ggtut 0.2.0
VJ Carey
| Snapshot Date: 2014-10-04 07:15:22 -0700 (Sat, 04 Oct 2014) | | URL: https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_2_14/experiment/pkgs/ggtut | | Last Changed Rev: 2799 / Revision: 3055 | | Last Changed Date: 2014-04-11 14:27:08 -0700 (Fri, 11 Apr 2014) |
| zin2 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK |
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### Running command:
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### /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings ggtut_0.2.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-2.14-data-experiment/meat/ggtut.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ggtut/DESCRIPTION’ ... OK
* this is package ‘ggtut’ version ‘0.2.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
‘GGtools’ ‘ff’ ‘GenomicRanges’ ‘snpStats’ ‘GGdata’ ‘GenomicFeatures’
‘ChIPpeakAnno’ ‘Rsamtools’ ‘cheung2010’
‘SNPlocs.Hsapiens.dbSNP.20120608’ ‘hmyriB36’
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 ‘ggtut’ can be installed ... [40s/42s] OK
* checking installed package size ... NOTE
installed size is 189.4Mb
sub-directories of 1Mb or more:
bam 15.1Mb
data 22.3Mb
ffarchives 136.9Mb
ffobjects 1.6Mb
images 12.9Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘GenomicFeatures’ ‘ChIPpeakAnno’
A package should be listed in only one of these fields.
* 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:
‘ChIPpeakAnno’ ‘GGdata’ ‘GGtools’ ‘GenomicFeatures’ ‘GenomicRanges’
‘Rsamtools’ ‘SNPlocs.Hsapiens.dbSNP.20120608’ ‘cheung2010’ ‘ff’
‘hmyriB36’ ‘snpStats’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File ‘ggtut/R/zzz.R’:
.onLoad calls:
packageStartupMessage("\n\nggtut: as of 10 Jan 2013, SNPlocs requested are hg19-based, but all serialized")
packageStartupMessage("objects have hg18 coordinates. Liftovers will be conducted soon.")
packageStartupMessage("In the mean time, this package is primarily for demonstration that the software functions.\n")
See section ‘Good practice’ in '?.onAttach'.
* 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 files in ‘vignettes’ ... OK
* checking examples ... [28s/29s] OK
* checking PDF version of manual ... OK
NOTE: There were 5 notes.
See
‘/home/biocbuild/bbs-2.14-data-experiment/meat/ggtut.Rcheck/00check.log’
for details.