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Package 162/264HostnameOS / ArchBUILDCHECKBUILD BIN
oligo 1.3.18
Benilton Carvalho
Snapshot Date: 2008-04-09 00:13:10 -0700 (Wed, 09 Apr 2008)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo
Last Changed Rev: 30606 / Revision: 30951
Last Changed Date: 2008-03-21 01:53:31 -0700 (Fri, 21 Mar 2008)
lamb1 Linux (SUSE 10.1) / x86_64  OK  WARNINGS 
wilson2 Linux (openSUSE 10.3) / x86_64  OK  WARNINGS 
wellington Linux (openSUSE 10.3) / i686  OK  WARNINGS 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK [ WARNINGS ] OK 
pelham Mac OS X Leopard (10.5.1) / i386  OK  WARNINGS  OK 
Package: oligo
Version: 1.3.18
Command: E:\biocbld\bbs-2.2-bioc\R\bin\R.exe CMD check oligo_1.3.18.tar.gz
StartedAt: 2008-04-09 06:47:35 -0700 (Wed, 09 Apr 2008)
EndedAt: 2008-04-09 06:54:34 -0700 (Wed, 09 Apr 2008)
EllapsedTime: 418.5 seconds
RetCode: 0
Status: WARNINGS
CheckDir: oligo.Rcheck
Warnings: 1

Command output

* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.2-bioc/meat/oligo.Rcheck'
* using R version 2.7.0 Under development (unstable) (2008-03-10 r44730)
* using session charset: ISO8859-1
* checking for file 'oligo/DESCRIPTION' ... OK
* this is package 'oligo' version '1.3.18'
* 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'
justCRLMM2: no visible binding for global variable 'maleIndex'
justCRLMMv2: no visible binding for global variable 'maleIndex'
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 ... WARNING
Undocumented S4 methods:
  generic 'kind' and siglist 'AffyGeneSTPDInfo'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* 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

WARNING: There was 1 warning, see
  E:/biocbld/bbs-2.2-bioc/meat/oligo.Rcheck/00check.log
for details

oligo.Rcheck/00install.out:

installing R.css in E:/biocbld/bbs-2.2-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  -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/src/extra/zlib -DHAVE_ZLIB -Ie:/biocbld/bbs-2.2-bioc/R/include -I"e:/biocbld/bbs-2.2-bioc/R/library/preprocessCore/include"    -O3 -Wall  -c baseProfile.c -o baseProfile.o
gcc  -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/src/extra/zlib -DHAVE_ZLIB -Ie:/biocbld/bbs-2.2-bioc/R/include -I"e:/biocbld/bbs-2.2-bioc/R/library/preprocessCore/include"    -O3 -Wall  -c basecontent.c -o basecontent.o
gcc  -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/src/extra/zlib -DHAVE_ZLIB -Ie:/biocbld/bbs-2.2-bioc/R/include -I"e:/biocbld/bbs-2.2-bioc/R/library/preprocessCore/include"    -O3 -Wall  -c rma2.c -o rma2.o
gcc  -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/src/extra/zlib -DHAVE_ZLIB -Ie:/biocbld/bbs-2.2-bioc/R/include -I"e:/biocbld/bbs-2.2-bioc/R/library/preprocessCore/include"    -O3 -Wall  -c rma_background2.c -o rma_background2.o
gcc  -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/src/extra/zlib -DHAVE_ZLIB -Ie:/biocbld/bbs-2.2-bioc/R/include -I"e:/biocbld/bbs-2.2-bioc/R/library/preprocessCore/include"    -O3 -Wall  -c rma_common.c -o rma_common.o
gcc  -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/src/extra/zlib -DHAVE_ZLIB -Ie:/biocbld/bbs-2.2-bioc/R/include -I"e:/biocbld/bbs-2.2-bioc/R/library/preprocessCore/include"    -O3 -Wall  -c trimmed.c -o trimmed.o
windres --preprocessor="gcc -E -xc -DRC_INVOKED" -I e:/biocbld/bbs-2.2-bioc/R/include  -i oligo_res.rc -o oligo_res.o
gcc  -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  -Le:/biocbld/bbs-2.2-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
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* DONE (oligo)