HD2013SGI 1.11.0
Bernd Fischer
| Snapshot Date: 2015-11-25 07:17:28 -0800 (Wed, 25 Nov 2015) | | URL: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/HD2013SGI | | Last Changed Rev: 3462 / Revision: 3504 | | Last Changed Date: 2015-10-13 13:20:35 -0700 (Tue, 13 Oct 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ OK ] | 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 HD2013SGI_1.11.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-data-experiment/meat/HD2013SGI.Rcheck’
* using R Under development (unstable) (2015-11-08 r69614)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HD2013SGI/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HD2013SGI’ version ‘1.11.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
‘RColorBrewer’ ‘gplots’ ‘geneplotter’ ‘splots’ ‘limma’ ‘vcd’ ‘LSD’
‘EBImage’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘HD2013SGI’ can be installed ... [10s/54s] OK
* checking installed package size ... NOTE
installed size is 526.8Mb
sub-directories of 1Mb or more:
data 524.1Mb
doc 1.6Mb
* 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
Packages in Depends field not imported from:
‘EBImage’ ‘LSD’ ‘RColorBrewer’ ‘geneplotter’ ‘gplots’ ‘limma’
‘splots’ ‘vcd’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘humanReadableNames’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
HD2013SGIHeatmapHuman: no visible global function definition for ‘unit’
HD2013SGIHeatmapHuman: no visible global function definition for
‘pushViewport’
HD2013SGIHeatmapHuman: no visible global function definition for
‘viewport’
HD2013SGIHeatmapHuman: no visible global function definition for
‘grid.layout’
HD2013SGIHeatmapHuman: no visible global function definition for
‘grid.rect’
HD2013SGIHeatmapHuman: no visible global function definition for
‘grid.raster’
HD2013SGIHeatmapHuman: no visible global function definition for
‘popViewport’
HD2013SGIHeatmapHuman: no visible global function definition for
‘grid.text’
HD2013SGIHeatmapHuman: no visible global function definition for ‘gpar’
Undefined global functions or variables:
gpar grid.layout grid.raster grid.rect grid.text popViewport
pushViewport unit viewport
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [60s/80s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
featuresPerWell 43.622 0.882 61.222
datamatrixfull 10.183 0.278 12.611
* checking for unstated dependencies in vignettes ... OK
* 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
Status: 4 NOTEs
See
‘/Users/biocbuild/bbs-3.3-data-experiment/meat/HD2013SGI.Rcheck/00check.log’
for details.