ontoTools 1.33.1
Vince Carey
| Snapshot Date: 2012-02-28 17:01:26 -0800 (Tue, 28 Feb 2012) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ontoTools | | Last Changed Rev: 62450 / Revision: 63265 | | Last Changed Date: 2012-02-01 10:40:39 -0800 (Wed, 01 Feb 2012) |
| lamb2 | Linux (openSUSE 11.4) / x86_64 | OK | OK | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| petty | Mac OS X Snow Leopard (10.6.7) / i386 | OK | [ OK ] | OK |
* using log directory '/Users/biocbuild/bbs-2.10-bioc/meat/ontoTools.Rcheck'
* using R Under development (unstable) (2012-02-12 r58325)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'ontoTools/DESCRIPTION' ... OK
* this is package 'ontoTools' version '1.33.1'
* 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 'ontoTools' can be installed ... OK
* 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 'ontoTools/R/zzz.R':
.onLoad calls:
require("Biobase")
Package startup functions should not change the search path.
See section 'Good practice' in ?.onAttach.
child2parentMatDense: warning in matrix(0, nr = length(nd), nc =
length(nd)): partial argument match of 'nr' to 'nrow'
child2parentMatDense: warning in matrix(0, nr = length(nd), nc =
length(nd)): partial argument match of 'nc' to 'ncol'
child2parentMatSparse: warning in assign(nd[i], i, env = mape): partial
argument match of 'env' to 'envir'
daughterMat: warning in matrix(0, nr = length(nd), nc = length(nd)):
partial argument match of 'nr' to 'nrow'
daughterMat: warning in matrix(0, nr = length(nd), nc = length(nd)):
partial argument match of 'nc' to 'ncol'
depthStruct: warning in assign(nms[i], dps[i], env = tag2depth):
partial argument match of 'env' to 'envir'
depthStruct: warning in assign(as.character(d), nms[round(dvec, 0) ==
d], env = depth2tags): partial argument match of 'env' to 'envir'
otkvEnv2namedSparse: warning in ls(env = otkvEnv): partial argument
match of 'env' to 'envir'
* checking Rd files ... NOTE
prepare_Rd: A.csr.Rd:20-22: Dropping empty section \references
prepare_Rd: GDI.Rd:32-33: Dropping empty section \value
prepare_Rd: GDI.Rd:34: Dropping empty section \references
prepare_Rd: SGDIvocab.Rd:37: Dropping empty section \references
prepare_Rd: STMA.Rd:8-9: Dropping empty section \details
prepare_Rd: STMA.Rd:10-11: Dropping empty section \value
prepare_Rd: STMA.Rd:12: Dropping empty section \references
prepare_Rd: accessMat.Rd:21-22: Dropping empty section \details
prepare_Rd: accessMat.Rd:32-33: Dropping empty section \examples
prepare_Rd: compoundGraph-class.Rd:41-42: Dropping empty section \examples
prepare_Rd: litOnto.Rd:42-44: Dropping empty section \source
prepare_Rd: litOnto.Rd:45-47: Dropping empty section \references
prepare_Rd: ooMapLL2GOMFdemo.Rd:31-33: Dropping empty section \references
prepare_Rd: rootedDAG-class.Rd:44-45: Dropping empty section \examples
prepare_Rd: taggedHierNomenclature-class.Rd:47: Dropping empty section \references
* 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 ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* 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
NOTE: There were 2 notes.
See
'/Users/biocbuild/bbs-2.10-bioc/meat/ontoTools.Rcheck/00check.log'
for details.
* installing *source* package 'ontoTools' ...
** R
** data
** inst
** preparing package for lazy loading
Warning in .simpleDuplicateClass(def, prev) :
A specification for S3 class "connection" in package 'BiocGenerics' seems equivalent to one from package 'graph' and is not turning on duplicate class definitions for this class
Warning in .simpleDuplicateClass(def, prev) :
A specification for S3 class "file" in package 'BiocGenerics' seems equivalent to one from package 'graph' and is not turning on duplicate class definitions for this class
Warning in .simpleDuplicateClass(def, prev) :
A specification for S3 class "gzfile" in package 'BiocGenerics' seems equivalent to one from package 'graph' and is not turning on duplicate class definitions for this class
Warning in .simpleDuplicateClass(def, prev) :
A specification for S3 class "url" in package 'BiocGenerics' seems equivalent to one from package 'graph' and is not turning on duplicate class definitions for this class
Warning: replacing previous import 'coerce' when loading 'SparseM'
Creating a generic function for 'grep' from package 'base' in package 'ontoTools'
** help
*** installing help indices
** building package indices
** installing vignettes
'ontoTools.Rnw'
'ontoToolsArchiving.Rnw'
'sgdiOnto.Rnw'
** testing if installed package can be loaded
Warning in .simpleDuplicateClass(def, prev) :
A specification for S3 class "connection" in package 'BiocGenerics' seems equivalent to one from package 'graph' and is not turning on duplicate class definitions for this class
Warning in .simpleDuplicateClass(def, prev) :
A specification for S3 class "file" in package 'BiocGenerics' seems equivalent to one from package 'graph' and is not turning on duplicate class definitions for this class
Warning in .simpleDuplicateClass(def, prev) :
A specification for S3 class "gzfile" in package 'BiocGenerics' seems equivalent to one from package 'graph' and is not turning on duplicate class definitions for this class
Warning in .simpleDuplicateClass(def, prev) :
A specification for S3 class "url" in package 'BiocGenerics' seems equivalent to one from package 'graph' and is not turning on duplicate class definitions for this class
Warning: replacing previous import 'coerce' when loading 'SparseM'
* DONE (ontoTools)