segmentSeq 1.5.1
Thomas J. Hardcastle
| Snapshot Date: 2011-07-06 19:21:50 -0700 (Wed, 06 Jul 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/segmentSeq | | Last Changed Rev: 55431 / Revision: 56603 | | Last Changed Date: 2011-05-11 08:17:57 -0700 (Wed, 11 May 2011) |
| wilson2 | Linux (openSUSE 11.4) / x86_64 | OK | [ WARNINGS ] | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | WARNINGS | OK |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | WARNINGS | OK |
| moscato1 | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | WARNINGS | OK |
| pitt | Mac OS X Leopard (10.5.8) / i386 | OK | WARNINGS | OK |
* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/segmentSeq.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-06-15 r56138)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘segmentSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘segmentSeq’ version ‘1.5.1’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘segmentSeq’ 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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
plotGenome: no visible binding for global variable ‘ss’
* 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 'plotGenome':
plotGenome
Code: function(aD, sD, chr = 1, limits = c(0, 10000), samples = NULL,
plotType = "pileup", plotDuplicated = FALSE, density =
0, showNumber = TRUE, logScale = FALSE, ...)
Docs: function(aD, sD, chr = 1, limits = c(0, 10000), samples = NULL,
plotType = "chunk", plotDuplicated = FALSE, ...)
Argument names in code not in docs:
density showNumber logScale
Mismatches in argument names:
Position: 8 Code: density Docs: ...
Mismatches in argument default values:
Name: 'plotType' Code: "pileup" Docs: "chunk"
Codoc mismatches from documentation object 'processTags':
processTags
Code: function(files, dir = ".", replicates, libnames, chrs, chrlens,
cols, header = TRUE, gap = 200, verbose = TRUE, strand
= NA, ...)
Docs: function(files, dir = ".", replicates, libnames, chrs, chrlens,
cols, header = TRUE, gap = 200, verbose = TRUE, ...)
Argument names in code not in docs:
strand
Mismatches in argument names:
Position: 11 Code: strand Docs: ...
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... 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, see
‘/loc/home/biocbuild/bbs-2.9-bioc/meat/segmentSeq.Rcheck/00check.log’
for details
* installing *source* package ‘segmentSeq’ ...
** R
** inst
** preparing package for lazy loading
Attaching package: ‘baySeq’
The following object(s) are masked from ‘package:base’:
rbind
Loading required package: IRanges
Attaching package: ‘IRanges’
The following object(s) are masked from ‘package:baySeq’:
rbind
The following object(s) are masked from ‘package:base’:
Map, cbind, eval, intersect, mapply, order, paste, pmax, pmax.int,
pmin, pmin.int, rbind, rep.int, setdiff, table, union
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: lattice
Loading required package: Rsamtools
Loading required package: latticeExtra
Loading required package: RColorBrewer
Creating a new generic function for “cbind” in package “segmentSeq”
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
‘segmentSeq.Rnw’
** testing if installed package can be loaded
* DONE (segmentSeq)