farms 1.11.0
Djork-Arne Clevert
| Snapshot Date: 2013-03-24 17:01:43 -0700 (Sun, 24 Mar 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/farms | | Last Changed Rev: 70052 / Revision: 74774 | | Last Changed Date: 2012-10-01 15:43:56 -0700 (Mon, 01 Oct 2012) |
| george2 | Linux (Ubuntu 12.04.1 LTS) / x86_64 | OK | OK | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | [ OK ] | OK |
| petty | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/farms.Rcheck'
* using R version 3.0.0 beta (2013-03-19 r62328)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'farms/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'farms' version '1.11.0'
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'farms' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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
File 'farms/R/zzz.R':
.onLoad calls:
require("methods", quietly = TRUE)
packageStartupMessage(" _ ", "\n", "| | ", "\n", "| | __, ,_ _ _ _ , ", "\n", "|/ / | / | / |/ |/ | / \\_", "\n", "|__/\\_/|_/ |_/ | | |_/ \\/ ", "\n", "|\\ ", "\n", "|/ ", "\n")
require(utils)
require(Biobase, quietly = TRUE)
require(affy, quietly = TRUE)
packageStartupMessage("Citation: S. Hochreiter et al.,", "\n", "A new summarization method for affymetrix probe level data,", "\n", "Bioinformatics, 22, 8, 943-949, 2006", "\n", "\n", "Citation: W. Talloen et al.,", "\n", "I/NI-calls for the exclusion of non-informative genes: a highly effective filtering tool for microarray data,", "\n", "Bioinformatics, 23, 21, 2897-2902, 2007", "\n", "BibTex: enter 'toBibtex(citation(\"farms\"))'", "\n\n", "Homepage: http://www.bioinf.jku.at/software/farms/farms.html", "\n\n", "FARMS Package Version ", version, "\n")
packageStartupMessage("\n", "Changes in FARMS:", "\n", "For all changes previous to 1.3.0, see the farms vignette.", "\n", "Version 1.3.0: Added I/NI-calls for filtering", "\n", " Adjusted Hyperparameters for alternative CDFs,", "\n", " probes set standardized, weighted mean", "\n", " Works now with R >= 2.8 and Bioconductor 2.3,", "\n", " Changed termination criterion, initialization values,", "\n", " factors and loadings scaled, added argument robust", "\n", " Update for R-2.11", "\n", " Updated I/NI-Call for Laplace-FARMS version,", "\n", " Maximum likelihood correlation structure given", "\n", " non-negative constraints", "\n", "Version 1.4.0: Default centering changed to median", "\n", "Version 1.8.x: Suppression of spurious correlation (Laplace-FARMS)", "\n")
Package startup functions should not change the search path.
See section 'Good practice' in '?.onAttach'.
* 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 ... OK
* checking installed files from 'inst/doc' ... NOTE
The following files should probably not be installed:
'bioinf.cls', 'farms_defs.sty', 'natbib.bst', 'natbib.sty'
Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking examples ...
** running examples for arch 'i386' ... [3s] OK
** running examples for arch 'x64' ... [3s] 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
'E:/biocbld/bbs-2.12-bioc/meat/farms.Rcheck/00check.log'
for details.