bsseq 0.7.4
Kasper Daniel Hansen
| Snapshot Date: 2013-01-15 17:01:14 -0800 (Tue, 15 Jan 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq | | Last Changed Rev: 71547 / Revision: 72575 | | Last Changed Date: 2012-11-29 07:04:40 -0800 (Thu, 29 Nov 2012) |
| george2 | Linux (Ubuntu 12.04.1 LTS) / x86_64 | OK | WARNINGS | |
| lamb2 | Linux (openSUSE 11.4) / x86_64 | OK | [ WARNINGS ] | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | WARNINGS | OK |
| petty | Mac OS X Leopard (10.5.8) / i386 | OK | WARNINGS | OK |
* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/bsseq.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘bsseq/DESCRIPTION’ ... OK
* this is package ‘bsseq’ version ‘0.7.4’
* 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 ‘bsseq’ can be installed ... 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 for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.bsPlotPoints: no visible binding for global variable ‘pointsMinCov’
.plotSmoothData: no visible binding for global variable ‘Bsseq’
plotRegion: no visible binding for global variable ‘positions’
plotRegion: no visible binding for global variable ‘plotRange’
* 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 ... WARNING
Files not of a type allowed in a ‘data’ directory:
‘CpG_context_test_data.fastq_bismark.bedGraph’
Please use e.g. ‘inst/extdata’ for non-R data files
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
BSmooth.tstat 10.581 0.78 11.832
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running ‘runTests.R’
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 vignettes ... SKIPPED
* checking PDF version of manual ... OK
WARNING: There was 1 warning.
NOTE: There was 1 note.
See
‘/loc/home/biocbuild/bbs-2.12-bioc/meat/bsseq.Rcheck/00check.log’
for details.
* installing *source* package ‘bsseq’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
‘bsseq.Rnw’
‘bsseq_analysis.Rnw’
** testing if installed package can be loaded
* DONE (bsseq)