bigmemoryExtras 1.14.2
Peter M. Haverty
| Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/bigmemoryExtras | | Last Changed Rev: 113993 / Revision: 116712 | | Last Changed Date: 2016-02-24 09:05:35 -0800 (Wed, 24 Feb 2016) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ WARNINGS ] | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED... |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | WARNINGS | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings bigmemoryExtras_1.14.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/bigmemoryExtras.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* 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 ‘1.14.2’
* 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)
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 ... [1s/1s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘prove.R’ [2s/2s]
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/RtmpaOiXJw/file453c50b663b0...
---
> 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/RtmpaOiXJw/file453c50b663b0...
---
> Attaching to on-disk data:/tmp/Rtmpvp2xij/file6f6030905843...
10c19
< Attaching to on-disk data:/tmp/RtmpaOiXJw/bigmat/ds...
---
> Attaching to on-disk data:/tmp/Rtmpvp2xij/bigmat/ds...
12c21
< Attaching to on-disk data:/tmp/RtmpaOiXJw/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
29,34c38,42
< Filter, Find, Map, Position, Reduce, anyDuplicated, append,
< as.data.frame, as.vector, cbind, colnames, do.call, duplicated,
< eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply,
< lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
< pmin.int, rank, rbind, 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
44c52
< RUNIT TEST PROTOCOL -- Fri Apr 22 22:27:31 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
‘/home/biocbuild/bbs-3.2-bioc/meat/bigmemoryExtras.Rcheck/00check.log’
for details.