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IMPORTANT NOTE: R was configured with --enable-strict-barrier on lamb1 |
Package 77/247 | Hostname | OS | Arch | BUILD | CHECK | BUILD BIN |
flowUtils0.2.7Florian HahneLast Changed Date: 2007-07-19 14:20:23 -0700 Last Changed Rev: 25895 | lamb1 | Linux (SUSE 10.1) | x86_64 | OK | [ ERROR ] | |
wellington | Linux (SUSE 9.2) | i686 | OK | ERROR | ||
liverpool | Windows Server 2003 R2 (32-bit) | x64 | OK | ERROR | OK | |
pitt | Mac OS X (10.4.10) | i386 | OK | ERROR | OK |
Package: flowUtils |
Version: 0.2.7 |
Command: /home/biocbuild/bbs-2.1-bioc/R/bin/R CMD check flowUtils_0.2.7.tar.gz |
RetCode: 1 |
Time: 34.5 seconds |
Status: ERROR |
CheckDir: flowUtils.Rcheck |
Warnings: NA |
* checking for working latex ... OK * using log directory '/home/biocbuild/bbs-2.1-bioc/meat/flowUtils.Rcheck' * using R version 2.6.0 Under development (unstable) (2007-08-06 r42439) * checking for file 'flowUtils/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'flowUtils' version '0.2.7' * checking package name space information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking whether package 'flowUtils' 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 ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the name space 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 cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * creating flowUtils-Ex.R ... OK * checking examples ... ERROR Running examples in 'flowUtils-Ex.R' failed. The error most likely occurred in: > ### * read.gatingML > > flush(stderr()); flush(stdout()) > > ### Name: read.gatingML > ### Title: Function to parse xml gating file into a structured filter > ### Aliases: read.gatingML > ### Keywords: methods > > ### ** Examples > > > EGate <-read.gatingML(system.file("xml", + "EllipsoidGates.xml", package="flowUtils")) List of 10 $ EllipsoidGate:List of 5 ..$ dimension: list() .. ..- attr(*, "class")= chr [1:2] "gating_dimension" "XMLNode" ..$ dimension: list() .. ..- attr(*, "class")= chr [1:2] "gating_dimension" "XMLNode" ..$ focus :List of 2 .. ..$ coordinate: list() .. .. ..- attr(*, "class")= chr [1:2] "gating_coordinate" "XMLNode" .. ..$ coordinate: list() .. .. ..- attr(*, "class")= chr [1:2] "gating_coordinate" "XMLNode" .. ..- attr(*, "class")= chr [1:2] "gating_focus" "XMLNode" ..$ focus :List of 2 .. ..$ coordinate: list() .. .. ..- attr(*, "class")= chr [1:2] "gating_coordinate" "XMLNode" .. ..$ coordinate: list() .. .. ..- attr(*, "class")= chr [1:2] "gating_coordinate" "XMLNode" .. ..- attr(*, "class")= chr [1:2] "gating_focus" "XMLNode" ..$ distance :List of 1 .. ..$ text: list() .. .. ..- attr(*, "class")= chr [1:2] "XMLTextNode" "XMLNode" .. ..- attr(*, "class")= chr [1:2] "gating_distance" "XMLNode" ..- attr(*, "class")= chr [1:2] "gating_EllipsoidGate" "XMLNode" $ EllipsoidGate:List of 5 ..$ dimension: list() .. ..- attr(*, "class")= chr [1:2] "gating_dimension" "XMLNode" ..$ dimension: list() .. ..- attr(*, "class")= chr [1:2] "gating_dimension" "XMLNode" ..$ focus :List of 2 .. ..$ coordinate: list() .. .. ..- attr(*, "class")= chr [1:2] "gating_coordinate" "XMLNode" .. ..$ coordinate: list() .. .. ..- attr(*, "class")= chr [1:2] "gating_coordinate" "XMLNode" .. ..