Package: gene2pathway

Version: 2.10.1

Command: rm -rf gene2pathway.buildbin-libdir && mkdir gene2pathway.buildbin-libdir && E:\biocbld\bbs-2.10-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=gene2pathway.buildbin-libdir gene2pathway_2.10.1.tar.gz >gene2pathway-install.out 2>&1 && E:\biocbld\bbs-2.10-bioc\R\bin\R.exe CMD check --library=gene2pathway.buildbin-libdir --install="check:gene2pathway-install.out" --force-multiarch --no-vignettes --timings gene2pathway_2.10.1.tar.gz && mv gene2pathway.buildbin-libdir/* gene2pathway.Rcheck/ && rmdir gene2pathway.buildbin-libdir

StartedAt: 2012-09-24 00:43:21 -0700 (Mon, 24 Sep 2012)

EndedAt: 2012-09-24 00:49:44 -0700 (Mon, 24 Sep 2012)

EllapsedTime: 383.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: gene2pathway.Rcheck

Warnings: 2

* using log directory 'E:/biocbld/bbs-2.10-bioc/meat/gene2pathway.Rcheck'
* using R version 2.15.1 (2012-06-22)
* 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 '2.10.1'
* 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-2.10-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
* loading checks for arch 'i386'
** 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 ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** 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 ... OK
** 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
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 ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                                         old_size new_size compress
  classificationModelSignalTrans_dme.rda    184Kb     26Kb       xz
  classificationModel_dme.rda               1.3Mb    351Kb       xz
* checking installed files from 'inst/doc' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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.
NOTE: There were 2 notes.
See
  'E:/biocbld/bbs-2.10-bioc/meat/gene2pathway.Rcheck/00check.log'
for details.

install for i386

* 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
** help
*** installing help indices
** building package indices
** installing vignettes
   '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
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

install for x64

* installing *source* package 'gene2pathway' ...
** 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
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
* MD5 sums
packaged installation of 'gene2pathway' as gene2pathway_2.10.1.zip

* DONE (gene2pathway)