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Package 67/233HostnameOS / ArchBUILDCHECKBUILD BIN
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 
Package: exonmap
Version: 1.4.3
Command: D:\biocbld\bbs-2.1-bioc\R\bin\R.exe CMD check exonmap_1.4.3.tar.gz
StartedAt: 2008-04-09 19:10:17 -0700 (Wed, 09 Apr 2008)
EndedAt: 2008-04-09 19:13:41 -0700 (Wed, 09 Apr 2008)
EllapsedTime: 203.4 seconds
RetCode: 0
Status: WARNINGS
CheckDir: exonmap.Rcheck
Warnings: 1

Command output

* 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

exonmap.Rcheck/00install.out:

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)