BioC 2.13: CHECK report for DBChIP on perceval
This page was generated on 2014-04-05 09:52:53 -0700 (Sat, 05 Apr 2014).
DBChIP 1.6.0 Kun Liang
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014) | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/DBChIP | Last Changed Rev: 81642 / Revision: 88450 | Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | |
moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | [ OK ] | OK |
Summary
Package: DBChIP |
Version: 1.6.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch DBChIP_1.6.0.tar.gz |
StartedAt: 2014-04-05 00:41:06 -0700 (Sat, 05 Apr 2014) |
EndedAt: 2014-04-05 00:44:29 -0700 (Sat, 05 Apr 2014) |
EllapsedTime: 203.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: DBChIP.Rcheck |
Warnings: 0 |
Command output
* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/DBChIP.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DBChIP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DBChIP’ version ‘1.6.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘DBChIP’ can be installed ... [16s/16s] OK
* checking installed package size ... OK
* 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 dependencies in R code ... NOTE
‘library’ or ‘require’ calls to packages already attached by Depends:
‘DESeq’ ‘edgeR’
Please remove these calls from your code.
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
test.diff.binding.edgeR: possible error in estimateTagwiseDisp(d,
prior.n = prior.n, verbose = FALSE): unused argument (prior.n =
prior.n)
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
‘DBChIP.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [22s/22s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
DBChIP 5.927 0.535 6.487
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running ‘runTests.R’ [11s/12s]
[12s/12s] OK
* 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
NOTE: There were 3 notes.
See
‘/Users/biocbuild/bbs-2.13-bioc/meat/DBChIP.Rcheck/00check.log’
for details.
DBChIP.Rcheck/00install.out:
* installing *source* package ‘DBChIP’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DBChIP)
DBChIP.Rcheck/DBChIP-Ex.timings:
name | user | system | elapsed
|
DBChIP-package | 3.911 | 0.109 | 4.024 |
|
DBChIP | 5.927 | 0.535 | 6.487 |
|
binding.site.list | 0.229 | 0.036 | 0.265 |
|
chip.data.list | 0.231 | 0.047 | 0.278 |
|
conds | 0.225 | 0.043 | 0.269 |
|
input.data.list | 0.220 | 0.032 | 0.252 |
|
load.data | 0.779 | 0.110 | 0.889 |
|
read.binding.site.list | 0.476 | 0.034 | 0.510 |
|