ChromoViz 1.10.2
Jihoon Kim
| 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/ChromoViz | | Last Changed Rev: 28381 / Revision: 30966 | | Last Changed Date: 2007-11-01 15:45:34 -0700 (Thu, 01 Nov 2007) |
| 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/ChromoViz.Rcheck'
* using R version 2.6.2 (2008-02-08)
* checking for file 'ChromoViz/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ChromoViz' version '1.10.2'
* 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 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
D:/biocbld/bbs-2.1-bioc/meat/ChromoViz.Rcheck/00check.log
for details
installing R.css in D:/biocbld/bbs-2.1-bioc/meat/ChromoViz.Rcheck
---------- Making package ChromoViz ------------
adding build stamp to DESCRIPTION
installing R files
installing data files
installing man source files
installing indices
not zipping data
installing help
>>> Building/Updating help pages for package 'ChromoViz'
Formats: text html latex example chm
cViz text html latex example chm
cViz.addAnnoNodes2SVG text html latex chm
cViz.addZeroToTheSingleDigit text html latex chm
cViz.distinctNames text html latex chm
cViz.drawChr text html latex chm
cViz.drawFeature text html latex chm
cViz.getHeightOfPolylinePoints text html latex chm
cViz.incPolylineAttrValue text html latex chm
cViz.incSVGviewBoxValue text html latex chm
cViz.incSingleAttrValue text html latex chm
cViz.incTextAttrValue text html latex chm
cViz.insertNewAttrValue text html latex chm
cViz.loadFiles text html latex chm
cViz.makeChromWrapperHtml text html latex chm
cViz.makeFrameHtml text html latex chm
cViz.makeHeaderHtml text html latex chm
cViz.mergeSVG text html latex chm
exprKnockout text html latex example chm
exprStemcell text html latex example chm
humanBand text html latex example chm
mouseBand text html latex example chm
svgControl text html latex chm
HHC5012: Error: Cannot create a temporary file in your TEMP path.
HHC4016: Warning: Cannot open "Resource Kits\Tools\;c:\Program Files\Affymetrix\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\ChromoViz.Rcheck\00_pkg_src\ChromoViz\chm\ChromoViz.chm
HHC4016: Warning: Cannot open "Resource Kits\Tools\;c:\Program Files\Affymetrix\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:
adding MD5 sums
* DONE (ChromoViz)