nem 2.2.1
Florian Markowetz
| Snapshot Date: 2008-04-09 12:13:20 -0700 (Wed, 09 Apr 2008) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_1/madman/Rpacks/nem | | Last Changed Rev: 27801 / Revision: 30966 | | 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 'D:/biocbld/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 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 R.css in D:/biocbld/bbs-2.1-bioc/meat/nem.Rcheck
---------- Making package nem ------------
adding build stamp to DESCRIPTION
installing R files
installing inst files
installing data files
installing man source files
installing indices
not zipping data
installing help
Note: unmatched right brace in 'nem.greedy' on or after line 41
Note: unmatched right brace in 'nem.greedy.Rd' on or after line 41
>>> Building/Updating help pages for package 'nem'
Formats: text html latex example chm
BFSlevel text html latex example chm
BoutrosRNAi2002 text html latex example chm
CONTmLL text html latex example chm
FULLmLL text html latex example chm
SCCgraph text html latex example chm
enumerate.models text html latex example chm
getDensityMatrix text html latex chm
internal text html latex chm
local.model.prior text html latex example chm
mLL text html latex example chm
moduleNetwork text html latex example chm
nem text html latex example chm
nem.cont.preprocess text html latex example chm
nem.discretize text html latex example chm
nem.greedy text html latex example chm
nemModelSelection text html latex example chm
network.AIC text html latex example chm
pairwise.posterior text html latex example chm
plot.effects text html latex example chm
plot.nem text html latex chm
prune.graph text html latex example chm
score text html latex example chm
selectEGenes text html latex example chm
subsets text html latex example chm
transitive.closure text html latex example chm
transitive.reduction text html latex example chm
triples.posterior text html latex example chm
HHC5012: Error: Cannot create a temporary file in your TEMP path.
HHC4016: Warning: Cannot open "am Files\Java\jdk1.5.0_06\bin;c:\program files\imagemagick-6.3.2-q16;c:\Program Files\MySQL\MySQL Server 5.0\bin;c:\Program Files\ggobi".
Microsoft HTML Help Compiler 4.74.8702
Compiling d:\biocbld\bbs-2.1-bioc\meat\nem.Rcheck\00_pkg_src\nem\chm\nem.chm
HHC4016: Warning: Cannot open "am Files\Java\jdk1.5.0_06\bin;c:\program files\imagemagick-6.3.2-q16;c:\Program Files\MySQL\MySQL Server 5.0\bin;c:\Program Files\ggobi".
The following files were not compiled:
preparing package nem 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
adding MD5 sums
* DONE (nem)