nem 2.2.1
Florian Markowetz
| Snapshot Date: 2008-04-02 12:12:36 -0700 (Wed, 02 Apr 2008) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_1/madman/Rpacks/nem | | Last Changed Rev: 27801 / Revision: 30807 | | Last Changed Date: 2007-10-05 17:10:29 -0700 (Fri, 05 Oct 2007) |
| lamb1 | Linux (SUSE 10.1) / x86_64 | OK | OK | |
| wilson2 | Linux (openSUSE 10.3) / x86_64 | OK | [ OK ] | |
| wellington | Linux (openSUSE 10.3) / i686 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | OK |
| lemming | Windows Server 2003 (32-bit) / x64 | OK | OK | OK |
| pitt | Mac OS X Tiger (10.4.11) / i386 | OK | OK | OK |
* checking for working latex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.1-bioc/meat/nem.Rcheck'
* using R version 2.6.2 (2008-02-08)
* checking for file 'nem/DESCRIPTION' ... OK
* this is package 'nem' version '2.2.1'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'nem' can be installed ... 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 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
filterEGenes : clusterData: no visible global function definition for
'silhouette'
nem: no visible global function definition for 'RelNet'
selectEGenes: no visible binding for global variable 'a'
selectEGenes: no visible binding for global variable 'b'
Found possibly global 'T' or 'F' in the following functions:
bum.qalt qbum
* checking Rd files ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... NOTE
S3 methods shown with full name in documentation object 'moduleNetwork':
print.ModuleNetwork
S3 methods shown with full name in documentation object 'pairwise.posterior':
print.pairwise
S3 methods shown with full name in documentation object 'plot.effects':
plot.effects
S3 methods shown with full name in documentation object 'plot.nem':
plot.nem
S3 methods shown with full name in documentation object 'score':
print.score
S3 methods shown with full name in documentation object 'triples.posterior':
print.triples
The \usage entries for S3 methods should use the \method markup and not
their full name.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking data for non-ASCII characters ... OK
* creating nem-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating nem-manual.tex ... OK
* checking nem-manual.tex ... OK
* Installing *source* package 'nem' ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: e1071
Loading required package: class
Loading required package: graph
Loading required package: Rgraphviz
Loading required package: RBGL
Attaching package: 'RBGL'
The following object(s) are masked from package:e1071 :
extractPath
Loading required package: time
** help
Note: unmatched right brace in 'nem.greedy' on or after line 41
>>> Building/Updating help pages for package 'nem'
Formats: text html latex example
BFSlevel text html latex example
BoutrosRNAi2002 text html latex example
CONTmLL text html latex example
FULLmLL text html latex example
SCCgraph text html latex example
enumerate.models text html latex example
getDensityMatrix text html latex
internal text html latex
local.model.prior text html latex example
mLL text html latex example
moduleNetwork text html latex example
nem text html latex example
nem.cont.preprocess text html latex example
nem.discretize text html latex example
nem.greedy text html latex example
nemModelSelection text html latex example
network.AIC text html latex example
pairwise.posterior text html latex example
plot.effects text html latex example
plot.nem text html latex
prune.graph text html latex example
score text html latex example
selectEGenes text html latex example
subsets text html latex example
transitive.closure text html latex example
transitive.reduction text html latex example
triples.posterior text html latex example
** building package indices ...
* DONE (nem)