* using log directory 'd:/Rcompile/CRANpkg/local/2.9/caMassClass.Rcheck'
* using R version 2.9.2 Patched (2009-09-02 r49531)
* using session charset: ISO8859-1
* checking for file 'caMassClass/DESCRIPTION' ... OK
* this is package 'caMassClass' version '1.8'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'caMassClass' 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 ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd files against version 2 parser ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking examples ... ERROR
Running examples in 'caMassClass-Ex.R' failed.
The error most likely occurred in:

> ### * mzXML
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: read.mzXML & write.mzXML
> ### Title: Read and Write mzXML Files
> ### Aliases: read.mzXML write.mzXML new.mzXML
> ### Keywords: file
> 
> ### ** Examples
> 
>   directory = system.file("Test", package = "caMassClass")
>   FileName = file.path(directory,"test1.xml")
>   xml = read.mzXML(FileName)
>   xml
$header
[1] "\"mzXML xsi:schemaLocation=\"http://sashimi.sourceforge.net/schema_revision/mzXML_2.\" http://sashimi.sourceforge.net/schema_revision/mzXML_2.\"/mzXML_idx_2.\".xsd\" xmlns=\"http://sashimi.sourceforge.net/schema_revision/mzXML_2.\"\" xmlns:xsi=\"http://www.w\".org/2\"\"1/XMLSchema-instance\"\"\n"

$parentFile
[1] "    <parentFile fileName=\"file://unknown\" fileType=\"RAWData\" fileSha1=\"957f3baf650d4de3d87c04a9fc64baa13f6b363e\"/>\n    <parentFile filename='file://d:/Rcompile/CRANpkg/lib/2.9/caMassClass/Test/test1.xml' fileType='processedData' fileSha1='0563f3b02b407a13c2292d5c6d89552469408c6d'/>\n"

$dataProcessing
[1] "    <dataProcessing>\n      <software type=\"conversion\" name=\"edu.duke.cabig.rproteomics.utils.ProteomicsDataTranslator\" version=\"1\"/>\n    </dataProcessing>\n"

$scan
$scan[[1]]
$scan[[1]]$mass
 [1]  428.8388  666.1218  856.0161  956.2572  959.4442 1054.5771 1074.7927
 [8] 1089.9229 1121.0698 1124.1724 1139.9790 1146.2075 1155.8115 1159.5918
[15] 1172.8542 1181.4463 1190.8564 1193.3604 1218.6665 1229.0952 1257.6169
[22] 1361.0352 1361.7271 1389.2571 1445.6738 1717.3994 1736.9541 1852.5127
[29] 1862.7773 1900.6785

$scan[[1]]$peaks
 [1]  1199   368  2242  3430  2837   602  4585   690  3333  1574   411   590
[13]  1334  2503  1598  4289   610  3388   596  3143  1571 13764  3401  4053
[25]  3022  1583  1651  1308  2199   316

$scan[[1]]$num
[1] 1

$scan[[1]]$parentNum
[1] 1

$scan[[1]]$msLevel
[1] 1

$scan[[1]]$scanAttr
[1] " scanType=\"generic\""

$scan[[1]]$maldi
NULL

$scan[[1]]$scanOrigin
[1] "<scanOrigin parentFileID='0563f3b02b407a13c2292d5c6d89552469408c6d' num='1'/>\n"

$scan[[1]]$precursorMz
character(0)

$scan[[1]]$nameValue
NULL


$scan[[2]]
$scan[[2]]$mass
 [1]  182.6632  225.5469  247.1612  323.8478  346.5691  360.3236  478.8156
 [8]  527.1956  596.2330  717.2694  785.1747 1227.2649

$scan[[2]]$peaks
 [1]  812  525 2216 1254 1426 3880 1641 2260 3356 2181 5533 3539

$scan[[2]]$num
[1] 2

$scan[[2]]$parentNum
[1] 2

$scan[[2]]$msLevel
[1] 1

$scan[[2]]$scanAttr
[1] ""

$scan[[2]]$maldi
NULL

$scan[[2]]$scanOrigin
[1] "<scanOrigin parentFileID='0563f3b02b407a13c2292d5c6d89552469408c6d' num='2'/>\n"

$scan[[2]]$precursorMz
character(0)

$scan[[2]]$nameValue
NULL



attr(,"class")
[1] "mzXML"
>   
>   # test reading/writing
>   write.mzXML(xml, "temp.xml")
>   xml2 = read.mzXML("temp.xml")
Start tag expected, '<' not found
Error: 1: Start tag expected, '<' not found
Execution halted