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Package 176/553HostnameOS / ArchBUILDCHECKBUILD BIN
farms 1.8.2
Djork-Arne Clevert
Snapshot Date: 2012-09-23 17:01:39 -0700 (Sun, 23 Sep 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_10/madman/Rpacks/farms
Last Changed Rev: 65210 / Revision: 69725
Last Changed Date: 2012-04-17 05:38:44 -0700 (Tue, 17 Apr 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 Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: farms
Version: 1.8.2
Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch farms_1.8.2.tar.gz
StartedAt: 2012-09-24 00:03:00 -0700 (Mon, 24 Sep 2012)
EndedAt: 2012-09-24 00:03:55 -0700 (Mon, 24 Sep 2012)
EllapsedTime: 54.7 seconds
RetCode: 0
Status:  OK 
CheckDir: farms.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.10-bioc/meat/farms.Rcheck'
* using R version 2.15.1 (2012-06-22)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'farms/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'farms' version '1.8.2'
* 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 'farms' 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 'farms/R/zzz.R':
  .onLoad calls:
    require("methods", quietly = TRUE)
    require(utils)
    require(Biobase, quietly = TRUE)
    require(affy, quietly = TRUE)

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 sizes of PDF files under 'inst/doc' ... 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 ... 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/farms.Rcheck/00check.log'
for details.

farms.Rcheck/00install.out:

* installing *source* package 'farms' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'farms.Rnw' 
** testing if installed package can be loaded

* DONE (farms)

farms.Rcheck/farms-Ex.timings:

nameusersystemelapsed
INI_Calls-class0.2170.0070.224
INIcalls-methods0.0810.0040.085
expFarms0.0500.0010.050
generateExprVal.method.farms0.0060.0010.035
getI_Eset-methods0.0770.0020.079
getI_ProbeSets-methods0.0770.0020.080
getNI_Eset-methods0.0770.0020.079
getNI_ProbeSets-methods0.0880.0030.117
lFarms0.0630.0020.065
plot-methods0.0880.0020.091
qFarms0.1000.0010.100
summary-methods0.0840.0040.087