- attr(*, "class")= chr [1:2] "gating_focus" "XMLNode" ..$ focus :List of 2 .. ..$ coordinate: list() .. .. ..- attr(*, "class")= chr [1:2] "gating_coordinate" "XMLNode" .. ..$ coordinate: list() .. .. ..- attr(*, "class")= chr [1:2] "gating_coordinate" "XMLNode" .. ..- attr(*, "class")= chr [1:2] "gating_focus" "XMLNode" ..$ distance :List of 1 .. ..$ text: list() .. .. ..- attr(*, "class")= chr [1:2] "XMLTextNode" "XMLNode" .. ..- attr(*, "class")= chr [1:2] "gating_distance" "XMLNode" ..- attr(*, "class")= chr [1:2] "gating_EllipsoidGate" "XMLNode" $ EllipsoidGate:List of 5 ..$ dimension: list() .. ..- attr(*, "class")= chr [1:2] "gating_dimension" "XMLNode" ..$ dimension: list() .. ..- attr(*, "class")= chr [1:2] "gating_dimension" "XMLNode" ..$ focus :List of 2 .. ..$ coordinate: list() .. .. ..- attr(*, "class")= chr [1:2] "gating_coordinate" "XMLNode" .. ..$ coordinate: list() .. .. ..- attr(*, "class")= chr [1:2] "gating_coordinate" "XMLNode" .. ..- attr(*, "class")= chr [1:2] "gating_focus" "XMLNode" ..$ focus :List of 2 .. ..$ coordinate: list() .. .. ..- attr(*, "class")= chr [1:2] "gating_coordinate" "XMLNode" .. ..$ coordinate: list() .. .. ..- attr(*, "class")= chr [1:2] "gating_coordinate" "XMLNode" .. ..- attr(*, "class")= chr [1:2] "gating_focus" "XMLNode" ..$ distance :List of 1 .. ..$ text: list() .. .. ..- attr(*, "class")= chr [1:2] "XMLTextNode" "XMLNode" .. ..- attr(*, "class")= chr [1:2] "gating_distance" "XMLNode" ..- attr(*, "class")= chr [1:2] "gating_EllipsoidGate" "XMLNode" $ EllipsoidGate:List of 6 ..$ dimension: list() .. ..- attr(*, "class")= chr [1:2] "gating_dimension" "XMLNode" ..$ dimension: list() .. ..- attr(*, "class")= chr [1:2] "gating_dimension" "XMLNode" ..$ dimension: list() .. ..- attr(*, "class")= chr [1:2] "gating_dimension" "XMLNode" ..$ focus :List of 3 .. ..$ coordinate: list() .. .. ..- attr(*, "class")= chr [1:2] "gating_coordinate" "XMLNode" .. ..$ coordinate: list() .. .. ..- attr(*, "class")= chr [1:2] "gating_coordinate" "XMLNode" .. ..$ coordinate: list() .. .. ..- attr(*, "class")= chr [1:2] "gating_coordinate" "XMLNode" .. ..- attr(*, "class")= chr [1:2] "gating_focus" "XMLNode" ..$ focus :List of 3 .. ..$ coordinate: list() .. .. ..- attr(*, "class")= chr [1:2] "gating_coordinate" "XMLNode" .. ..$ coordinate: list() .. .. ..- attr(*, "class")= chr [1:2] "gating_coordinate" "XMLNode" .. ..$ coordinate: list() .. .. ..- attr(*, "class")= chr [1:2] "gating_coordinate" "XMLNode" .. ..- attr(*, "class")= chr [1:2] "gating_focus" "XMLNode" ..$ distance :List of 1 .. ..$ text: list() .. .. ..- attr(*, "class")= chr [1:2] "XMLTextNode" "XMLNode" .. ..- attr(*, "class")= chr [1:2] "gating_distance" "XMLNode" ..- attr(*, "class")= chr [1:2] "gating_EllipsoidGate" "XMLNode" $ EllipsoidGate:List of 6 ..$ dimension: list() .. ..- attr(*, "class")= chr [1:2] "gating_dimension" "XMLNode" ..$ dimension: list() .. ..- attr(*, "class")= chr [1:2] "gating_dimension" "XMLNode" ..$ dimension: list() .. ..- attr(*, "class")= chr [1:2] "gating_dimension" "XMLNode" ..$ focus :List of 3 .. ..$ coordinate: list() .. .. ..- attr(*, "class")= chr [1:2] "gating_coordinate" "XMLNode" .. ..$ coordinate: list() .. .. ..