exonmap 1.5.4
Crispin Miller
| Snapshot Date: 2008-04-09 00:13:10 -0700 (Wed, 09 Apr 2008) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/exonmap | | Last Changed Rev: 30208 / Revision: 30951 | | Last Changed Date: 2008-02-26 11:58:14 -0800 (Tue, 26 Feb 2008) |
| lamb1 | Linux (SUSE 10.1) / x86_64 | OK | WARNINGS | |
| wilson2 | Linux (openSUSE 10.3) / x86_64 | OK | WARNINGS | |
| wellington | Linux (openSUSE 10.3) / i686 | OK | WARNINGS | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | WARNINGS | OK |
| pelham | Mac OS X Leopard (10.5.1) / i386 | OK | [ WARNINGS ] | OK |
* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.2-bioc/meat/exonmap.Rcheck'
* using R version 2.7.0 beta (2008-04-07 r45159)
* using session charset: ASCII
* checking for file 'exonmap/DESCRIPTION' ... OK
* this is package 'exonmap' version '1.5.4'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'exonmap' can be installed ... 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 for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... WARNING
plot:
function(x, ...)
plot.gene:
function(gene, data, gps, scale.to.gene, type, use.symbol, use.mt,
probes.min, f, f.extra.params, col, col.range, col.f, main,
xlab, ylab, xlim, ylim, border.col, no.data.col, text.col,
text.bg, exon.borders, pad, transcript.height, show.legend)
See section 'Generic functions and methods' of the 'Writing R Extensions'
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.doStoredProcedureFetch: no visible binding for global variable
'.ExonmapConnection'
.doStoredProcedureOtherFeaturesFetch: no visible binding for global
variable '.ExonmapOtherFeaturesConnection'
.xmapDisconnect: no visible binding for global variable
'.ExonmapConnection'
.xmapOtherFeaturesDisconnect: no visible binding for global variable
'.ExonmapOtherFeaturesConnection'
exon.details: no visible binding for global variable 'a'
xmapBridge: no visible binding for global variable '.ExonmapSpecies'
* checking Rd files ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... NOTE
S3 methods shown with full name in documentation object 'plot.gene':
plot.gene
The \usage entries for S3 methods should use the \method markup and not
their full name.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking data for non-ASCII characters ... OK
* creating exonmap-Ex.R ... OK
* checking examples ... OK
* creating exonmap-manual.tex ... OK
* checking exonmap-manual.tex using pdflatex ... OK
WARNING: There was 1 warning, see
/Users/biocbuild/bbs-2.2-bioc/meat/exonmap.Rcheck/00check.log
for details
* Installing *source* package 'exonmap' ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: affy
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
Loading required package: affyio
Loading required package: preprocessCore
Loading required package: simpleaffy
Loading required package: genefilter
Loading required package: survival
Loading required package: splines
Loading required package: gcrma
Loading required package: matchprobes
Loading required package: RColorBrewer
Loading required package: RMySQL
Loading required package: DBI
Loading required package: plier
** help
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>>> Building/Updating help pages for package 'exonmap'
Formats: text html latex example
PC-class text html latex example
Splanova-class text html latex example
X.toY text html latex example
array.subset text html latex example
gene.details text html latex example
gene.legend text html latex example
gene.strip text html latex example
gene.to.exon.probeset text html latex example
group.indices text html latex example
pc text html latex example
plot.gene text html latex example
plot.gene.graph text html latex example
probeset.stats text html latex example
probesets.in.range text html latex example
read.exon text html latex example
select.probewise text html latex example
splanova text html latex example
splicing.index text html latex example
x.rma text html latex
xmapBridge text html latex example
xmapDatabase text html latex example
xmapGene text html latex example
** building package indices ...
* DONE (exonmap)