Package: ChromoViz

Version: 1.10.0

Command: /loc/biocbuild/bbs-2.1-bioc/R/bin/R CMD check ChromoViz_1.10.0.tar.gz

RetCode: 0

Time: 49.8 seconds

Status: WARNINGS

CheckDir: ChromoViz.Rcheck

Warnings: 1

* checking for working latex ... OK
* using log directory '/extra/loc/biocbuild/bbs-2.1-bioc/meat/ChromoViz.Rcheck'
* using R version 2.6.0 (2007-10-03)
* checking for file 'ChromoViz/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ChromoViz' version '1.10.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'ChromoViz' 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 ... WARNING
Warnings in file 'R/cViz.addAnnoNodes2SVG.R':
  '\:' is an unrecognized escape in a character string
  unrecognized escape removed from "xmlns\:xlink"
  '\_' is an unrecognized escape in a character string
  unrecognized escape removed from "\_"
  '\:' is an unrecognized escape in a character string
  unrecognized escape removed from "xlink\:href"
  '\#' is an unrecognized escape in a character string
  unrecognized escape removed from "\#"
  '\<' is an unrecognized escape in a character string
  '\>' is an unrecognized escape in a character string
  unrecognized escapes removed from "\<?xml version=\"1.0\" standalone=\"yes\"?\>"

Warnings in file 'R/cViz.makeChromWrapperHtml.R':
  '\;' is an unrecognized escape in a character string
  unrecognized escape removed from "<input type=\"button\" value=\"Search\" onClick=\"FindAccNum(\'Chromosome\')\;\"><br><br><br>"
  '\_' is an unrecognized escape in a character string
  unrecognized escape removed from "\_"
  '\;' is an unrecognized escape in a character string
  unrecognized escape removed from "\" unchecked onClick=\"MovetoZero(\'Chromosome\', this)\;\">"

Warnings in file 'R/cViz.mergeSVG.R':
  '\:' is an unrecognized escape in a character string
  unrecognized escape removed from "xmlns\:xlink"
* 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 ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
cViz: no visible binding for global variable 'begin'
cViz: no visible binding for global variable 'value'
cViz: no visible binding for global variable 'chrom'
cViz: no visible binding for global variable 'svgControl'
cViz.drawFeature: no visible binding for global variable 'track'
cViz.drawFeature: no visible binding for global variable 'chrom'
cViz.drawFeature: no visible binding for global variable 'value'
cViz.loadFiles: no visible binding for global variable 'track'
Found possibly global 'T' or 'F' in the following functions:
  cViz.addAnnoNodes2SVG cViz.drawChr cViz.drawFeature cViz.loadFiles
  cViz.mergeSVG
* 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 ... OK
* checking data for non-ASCII characters ... OK
* creating ChromoViz-Ex.R ... OK
* checking examples ... OK
* creating ChromoViz-manual.tex ... OK
* checking ChromoViz-manual.tex ... OK

WARNING: There was 1 warning, see
  /extra/loc/biocbuild/bbs-2.1-bioc/meat/ChromoViz.Rcheck/00check.log
for details

* Installing *source* package 'ChromoViz' ...
** R
** data
** help
 >>> Building/Updating help pages for package 'ChromoViz'
     Formats: text html latex example 
  cViz                              text    html    latex   example
  cViz.addAnnoNodes2SVG             text    html    latex
  cViz.addZeroToTheSingleDigit      text    html    latex
  cViz.distinctNames                text    html    latex
  cViz.drawChr                      text    html    latex
  cViz.drawFeature                  text    html    latex
  cViz.getHeightOfPolylinePoints    text    html    latex
  cViz.incPolylineAttrValue         text    html    latex
  cViz.incSVGviewBoxValue           text    html    latex
  cViz.incSingleAttrValue           text    html    latex
  cViz.incTextAttrValue             text    html    latex
  cViz.insertNewAttrValue           text    html    latex
  cViz.loadFiles                    text    html    latex
  cViz.makeChromWrapperHtml         text    html    latex
  cViz.makeFrameHtml                text    html    latex
  cViz.makeHeaderHtml               text    html    latex
  cViz.mergeSVG                     text    html    latex
  exprKnockout                      text    html    latex   example
  exprStemcell                      text    html    latex   example
  humanBand                         text    html    latex   example
  mouseBand                         text    html    latex   example
  svgControl                        text    html    latex
** building package indices ...
* DONE (ChromoViz)