- attr(*, "class")= chr [1:2] "gating_coordinate" "XMLNode" .. ..$ coordinate: list() .. .. ..- attr(*, "class")= chr [1:2] "gating_coordinate" "XMLNode" .. ..- attr(*, "class")= chr [1:2] "gating_focus" "XMLNode" ..$ focus :List of 3 .. ..$ coordinate: list() .. .. ..- attr(*, "class")= chr [1:2] "gating_coordinate" "XMLNode" .. ..$ coordinate: list() .. .. ..- attr(*, "class")= chr [1:2] "gating_coordinate" "XMLNode" .. ..$ coordinate: list() .. .. ..- attr(*, "class")= chr [1:2] "gating_coordinate" "XMLNode" .. ..- attr(*, "class")= chr [1:2] "gating_focus" "XMLNode" ..$ distance :List of 1 .. ..$ text: list() .. .. ..- attr(*, "class")= chr [1:2] "XMLTextNode" "XMLNode" .. ..- attr(*, "class")= chr [1:2] "gating_distance" "XMLNode" ..- attr(*, "class")= chr [1:2] "gating_EllipsoidGate" "XMLNode" $ EllipsoidGate:List of 6 ..$ dimension: list() .. ..- attr(*, "class")= chr [1:2] "gating_dimension" "XMLNode" ..$ dimension: list() .. ..- attr(*, "class")= chr [1:2] "gating_dimension" "XMLNode" ..$ dimension: list() .. ..- attr(*, "class")= chr [1:2] "gating_dimension" "XMLNode" ..$ focus :List of 3 .. ..$ coordinate: list() .. .. ..- attr(*, "class")= chr [1:2] "gating_coordinate" "XMLNode" .. ..$ coordinate: list() .. .. ..- attr(*, "class")= chr [1:2] "gating_coordinate" "XMLNode" .. ..$ coordinate: list() .. .. ..- attr(*, "class")= chr [1:2] "gating_coordinate" "XMLNode" .. ..- attr(*, "class")= chr [1:2] "gating_focus" "XMLNode" ..$ focus :List of 3 .. ..$ coordinate: list() .. .. ..- attr(*, "class")= chr [1:2] "gating_coordinate" "XMLNode" .. ..$ coordinate: list() .. .. ..- attr(*, "class")= chr [1:2] "gating_coordinate" "XMLNode" .. ..$ coordinate: list() .. .. ..- attr(*, "class")= chr [1:2] "gating_coordinate" "XMLNode" .. ..- attr(*, "class")= chr [1:2] "gating_focus" "XMLNode" ..$ distance :List of 1 .. ..$ text: list() .. .. ..- attr(*, "class")= chr [1:2] "XMLTextNode" "XMLNode" .. ..- attr(*, "class")= chr [1:2] "gating_distance" "XMLNode" ..- attr(*, "class")= chr [1:2] "gating_EllipsoidGate" "XMLNode" $ EllipsoidGate:List of 5 ..$ dimension: list() .. ..- attr(*, "class")= chr [1:2] "gating_dimension" "XMLNode" ..$ dimension: list() .. ..- attr(*, "class")= chr [1:2] "gating_dimension" "XMLNode" ..$ focus :List of 2 .. ..$ coordinate: list() .. .. ..- attr(*, "class")= chr [1:2] "gating_coordinate" "XMLNode" .. ..$ coordinate: list() .. .. ..- attr(*, "class")= chr [1:2] "gating_coordinate" "XMLNode" .. ..- attr(*, "class")= chr [1:2] "gating_focus" "XMLNode" ..$ focus :List of 2 .. ..$ coordinate: list() .. .. ..- attr(*, "class")= chr [1:2] "gating_coordinate" "XMLNode" .. ..$ coordinate: list() .. .. ..- attr(*, "class")= chr [1:2] "gating_coordinate" "XMLNode" .. ..- attr(*, "class")= chr [1:2] "gating_focus" "XMLNode" ..$ distance :List of 1 .. ..$ text: list() .. .. ..- attr(*, "class")= chr [1:2] "XMLTextNode" "XMLNode" .. ..- attr(*, "class")= chr [1:2] "gating_distance" "XMLNode" ..- attr(*, "class")= chr [1:2] "gating_EllipsoidGate" "XMLNode" $ EllipsoidGate:List of 5 ..$ dimension: list() .. ..- attr(*, "class")= chr [1:2] "gating_dimension" "XMLNode" ..$ dimension: list() .. ..- attr(*, "class")= chr [1:2] "gating_dimension" "XMLNode" ..