ggbio 1.2.0
Tengfei Yin
| Snapshot Date: 2012-03-31 17:01:49 -0700 (Sat, 31 Mar 2012) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_10/madman/Rpacks/ggbio | | Last Changed Rev: 64678 / Revision: 64719 | | Last Changed Date: 2012-03-30 15:05:02 -0700 (Fri, 30 Mar 2012) |
| lamb2 | Linux (openSUSE 11.4) / x86_64 | OK | WARNINGS | |
| puck5 | Linux (Ubuntu 12.04) / 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/hpages/test-puck5/bbs-2.10-bioc/meat/ggbio.Rcheck'
* using R version 2.15.0 RC (2012-03-22 r58802)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ggbio/DESCRIPTION' ... OK
* this is package 'ggbio' version '1.2.0'
* 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 whether package 'ggbio' can be installed ... WARNING
Found the following significant warnings:
Warning: found methods to import for function 'as.list' but not the generic itself
Warning: found methods to import for function 'chartr' but not the generic itself
Warning: found methods to import for function 'IQR' but not the generic itself
Warning: found methods to import for function 'NROW' but not the generic itself
Warning: found methods to import for function 'aggregate' but not the generic itself
Warning: found methods to import for function 'cor' but not the generic itself
See '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/ggbio.Rcheck/00install.out' for details.
* 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
linkInter: no visible binding for global variable '.biovizBase.start'
linkInter: no visible binding for global variable '.biovizBase.x'
linkInter: no visible binding for global variable '.biovizBase.y'
linkInter : <anonymous>: no visible binding for global variable
'from.x'
linkInter : <anonymous>: no visible binding for global variable
'from.y'
linkInter : <anonymous>: no visible binding for global variable 'to.x'
linkInter : <anonymous>: no visible binding for global variable 'to.y'
plotSingleChrom: no visible binding for global variable 'x1'
plotSingleChrom: no visible binding for global variable 'x2'
plotStackedOverview: warning in getIdeogram(cytoband = cytoband):
partial argument match of 'cytoband' to 'cytobands'
* checking Rd files ... NOTE
prepare_Rd: stat_aggregate-method.Rd:91-92: Dropping empty section \examples
prepare_Rd: stat_coverage-method.Rd:64-65: Dropping empty section \examples
prepare_Rd: stat_table-method.Rd:46-47: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link(s) in documentation object '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/ggbio.Rcheck/00_pkg_src/ggbio/man/tracks.Rd':
'align.plots'
See the information in section 'Cross-references' of the 'Writing R
Extensions' manual.
* checking for missing documentation entries ... WARNING
Undocumented code objects:
'align.plots'
All user-level objects in a package should have documentation entries.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... 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 were 3 warnings.
NOTE: There were 2 notes.
See
'/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/ggbio.Rcheck/00check.log'
for details.
* installing *source* package 'ggbio' ...
** R
** inst
** preparing package for lazy loading
Warning: found methods to import for function 'as.list' but not the generic itself
Warning: found methods to import for function 'chartr' but not the generic itself
Warning: found methods to import for function 'IQR' but not the generic itself
Warning: found methods to import for function 'NROW' but not the generic itself
Warning: found methods to import for function 'aggregate' but not the generic itself
Warning: found methods to import for function 'chartr' but not the generic itself
Warning: found methods to import for function 'cor' but not the generic itself
Creating a new generic function for 'rescale' in package 'ggbio'
Warning in .simpleDuplicateClass(def, prev) :
A specification for class "characterORNULL" in package 'ggbio' seems equivalent to one from package 'IRanges' and is not turning on duplicate class definitions for this class
Creating a generic function for 'summary' from package 'base' in package 'ggbio'
Creating a generic function for 'print' from package 'base' in package 'ggbio'
Creating a new generic function for 'xlim' in package 'ggbio'
Creating a generic function for 'update' from package 'stats' in package 'ggbio'
Creating a new generic function for 'geom_rect' in package 'ggbio'
Creating a new generic function for 'geom_segment' in package 'ggbio'
Creating a new generic function for 'stat_identity' in package 'ggbio'
Warning in FUN(X[[1L]], ...) :
Created a package name, '2012-04-01 01:18:35', when none found
** help
*** installing help indices
** building package indices
** installing vignettes
'intro.Rnw'
** testing if installed package can be loaded
Warning: found methods to import for function 'as.list' but not the generic itself
Warning: found methods to import for function 'chartr' but not the generic itself
Warning: found methods to import for function 'IQR' but not the generic itself
Warning: found methods to import for function 'NROW' but not the generic itself
Warning: found methods to import for function 'aggregate' but not the generic itself
Warning: found methods to import for function 'chartr' but not the generic itself
Warning: found methods to import for function 'cor' but not the generic itself
* DONE (ggbio)