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Package 161/260HostnameOS / ArchBUILDCHECKBUILD BIN
oligo 1.4.0
Benilton Carvalho
Snapshot Date: 2008-08-08 00:12:03 -0700 (Fri, 08 Aug 2008)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_2/madman/Rpacks/oligo
Last Changed Rev: 31430 / Revision: 33132
Last Changed Date: 2008-04-29 16:50:18 -0700 (Tue, 29 Apr 2008)
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 
pitt Mac OS X Tiger (10.4.11) / i386  OK [ OK ] OK 
Package: oligo
Version: 1.4.0
Command: /Library/Frameworks/R.framework/Versions/2.7/Resources/bin/R CMD check oligo_1.4.0.tar.gz
StartedAt: 2008-08-08 05:24:07 -0700 (Fri, 08 Aug 2008)
EndedAt: 2008-08-08 05:32:19 -0700 (Fri, 08 Aug 2008)
EllapsedTime: 492.4 seconds
RetCode: 0
Status: OK
CheckDir: oligo.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.2-bioc/meat/oligo.Rcheck'
* using R version 2.7.1 (2008-06-23)
* using session charset: ASCII
* checking for file 'oligo/DESCRIPTION' ... OK
* this is package 'oligo' version '1.4.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'oligo' 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 ... NOTE
LLR2conf: no visible binding for global variable 'HmzK3'
LLR2conf: no visible binding for global variable 'lm1'
LLR2conf: no visible binding for global variable 'HmzK2'
LLR2conf: no visible binding for global variable 'HtzK3'
LLR2conf: no visible binding for global variable 'lm2'
LLR2conf: no visible binding for global variable 'HtzK2'
LLR2conf: no visible binding for global variable 'SNRK'
LLR2conf: no visible binding for global variable 'SNRlm'
justCRLMM: no visible binding for global variable 'maleIndex'
justCRLMM2: no visible binding for global variable 'maleIndex'
justCRLMMv2: no visible binding for global variable 'maleIndex'
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $BLAS_LIBS ... OK
* creating oligo-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating oligo-manual.tex ... OK
* checking oligo-manual.tex using pdflatex ... OK

oligo.Rcheck/00install.out:

* Installing *source* package 'oligo' ...
** libs
** arch - i386
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3 -I"/Library/Frameworks/R.framework/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -march=nocona -c baseProfile.c -o baseProfile.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3 -I"/Library/Frameworks/R.framework/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -march=nocona -c basecontent.c -o basecontent.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3 -I"/Library/Frameworks/R.framework/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -march=nocona -c rma2.c -o rma2.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3 -I"/Library/Frameworks/R.framework/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -march=nocona -c rma_background2.c -o rma_background2.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3 -I"/Library/Frameworks/R.framework/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -march=nocona -c rma_common.c -o rma_common.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3 -I"/Library/Frameworks/R.framework/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -march=nocona -c trimmed.c -o trimmed.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -mmacosx-version-min=10.4 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o oligo.so baseProfile.o basecontent.o rma2.o rma_background2.o rma_common.o trimmed.o   -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** arch - ppc
gcc -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -c baseProfile.c -o baseProfile.o
gcc -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -c basecontent.c -o basecontent.o
gcc -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -c rma2.c -o rma2.o
gcc -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -c rma_background2.c -o rma_background2.o
gcc -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -c rma_common.c -o rma_common.o
gcc -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -c trimmed.c -o trimmed.o
gcc -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -mmacosx-version-min=10.4 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o oligo.so baseProfile.o basecontent.o rma2.o rma_background2.o rma_common.o trimmed.o   -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** R
** inst
** preparing package for lazy loading
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: splines
Loading required package: RSQLite
Loading required package: DBI
Loading required package: preprocessCore
Loading required package: AnnotationDbi
Loading required package: affxparser
Loading required package: oligoClasses
** help
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 >>> Building/Updating help pages for package 'oligo'
     Formats: text html latex example 
  DBPDInfo-class                    text    html    latex   example
  FeatureSet-class                  text    html    latex   example
  FeatureSetExtensions-class        text    html    latex   example
  Index-methods                     text    html    latex
  IntensityMatrix-methods           text    html    latex
  MAplot-methods                    text    html    latex
  PDInfo-class                      text    html    latex   example
  PDInfo-methods                    text    html    latex
  Sequences-methods                 text    html    latex
  SnpQSet-class                     text    html    latex   example
  SnpQSet-methods                   text    html    latex
  SnpSetExtensions-class            text    html    latex   example
  basecontent                       text    html    latex   example
  boxplot                           text    html    latex
  chromosome                        text    html    latex
  crlmm                             text    html    latex   example
  featureIndex                      text    html    latex
  featureNames-methods              text    html    latex
  genomeBuild                       text    html    latex
  getCrlmmSummaries                 text    html    latex
  getPlatformDesign                 text    html    latex
  hist                              text    html    latex
  image                             text    html    latex
  internals                         text    html    latex
  justSNPRMA                        text    html    latex   example
  kind                              text    html    latex
  list.celfiles                     text    html    latex
  manufacturer                      text    html    latex
  nProbes                           text    html    latex
  ncol                              text    html    latex
  oligo-package                     text    html    latex   example
  platform                          text    html    latex
  platformDesign-class              text    html    latex   example
  plotDensity                       text    html    latex
  pmAllele                          text    html    latex
  pmPosition                        text    html    latex
  pmStrand                          text    html    latex
  probeNames                        text    html    latex
  read.celfiles                     text    html    latex
  read.xysfiles                     text    html    latex
  readSummaries                     text    html    latex
  rma                               text    html    latex
  sequenceDesignMatrix              text    html    latex
  snprma                            text    html    latex
  snprmaSummaries                   text    html    latex
** building package indices ...
* DONE (oligo)