exonmap 1.4.3
Crispin Miller
| Snapshot Date: 2008-04-09 12:13:20 -0700 (Wed, 09 Apr 2008) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_1/madman/Rpacks/exonmap | | Last Changed Rev: 30144 / Revision: 30966 | | Last Changed Date: 2008-02-25 02:35:34 -0800 (Mon, 25 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 |
| lemming | Windows Server 2003 (32-bit) / x64 | OK | [ WARNINGS ] | OK |
| pitt | Mac OS X Tiger (10.4.11) / i386 | OK | WARNINGS | OK |
* checking for working latex ... OK
* using log directory 'D:/biocbld/bbs-2.1-bioc/meat/exonmap.Rcheck'
* using R version 2.6.2 (2008-02-08)
* checking for file 'exonmap/DESCRIPTION' ... OK
* this is package 'exonmap' version '1.4.3'
* 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 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 ... OK
WARNING: There was 1 warning, see
D:/biocbld/bbs-2.1-bioc/meat/exonmap.Rcheck/00check.log
for details
installing R.css in D:/biocbld/bbs-2.1-bioc/meat/exonmap.Rcheck
---------- Making package exonmap ------------
adding build stamp to DESCRIPTION
installing R files
installing inst files
installing data files
installing man source files
installing indices
not zipping data
installing help
>>> Building/Updating help pages for package 'exonmap'
Formats: text html latex example chm
PC-class text html latex example chm
Splanova-class text html latex example chm
X.toY text html latex example chm
array.subset text html latex example chm
gene.details text html latex example chm
gene.legend text html latex example chm
gene.strip text html latex example chm
gene.to.exon.probeset text html latex example chm
group.indices text html latex example chm
pc text html latex example chm
plot.gene text html latex example chm
plot.gene.graph text html latex example chm
probeset.stats text html latex example chm
probesets.in.range text html latex example chm
read.exon text html latex example chm
select.probewise text html latex example chm
splanova text html latex example chm
splicing.index text html latex example chm
x.rma text html latex chm
xmapBridge text html latex example chm
xmapDatabase text html latex example chm
xmapGene text html latex example chm
HHC5012: Error: Cannot create a temporary file in your TEMP path.
HHC4016: Warning: Cannot open "etrix\GDAC NetAffx;c:\gs\gs8.51\bin;c:\Program Files\Java\jdk1.5.0_06\bin;c:\program files\imagemagick-6.3.2-q16;c:\Program Files\MySQL\MySQL Server 5.0\bin;c:\Program Files\ggobi".
Microsoft HTML Help Compiler 4.74.8702
Compiling d:\biocbld\bbs-2.1-bioc\meat\exonmap.Rcheck\00_pkg_src\exonmap\chm\exonmap.chm
HHC4016: Warning: Cannot open "etrix\GDAC NetAffx;c:\gs\gs8.51\bin;c:\Program Files\Java\jdk1.5.0_06\bin;c:\program files\imagemagick-6.3.2-q16;c:\Program Files\MySQL\MySQL Server 5.0\bin;c:\Program Files\ggobi".
The following files were not compiled:
preparing package exonmap 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
adding MD5 sums
* DONE (exonmap)