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Package 145/233HostnameOS / ArchBUILDCHECKBUILD BIN
oligo 1.2.2
Benilton Carvalho
Snapshot Date: 2008-04-02 12:12:36 -0700 (Wed, 02 Apr 2008)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_1/madman/Rpacks/oligo
Last Changed Rev: 28552 / Revision: 30807
Last Changed Date: 2007-11-07 14:46:28 -0800 (Wed, 07 Nov 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: oligo
Version: 1.2.2
Command: D:\biocbld\bbs-2.1-bioc\R\bin\R.exe CMD check oligo_1.2.2.tar.gz
StartedAt: 2008-04-02 20:45:17 -0700 (Wed, 02 Apr 2008)
EndedAt: 2008-04-02 20:59:42 -0700 (Wed, 02 Apr 2008)
EllapsedTime: 865.2 seconds
RetCode: 0
Status: OK
CheckDir: oligo.Rcheck
Warnings: 0

Command output

* checking for working latex ... OK
* using log directory 'D:/biocbld/bbs-2.1-bioc/meat/oligo.Rcheck'
* using R version 2.6.2 (2008-02-08)
* checking for file 'oligo/DESCRIPTION' ... OK
* this is package 'oligo' version '1.2.2'
* 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 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
justCRLMM: no visible binding for global variable 'maleIndex'
LLR2conf: no visible binding for global variable 'Dst'
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'
* 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 ... OK

oligo.Rcheck/00install.out:

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


---------- Making package oligo ------------
  adding build stamp to DESCRIPTION
  installing NAMESPACE file and metadata
  making DLL ...
making baseProfile.d from baseProfile.c
making basecontent.d from basecontent.c
making rma2.d from rma2.c
making rma_background2.d from rma_background2.c
making rma_common.d from rma_common.c
making trimmed.d from trimmed.c
gcc-sjlj  -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include"    -O3 -Wall  -c baseProfile.c -o baseProfile.o
gcc-sjlj  -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include"    -O3 -Wall  -c basecontent.c -o basecontent.o
gcc-sjlj  -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include"    -O3 -Wall  -c rma2.c -o rma2.o
gcc-sjlj  -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include"    -O3 -Wall  -c rma_background2.c -o rma_background2.o
gcc-sjlj  -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include"    -O3 -Wall  -c rma_common.c -o rma_common.o
gcc-sjlj  -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include"    -O3 -Wall  -c trimmed.c -o trimmed.o
windres --preprocessor="gcc-sjlj -E -xc -DRC_INVOKED" -I d:/biocbld/bbs-2.1-bioc/R/include  -i oligo_res.rc -o oligo_res.o
gcc-sjlj  -std=gnu99  -shared -s  -o oligo.dll oligo.def baseProfile.o basecontent.o rma2.o rma_background2.o rma_common.o trimmed.o oligo_res.o  -Ld:/biocbld/bbs-2.1-bioc/R/bin    -lR
  ... DLL made
  installing DLL
  installing R files
  installing inst files
  preparing package oligo 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
  installing man source files
  installing indices
  installing help
 >>> Building/Updating help pages for package 'oligo'
     Formats: text html latex example chm 
  DBPDInfo-class                    text    html    latex   example chm
  FeatureSet-class                  text    html    latex   example chm
  FeatureSetExtensions-class        text    html    latex   example chm
  Index-methods                     text    html    latex   example chm
  IntensityMatrix-methods           text    html    latex   example chm
  MAplot-methods                    text    html    latex           chm
  PDInfo-class                      text    html    latex   example chm
  PDInfo-methods                    text    html    latex   example chm
  Sequences-methods                 text    html    latex   example chm
  SnpCallSet-methods                text    html    latex   example chm
  SnpCopyNumberSet-methods          text    html    latex   example chm
  SnpQSet-class                     text    html    latex   example chm
  SnpQSet-methods                   text    html    latex   example chm
  SnpSetExtensions-class            text    html    latex   example chm
  basecontent                       text    html    latex   example chm
  boxplot                           text    html    latex   example chm
  chromosome                        text    html    latex   example chm
  crlmm                             text    html    latex   example chm
  featureIndex                      text    html    latex   example chm
  featureNames-methods              text    html    latex           chm
  genomeBuild                       text    html    latex   example chm
  getPlatformDesign                 text    html    latex   example chm
  hist                              text    html    latex   example chm
  image                             text    html    latex   example chm
  internals                         text    html    latex   example chm
  justSNPRMA                        text    html    latex   example chm
  kind                              text    html    latex   example chm
  list.celfiles                     text    html    latex   example chm
  manufacturer                      text    html    latex   example chm
  nProbes                           text    html    latex   example chm
  ncol                              text    html    latex   example chm
  oligo-package                     text    html    latex   example chm
  platform                          text    html    latex   example chm
  platformDesign-class              text    html    latex   example chm
  plotDensity                       text    html    latex   example chm
  pmAllele                          text    html    latex   example chm
  pmPosition                        text    html    latex   example chm
  pmStrand                          text    html    latex   example chm
  probeNames                        text    html    latex   example chm
  read.celfiles                     text    html    latex   example chm
  read.xysfiles                     text    html    latex   example chm
  rma                               text    html    latex   example chm
  sequenceDesignMatrix              text    html    latex   example chm
  snprma                            text    html    latex   example chm
  snprmaSummaries                   text    html    latex   example chm
HHC5012: Error: Cannot create a temporary file in your TEMP path.
HHC4016: Warning: Cannot open "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\oligo.Rcheck\00_pkg_src\oligo\chm\oligo.chm

HHC4016: Warning: Cannot open "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 (oligo)