biovizBase 1.7.5
Tengfei Yin
| Snapshot Date: 2013-01-15 17:01:14 -0800 (Tue, 15 Jan 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/biovizBase | | Last Changed Rev: 72531 / Revision: 72575 | | Last Changed Date: 2013-01-15 01:29:35 -0800 (Tue, 15 Jan 2013) |
| 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/biovizBase.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 ‘biovizBase/DESCRIPTION’ ... OK
* this is package ‘biovizBase’ version ‘1.7.5’
* 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 ‘biovizBase’ 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
transformToLinkInCircle: no visible binding for global variable
‘.circle.x’
transformToLinkInCircle: no visible binding for global variable
‘.circle.y’
transformToLinkInCircle : <anonymous>: no visible binding for global
variable ‘from.x’
transformToLinkInCircle : <anonymous>: no visible binding for global
variable ‘from.y’
transformToLinkInCircle : <anonymous>: no visible binding for global
variable ‘to.x’
transformToLinkInCircle : <anonymous>: no visible binding for global
variable ‘to.y’
validEven: no visible binding for global variable ‘gr’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'transformToGenome':
\S4method{transformToGenome}{GRanges}
Code: function(data, space.skip = 0.1, chr.weight = NULL)
Docs: function(data, space.skip = 0.1)
Argument names in code not in docs:
chr.weight
\S4method{transformToGenome}{GRangesList}
Code: function(data, space.skip = 0.1, chr.weight = NULL)
Docs: function(data, space.skip = 0.1)
Argument names in code not in docs:
chr.weight
transformToRectInCircle
Code: function(data, y = NULL, space.skip = 0.1, trackWidth = 10,
radius = 10, direction = c("clockwise",
"anticlockwise"), n = 100, mul = 0.05, chr.weight =
NULL)
Docs: function(data, y = NULL, space.skip = 0.1, trackWidth = 10,
radius = 10, direction = c("clockwise",
"anticlockwise"), n = 100, mul = 0.05)
Argument names in code not in docs:
chr.weight
transformToBarInCircle
Code: function(data, y = NULL, space.skip = 0.1, trackWidth = 10,
radius = 10, direction = c("clockwise",
"anticlockwise"), n = 100, mul = 0.05, chr.weight =
NULL)
Docs: function(data, y = NULL, space.skip = 0.1, trackWidth = 10,
radius = 10, direction = c("clockwise",
"anticlockwise"), n = 100, mul = 0.05)
Argument names in code not in docs:
chr.weight
transformToSegInCircle
Code: function(data, y = NULL, space.skip = 0.1, trackWidth = 10,
radius = 10, direction = c("clockwise",
"anticlockwise"), n = 100, chr.weight = NULL)
Docs: function(data, y = NULL, space.skip = 0.1, trackWidth = 10,
radius = 10, direction = c("clockwise",
"anticlockwise"), n = 100)
Argument names in code not in docs:
chr.weight
transformToLinkInCircle
Code: function(data, linked.to, space.skip = 0.1, trackWidth = 10,
radius = 10, link.fun = function(x, y, n = 100)
bezier(x, y, evaluation = n), direction =
c("clockwise", "anticlockwise"), chr.weight = NULL)
Docs: function(data, linked.to, space.skip = 0.1, trackWidth = 10,
radius = 10, link.fun = function(x, y, n = 100)
bezier(x, y, evaluation = n), direction =
c("clockwise", "anticlockwise"))
Argument names in code not in docs:
chr.weight
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... 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 was 1 warning.
NOTE: There was 1 note.
See
‘/loc/home/biocbuild/bbs-2.12-bioc/meat/biovizBase.Rcheck/00check.log’
for details.