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Package 206/233HostnameOS / ArchBUILDCHECKBUILD BIN
simpleaffy 2.14.05
Crispin Miller
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/simpleaffy
Last Changed Rev: 27980 / Revision: 30966
Last Changed Date: 2007-10-13 03:30:32 -0700 (Sat, 13 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 
Package: simpleaffy
Version: 2.14.05
Command: D:\biocbld\bbs-2.1-bioc\R\bin\R.exe CMD check simpleaffy_2.14.05.tar.gz
StartedAt: 2008-04-09 22:01:13 -0700 (Wed, 09 Apr 2008)
EndedAt: 2008-04-09 22:04:31 -0700 (Wed, 09 Apr 2008)
EllapsedTime: 198.3 seconds
RetCode: 0
Status: OK
CheckDir: simpleaffy.Rcheck
Warnings: 0

Command output

* checking for working latex ... OK
* using log directory 'D:/biocbld/bbs-2.1-bioc/meat/simpleaffy.Rcheck'
* using R version 2.6.2 (2008-02-08)
* checking for file 'simpleaffy/DESCRIPTION' ... OK
* this is package 'simpleaffy' version '2.14.05'
* 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 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 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
* creating simpleaffy-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating simpleaffy-manual.tex ... OK
* checking simpleaffy-manual.tex ... OK

simpleaffy.Rcheck/00install.out:

installing R.css in D:/biocbld/bbs-2.1-bioc/meat/simpleaffy.Rcheck


---------- Making package simpleaffy ------------
  adding build stamp to DESCRIPTION
  installing NAMESPACE file and metadata
  making DLL ...
making simpleaffy.d from simpleaffy.c
gcc-sjlj  -std=gnu99  -Id:/biocbld/bbs-2.1-bioc/R/include     -O3 -Wall  -c simpleaffy.c -o simpleaffy.o
windres --preprocessor="gcc-sjlj -E -xc -DRC_INVOKED" -I d:/biocbld/bbs-2.1-bioc/R/include  -i simpleaffy_res.rc -o simpleaffy_res.o
gcc-sjlj  -std=gnu99  -shared -s  -o simpleaffy.dll simpleaffy.def simpleaffy.o simpleaffy_res.o  -Ld:/biocbld/bbs-2.1-bioc/R/bin    -lR
  ... DLL made
  installing DLL
  installing R files
  installing inst files
  installing data files
  preparing package simpleaffy for lazy loading
Loading required package: affy
Loading required package: Biobase
Loading required package: tools

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: affyio
Loading required package: preprocessCore
Loading required package: genefilter
Loading required package: survival
Loading required package: splines
Loading required package: gcrma
Loading required package: matchprobes
  installing man source files
  installing indices
  not zipping data
  installing help
 >>> Building/Updating help pages for package 'simpleaffy'
     Formats: text html latex example chm 
  PairComp-class                    text    html    latex           chm
  QCStats-class                     text    html    latex           chm
  all.present                       text    html    latex   example chm
  all.present.in.group              text    html    latex   example chm
  bg.correct.sa                     text    html    latex   example chm
  call.exprs                        text    html    latex   example chm
  detection.p.val                   text    html    latex   example chm
  get.annotation                    text    html    latex   example chm
  get.array.indices                 text    html    latex   example chm
  get.array.subset                  text    html    latex   example chm
  get.array.subset.affy             text    html    latex   example chm
  get.fold.change.and.t.test        text    html    latex   example chm
  hmap.colors                       text    html    latex   example chm
  hmap.eset                         text    html    latex   example chm
  hmap.pc                           text    html    latex   example chm
  journalpng                        text    html    latex   example chm
  justMAS                           text    html    latex   example chm
  pairwise.comparison               text    html    latex   example chm
  pairwise.filter                   text    html    latex   example chm
  plot.pairwise.comparison          text    html    latex   example chm
  plot.qc.stats                     text    html    latex   example chm
  qc                                text    html    latex   example chm
  qc.affy                           text    html    latex   example chm
  qc.get.alpha1                     text    html    latex   example chm
  qc.get.array                      text    html    latex   example chm
  qc.get.probes                     text    html    latex   example chm
  qc.get.ratios                     text    html    latex   example chm
  qc.get.spikes                     text    html    latex   example chm
  qc.have.params                    text    html    latex   example chm
  qc.ok                             text    html    latex   example chm
  qc.read.file                      text    html    latex   example chm
  qc.stats                          text    html    latex   example chm
  read.affy                         text    html    latex   example chm
  read.affy.mixed                   text    html    latex   example chm
  setQCEnvironment                  text    html    latex   example chm
  simpleaffy-deprecated             text    html    latex   example chm
  standard.pearson                  text    html    latex   example chm
  trad.scatter.plot                 text    html    latex   example chm
HHC5012: Error: Cannot create a temporary file in your TEMP path.
HHC4016: Warning: Cannot open "es\Windows Resource Kits\Tools\;c:\Program Files\Affymetrix\GDAC NetAffx;c:\gs\gs8.51\bin;c:\Program 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\simpleaffy.Rcheck\00_pkg_src\simpleaffy\chm\simpleaffy.chm

HHC4016: Warning: Cannot open "es\Windows Resource Kits\Tools\;c:\Program Files\Affymetrix\GDAC NetAffx;c:\gs\gs8.51\bin;c:\Program 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:
  adding MD5 sums

* DONE (simpleaffy)