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Package 188/516HostnameOS / ArchBUILDCHECKBUILD BIN
gene2pathway 2.6.0
Holger Froehlich
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/gene2pathway
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: gene2pathway
Version: 2.6.0
Command: E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch gene2pathway_2.6.0.tar.gz
StartedAt: 2012-01-09 03:14:39 -0800 (Mon, 09 Jan 2012)
EndedAt: 2012-01-09 03:21:10 -0800 (Mon, 09 Jan 2012)
EllapsedTime: 391.5 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: gene2pathway.Rcheck
Warnings: 2

Command output

* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/gene2pathway.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 'gene2pathway/DESCRIPTION' ... OK
* this is package 'gene2pathway' version '2.6.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'doMC'
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package 'gene2pathway' can be installed ... WARNING
Found the following significant warnings:
  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'
See 'E:/biocbld/bbs-2.9-bioc/meat/gene2pathway.Rcheck/00install.out' for details.
* 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 'gene2pathway/R/zzz.R':
  .onLoad has wrong argument list 'lib, pkgname, where'

Package startup functions should have two arguments with names starting
  with 'lib' and 'pkg', respectively.
See section 'Good practice' in ?.onAttach.

gene2pathway: no visible global function definition for 'registerDoMC'
gene2pathway: no visible global function definition for '%dopar%'
gene2pathway: no visible global function definition for 'foreach'
gene2pathway: no visible binding for global variable 'g'
gene2pathway: no visible binding for global variable 'p'
gene2pathway.signaltrans: no visible global function definition for
  'registerDoMC'
gene2pathway.signaltrans: no visible global function definition for
  '%dopar%'
gene2pathway.signaltrans: no visible global function definition for
  'foreach'
gene2pathway.signaltrans: no visible binding for global variable 'p'
getKEGGHierarchy: no visible binding for global variable 'keggOrthDF'
predict.gene2pathway : testallBag: no visible global function
  definition for '%dopar%'
predict.gene2pathway : testallBag: no visible global function
  definition for 'foreach'
predict.gene2pathway : testallBag: no visible binding for global
  variable 'm'
predict.gene2pathway: no visible global function definition for
  'registerDoMC'
test.overrepresentation: no visible global function definition for
  'registerDoMC'
test.overrepresentation: no visible global function definition for
  '%dopar%'
test.overrepresentation: no visible global function definition for
  'foreach'
test.overrepresentation: no visible binding for global variable 'p'
trainallBag: no visible global function definition for 'registerDoMC'
trainallBag: no visible global function definition for '%dopar%'
trainallBag: no visible global function definition for 'foreach'
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... NOTE
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                                         old_size new_size compress
  classificationModelSignalTrans_dme.rda    440Kb    100Kb       xz
  classificationModel_dme.rda               2.5Mb    698Kb       xz
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There were 2 warnings, see
  'E:/biocbld/bbs-2.9-bioc/meat/gene2pathway.Rcheck/00check.log'
for details

gene2pathway.Rcheck/00install.out:

* installing *source* package 'gene2pathway' ...
** R
** data
** inst
** preparing package for lazy loading
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
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
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
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'gene2pathway.Rnw' using 'latin1' 
** 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 (gene2pathway)

gene2pathway.Rcheck/gene2pathway-Ex.timings:

nameusersystemelapsed
gene2pathway000
gene2pathway.signaltrans000
getComponents000
retrain000
retrain.signaltrans000
run.crossvalidation000