigmat/ds...
---
> Attaching to on-disk data:/tmp/Rtmpvp2xij/bigmat/ds...
12c21
< Attaching to on-disk data:/tmp/Rtmpv84AXg/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 Apr 20 23:36:29 2016
---
> RUNIT TEST PROTOCOL -- Fri Aug 9 09:52:34 2013
[3s/3s] 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.