Back to the "Multiple platform build/check report"

IMPORTANT NOTE: R was configured with --enable-strict-barrier on lamb1
Package 77/247HostnameOSArchBUILDCHECKBUILD BIN

flowUtils

0.2.7

Florian Hahne
Last 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: /loc/biocbuild/bbs-2.1-bioc/R/bin/R CMD check flowUtils_0.2.7.tar.gz
RetCode: 1
Time: 100.7 seconds
Status: ERROR
CheckDir: flowUtils.Rcheck
Warnings: NA

Command output

* checking for working latex ... OK
* using log directory '/extra/loc/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)