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Package 188/514HostnameOS / ArchBUILDCHECKBUILD BIN
gene2pathway 2.6.0
Holger Froehlich
Snapshot Date: 2012-03-23 18:21:46 -0700 (Fri, 23 Mar 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/gene2pathway
Last Changed Rev: 59920 / Revision: 64395
Last Changed Date: 2011-10-31 15:59:03 -0700 (Mon, 31 Oct 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  ERROR  skipped 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 [ ERROR ] skipped  skipped 
pitt Mac OS X Leopard (10.5.8) / i386  ERROR  skipped  skipped 

Summary

Package: gene2pathway
Version: 2.6.0
Command: chmod a+r gene2pathway -R && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data gene2pathway
StartedAt: 2012-03-23 23:24:38 -0700 (Fri, 23 Mar 2012)
EndedAt: 2012-03-23 23:25:34 -0700 (Fri, 23 Mar 2012)
EllapsedTime: 55.8 seconds
RetCode: 1
Status:  ERROR  
PackageFile: None
PackageFileSize: NA

Command output

* checking for file 'gene2pathway/DESCRIPTION' ... OK
* preparing 'gene2pathway':
* checking DESCRIPTION meta-information ... OK
* installing the package to re-build vignettes
* creating vignettes ... ERROR
Loading required package: kernlab
Loading required package: biomaRt
Loading required package: KEGGSOAP
Note: Method with signature "PrimitiveSOAPType#list" chosen for function "resolve",
 target signature "PrimitiveSOAPType#SchemaCollection".
 "SOAPType#SchemaCollection" would also be valid
Warning: 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'
Warning: 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'
Note: Method with signature "ArrayType#list" chosen for function "resolve",
 target signature "ArrayType#SchemaCollection".
 "SimpleSequenceType#SchemaCollection" would also be valid
Loading required package: RBGL
Loading required package: graph
Warning in .simpleDuplicateClass(def, prev) :
  A specification for S3 class "connection" in package 'graph' seems equivalent to one from package 'SSOAP' and is not turning on duplicate class definitions for this class
Loading required package: AnnotationDbi
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.

Warning in .simpleDuplicateClass(def, prev) :
  A specification for S3 class "connection" in package 'IRanges' seems equivalent to one from package 'SSOAP' and is not turning on duplicate class definitions for this class
Warning in .simpleDuplicateClass(def, prev) :
  A specification for S3 class "file" in package 'IRanges' seems equivalent to one from package 'graph' and is not turning on duplicate class definitions for this class
Loading required package: org.Dm.eg.db
Loading required package: DBI

Loading required package: keggorthology
Loading required package: hgu95av2.db
Loading required package: org.Hs.eg.db



Error: processing vignette 'gene2pathway.Rnw' failed with diagnostics:
 chunk 4 
Error in elems[which.gene] : invalid subscript type 'list'
Execution halted