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Package 281/319HostnameOS / ArchBUILDCHECKBUILD BIN
simpleaffy 2.20.0
Crispin Miller
Bioconductor Changelog
Snapshot Date: 2009-10-20 11:27:33 -0700 (Tue, 20 Oct 2009)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_4/madman/Rpacks/simpleaffy
Last Changed Rev: 39013 / Revision: 42512
Last Changed Date: 2009-04-20 16:24:12 -0700 (Mon, 20 Apr 2009)
wilson1 Linux (openSUSE 11.1) / x86_64  OK [ OK ]
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
pitt Mac OS X Tiger (10.4.11) / i386  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 
Package: simpleaffy
Version: 2.20.0
Command: /home/biocbuild/bbs-2.4-bioc/R/bin/R CMD check --no-vignettes simpleaffy_2.20.0.tar.gz
StartedAt: 2009-10-20 17:56:41 -0700 (Tue, 20 Oct 2009)
EndedAt: 2009-10-20 17:58:27 -0700 (Tue, 20 Oct 2009)
EllapsedTime: 106.5 seconds
RetCode: 0
Status: OK
CheckDir: simpleaffy.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.4-bioc/meat/simpleaffy.Rcheck'
* using R version 2.9.2 (2009-08-24)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'simpleaffy/DESCRIPTION' ... OK
* this is package 'simpleaffy' version '2.20.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'simpleaffy' 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 whether the name space 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 ... OK
* checking Rd files ... OK
* checking Rd files against version 2 parser ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking data for non-ASCII characters ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $BLAS_LIBS ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

simpleaffy.Rcheck/00install.out:

* Installing *source* package 'simpleaffy' ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c simpleaffy.c -o simpleaffy.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o simpleaffy.so simpleaffy.o -L/home/biocbuild/bbs-2.4-bioc/R/lib -lR
** R
** data
** inst
** preparing package for lazy loading
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: Biostrings
Loading required package: IRanges

Attaching package: 'IRanges'


	The following object(s) are masked from package:base :

	 cbind,
	 duplicated,
	 order,
	 pmax,
	 pmax.int,
	 pmin,
	 pmin.int,
	 rank,
	 rbind,
	 rep.int,
	 sapply,
	 sort,
	 table,
	 unique 

** help
*** installing help indices
 >>> Building/Updating help pages for package 'simpleaffy'
     Formats: text html latex example 
Note: removing empty section \seealso in file 'PairComp-class.Rd'
  PairComp-class                    text    html    latex
  QCStats-class                     text    html    latex
  all.present                       text    html    latex   example
  all.present.in.group              text    html    latex   example
  bg.correct.sa                     text    html    latex   example
Note: removing empty section \details in file 'call.exprs.Rd'
  call.exprs                        text    html    latex   example
  detection.p.val                   text    html    latex   example
  get.annotation                    text    html    latex   example
Note: removing empty section \seealso in file 'get.array.indices.Rd'
  get.array.indices                 text    html    latex   example
  get.array.subset                  text    html    latex   example
  get.array.subset.affy             text    html    latex   example
  get.fold.change.and.t.test        text    html    latex   example
  hmap.colors                       text    html    latex   example
  hmap.eset                         text    html    latex   example
  hmap.pc                           text    html    latex   example
  journalpng                        text    html    latex   example
  justMAS                           text    html    latex   example
  pairwise.comparison               text    html    latex   example
  pairwise.filter                   text    html    latex   example
  plot.pairwise.comparison          text    html    latex   example
  plot.qc.stats                     text    html    latex   example
  qc                                text    html    latex   example
  qc.affy                           text    html    latex   example
Note: removing empty section \note in file 'qc.get.alpha1.Rd'
  qc.get.alpha1                     text    html    latex   example
Note: removing empty section \note in file 'qc.get.array.Rd'
  qc.get.array                      text    html    latex   example
Note: removing empty section \note in file 'qc.get.probes.Rd'
  qc.get.probes                     text    html    latex   example
Note: removing empty section \note in file 'qc.get.ratios.Rd'
  qc.get.ratios                     text    html    latex   example
Note: removing empty section \note in file 'qc.get.spikes.Rd'
  qc.get.spikes                     text    html    latex   example
Note: removing empty section \note in file 'qc.have.params.Rd'
  qc.have.params                    text    html    latex   example
Note: removing empty section \note in file 'qc.ok.Rd'
Note: removing empty section \arguments in file 'qc.ok.Rd'
  qc.ok                             text    html    latex   example
Note: removing empty section \note in file 'qc.read.file.Rd'
  qc.read.file                      text    html    latex   example
  qc.stats                          text    html    latex   example
Note: removing empty section \details in file 'read.affy.Rd'
  read.affy                         text    html    latex   example
Note: removing empty section \details in file 'read.affy.mixed.Rd'
  read.affy.mixed                   text    html    latex   example
Note: removing empty section \note in file 'setQCEnvironment.Rd'
  setQCEnvironment                  text    html    latex   example
Note: removing empty section \value in file 'simpleaffy-deprecated.Rd'
Note: removing empty section \note in file 'simpleaffy-deprecated.Rd'
  simpleaffy-deprecated             text    html    latex   example
  standard.pearson                  text    html    latex   example
  trad.scatter.plot                 text    html    latex   example
** building package indices ...
* DONE (simpleaffy)