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Package 274/516HostnameOS / ArchBUILDCHECKBUILD BIN
KEGGSOAP 1.28.0
Bioconductor Package Maintainer
Snapshot Date: 2012-01-08 18:22:44 -0800 (Sun, 08 Jan 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/KEGGSOAP
Last Changed Rev: 59920 / Revision: 61898
Last Changed Date: 2011-10-31 15:59:03 -0700 (Mon, 31 Oct 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  WARNINGS 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK [ WARNINGS ] OK 
gewurz Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 

Summary

Package: KEGGSOAP
Version: 1.28.0
Command: E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch KEGGSOAP_1.28.0.tar.gz
StartedAt: 2012-01-09 03:56:27 -0800 (Mon, 09 Jan 2012)
EndedAt: 2012-01-09 03:58:56 -0800 (Mon, 09 Jan 2012)
EllapsedTime: 148.7 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: KEGGSOAP.Rcheck
Warnings: 1

Command output

* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/KEGGSOAP.Rcheck'
* using R version 2.14.1 (2011-12-22)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'KEGGSOAP/DESCRIPTION' ... OK
* this is package 'KEGGSOAP' version '1.28.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package 'KEGGSOAP' can be installed ... OK
* checking installed package size ... 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 whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... WARNING
Loading required package: methods
Error: .onLoad failed in loadNamespace() for 'KEGGSOAP', details:
  call: as(doc, "XMLInternalDocument")
  error: no method or default for coercing "XMLInternalElementNode" to "XMLInternalDocument"
Execution halted

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... 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
File 'KEGGSOAP/R/zzz.R':
  .onLoad calls:
    require("methods")

Package startup functions should not change the search path.
See section 'Good practice' in ?.onAttach.

* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... OK
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
  'E:/biocbld/bbs-2.9-bioc/meat/KEGGSOAP.Rcheck/00check.log'
for details

KEGGSOAP.Rcheck/00install.out:

* installing *source* package 'KEGGSOAP' ...
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
Note: Method with signature "PrimitiveSOAPType#list" chosen for function "resolve",
 target signature "PrimitiveSOAPType#SchemaCollection".
 "SOAPType#SchemaCollection" would also be valid
Note: Method with signature "ArrayType#list" chosen for function "resolve",
 target signature "ArrayType#SchemaCollection".
 "SimpleSequenceType#SchemaCollection" would also be valid
Warning messages:
1: Class "VirtualSOAPClass" is defined (with package slot 'SSOAP') but no metadata object found to revise subclass information---not exported?  Making a copy in package '.GlobalEnv' 
2: Class "VirtualXMLSchemaClass" is defined (with package slot 'XMLSchema') but no metadata object found to revise subclass information---not exported?  Making a copy in package '.GlobalEnv' 

* DONE (KEGGSOAP)

KEGGSOAP.Rcheck/KEGGSOAP-Ex.timings:

nameusersystemelapsed
bconv0.130.031.36
bget0.020.001.86
get.genes.by.motifs0.040.002.31
get.genes.by.organism0.000.000.53
get.genes.by.pathway0.060.002.06
get.ko.by.gene0.150.003.61
get.motifs.by.gene0.010.011.05
get.paralogs.by.gene0.060.001.16
get.pathways.by.genes0.070.002.15
getBestNeighbors0.140.002.32
list.organisms2.010.026.62
mark.pathway.by.objects0.030.001.72
search.compounds.by.name0.080.003.38
search.glycans.by.name0.140.023.50