GenomicFeatures 1.9.19
Bioconductor Package Maintainer
| Snapshot Date: 2012-06-20 15:22:40 -0700 (Wed, 20 Jun 2012) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicFeatures | | Last Changed Rev: 66860 / Revision: 66885 | | Last Changed Date: 2012-06-20 08:53:01 -0700 (Wed, 20 Jun 2012) |
| lamb1 | Linux (openSUSE 12.1) / x86_64 | OK | TIMEOUT | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | TIMEOUT | OK |
| pitt | Mac OS X Leopard (10.5.8) / i386 | OK | [ WARNINGS ] | OK |
| perceval | Mac OS X Leopard (10.5.8) / i386 | OK | WARNINGS | OK |
* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/GenomicFeatures.Rcheck'
* using R version 2.15.0 Patched (2012-04-26 r59216)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'GenomicFeatures/DESCRIPTION' ... OK
* this is package 'GenomicFeatures' version '1.9.19'
* 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 whether package 'GenomicFeatures' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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
.getBiomartDbVersion: no visible binding for global variable 'mart'
.getMetaDataValue: no visible global function definition for 'error'
.setseqnameStyle: no visible binding for global variable 'txdb'
.valid.FeatureDb: no visible global function definition for
'.valid.metadata.table'
.validate.colnames: no visible global function definition for
'.valid.colnames'
* checking Rd files ... OK
* checking Rd metadata ... WARNING
Rd files with duplicated alias 'exons_deprecated':
'defunct.Rd' 'regions.Rd'
Rd files with duplicated alias 'introns_deprecated':
'defunct.Rd' 'regions.Rd'
Rd files with duplicated alias 'transcripts_deprecated':
'defunct.Rd' 'regions.Rd'
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running 'GenomicFeatures_unit_tests.R'
OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' calls not declared from:
'DESeq' 'Rsamtools' 'xtable'
* 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 were 2 notes.
See
'/Users/biocbuild/bbs-2.11-bioc/meat/GenomicFeatures.Rcheck/00check.log'
for details.
* installing *source* package 'GenomicFeatures' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
'GenomicFeatures.Rnw'
'spliceGraph.Rnw'
** testing if installed package can be loaded
* DONE (GenomicFeatures)