$ focus :List of 2 .. ..$ coordinate: list() .. .. ..- attr(*, "class")= chr [1:2] "gating_coordinate" "XMLNode" .. ..$ coordinate: list() .. .. ..- attr(*, "class")= chr [1:2] "gating_coordinate" "XMLNode" .. ..- attr(*, "class")= chr [1:2] "gating_focus" "XMLNode" ..$ focus :List of 2 .. ..$ coordinate: list() .. .. ..- attr(*, "class")= chr [1:2] "gating_coordinate" "XMLNode" .. ..$ coordinate: list() .. .. ..- attr(*, "class")= chr [1:2] "gating_coordinate" "XMLNode" .. ..- attr(*, "class")= chr [1:2] "gating_focus" "XMLNode" ..$ distance :List of 1 .. ..$ text: list() .. .. ..- attr(*, "class")= chr [1:2] "XMLTextNode" "XMLNode" .. ..- attr(*, "class")= chr [1:2] "gating_distance" "XMLNode" ..- attr(*, "class")= chr [1:2] "gating_EllipsoidGate" "XMLNode" $ EllipsoidGate:List of 5 ..$ dimension: list() .. ..- attr(*, "class")= chr [1:2] "gating_dimension" "XMLNode" ..$ dimension: list() .. ..- attr(*, "class")= chr [1:2] "gating_dimension" "XMLNode" ..$ focus :List of 2 .. ..$ coordinate: list() .. .. ..- attr(*, "class")= chr [1:2] "gating_coordinate" "XMLNode" .. ..$ coordinate: list() .. .. ..- attr(*, "class")= chr [1:2] "gating_coordinate" "XMLNode" .. ..- attr(*, "class")= chr [1:2] "gating_focus" "XMLNode" ..$ focus :List of 2 .. ..$ coordinate: list() .. .. ..- attr(*, "class")= chr [1:2] "gating_coordinate" "XMLNode" .. ..$ coordinate: list() .. .. ..- attr(*, "class")= chr [1:2] "gating_coordinate" "XMLNode" .. ..- attr(*, "class")= chr [1:2] "gating_focus" "XMLNode" ..$ distance :List of 1 .. ..$ text: list() .. .. ..- attr(*, "class")= chr [1:2] "XMLTextNode" "XMLNode" .. ..- attr(*, "class")= chr [1:2] "gating_distance" "XMLNode" ..- attr(*, "class")= chr [1:2] "gating_EllipsoidGate" "XMLNode" $ EllipsoidGate:List of 5 ..$ dimension: list() .. ..- attr(*, "class")= chr [1:2] "gating_dimension" "XMLNode" ..$ dimension: list() .. ..- attr(*, "class")= chr [1:2] "gating_dimension" "XMLNode" ..$ focus :List of 2 .. ..$ coordinate: list() .. .. ..- attr(*, "class")= chr [1:2] "gating_coordinate" "XMLNode" .. ..$ coordinate: list() .. .. ..- attr(*, "class")= chr [1:2] "gating_coordinate" "XMLNode" .. ..- attr(*, "class")= chr [1:2] "gating_focus" "XMLNode" ..$ focus :List of 2 .. ..$ coordinate: list() .. .. ..- attr(*, "class")= chr [1:2] "gating_coordinate" "XMLNode" .. ..$ coordinate: list() .. .. ..- attr(*, "class")= chr [1:2] "gating_coordinate" "XMLNode" .. ..- attr(*, "class")= chr [1:2] "gating_focus" "XMLNode" ..$ distance :List of 1 .. ..$ text: list() .. .. ..- attr(*, "class")= chr [1:2] "XMLTextNode" "XMLNode" .. ..- attr(*, "class")= chr [1:2] "gating_distance" "XMLNode" ..- attr(*, "class")= chr [1:2] "gating_EllipsoidGate" "XMLNode" NULL Error in FUN(X[[1L]], ...) : no slot of name "parentId" for this object of class "ellipsoidGate" Calls: read.gatingML -> lapply -> FUN Execution halted
flowUtils.Rcheck/00install.out:
* Installing *source* package 'flowUtils' ... ** R ** inst ** help >>> Building/Updating help pages for package 'flowUtils' Formats: text html latex example flowUtil-package text html latex example read.gatingML text html latex example read.transformML text html latex example ** building package indices ... * DONE (flowUtils)