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Package 30/514HostnameOS / ArchBUILDCHECKBUILD BIN
altcdfenvs 2.16.0
Laurent Gautier
Snapshot Date: 2012-03-23 18:21:46 -0700 (Fri, 23 Mar 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/altcdfenvs
Last Changed Rev: 59920 / Revision: 64395
Last Changed Date: 2011-10-31 15:59:03 -0700 (Mon, 31 Oct 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: altcdfenvs
Version: 2.16.0
Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch altcdfenvs_2.16.0.tar.gz
StartedAt: 2012-03-23 23:11:24 -0700 (Fri, 23 Mar 2012)
EndedAt: 2012-03-23 23:15:02 -0700 (Fri, 23 Mar 2012)
EllapsedTime: 218.2 seconds
RetCode: 0
Status:  OK 
CheckDir: altcdfenvs.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/altcdfenvs.Rcheck'
* using R version 2.14.2 (2012-02-29)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'altcdfenvs/DESCRIPTION' ... OK
* this is package 'altcdfenvs' version '2.16.0'
* 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 whether package 'altcdfenvs' 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 'altcdfenvs/R/zzz.R':
  .First.lib has wrong argument list 'libname, pkgname, where'
  .First.lib calls:
    library(affy, pos = 3)

Package startup functions should have two arguments with names starting
  with 'lib' and 'pkg', respectively.
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 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

altcdfenvs.Rcheck/00install.out:

* installing *source* package 'altcdfenvs' ...
** R
** data
** inst
** preparing package for lazy loading
Warning in .simpleDuplicateClass(def, prev) :
  A specification for S3 class "connection" in package 'graph' seems equivalent to one from package 'IRanges' and is not turning on duplicate class definitions for this class
Warning in .simpleDuplicateClass(def, prev) :
  A specification for S3 class "file" in package 'graph' seems equivalent to one from package 'IRanges' and is not turning on duplicate class definitions for this class
NOTE: arguments in definition for validity method for class 'AffyProbesMatch' changed from (obj) to (object)
in method for 'toHypergraph' with signature '"CdfEnvAffy"': no definition for class "CdfEnvAffy"
Creating a generic function for 'plot' from package 'graphics' in package 'altcdfenvs'
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'altcdfenvs.Rnw' 
   'modify.Rnw' 
   'ngenomeschips.Rnw' 
** testing if installed package can be loaded

* DONE (altcdfenvs)

altcdfenvs.Rcheck/altcdfenvs-Ex.timings:

nameusersystemelapsed
AffyProbesMatch-class0.0020.0010.002
CdfEnvAffy-class10.310 0.09210.470
appendCdfEnvAffy0.0060.0010.008
cdfenv0.0000.0000.001
cdfenvEx0.0040.0010.004
getxy.probeseq0.0000.0000.001
index2xy000
matchAffyProbes14.792 1.29216.230
plot.CdfEnvAffy0.0000.0000.001
removeIndex27.480 0.16528.619
unique.CdfEnvAffy000
utils.FASTA0.0080.0020.009
validAffyBatch0.0000.0000.001