gene2pathway 2.6.0
Holger Froehlich
| Snapshot Date: 2012-03-07 18:21:26 -0800 (Wed, 07 Mar 2012) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/gene2pathway | | Last Changed Rev: 59920 / Revision: 63606 | | Last Changed Date: 2011-10-31 15:59:03 -0700 (Mon, 31 Oct 2011) |
| wilson2 | Linux (openSUSE 11.4) / x86_64 | OK | [ WARNINGS ] | |
| 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 |
* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/gene2pathway.Rcheck’
* using R version 2.14.2 (2012-02-29)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 ... OK
* 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 ‘/loc/home/biocbuild/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 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 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
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 699Kb 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 was 1 warning, see
‘/loc/home/biocbuild/bbs-2.9-bioc/meat/gene2pathway.Rcheck/00check.log’
for details
* 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)