oligo 1.6.0
Benilton Carvalho
| Bioconductor Changelog | | Snapshot Date: 2009-04-18 11:27:48 -0700 (Sat, 18 Apr 2009) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_3/madman/Rpacks/oligo | | Last Changed Rev: 34811 / Revision: 38965 | | Last Changed Date: 2008-10-21 15:32:58 -0700 (Tue, 21 Oct 2008) |
| wilson2 | 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 (10.5.6) / i386 | OK | OK | OK |
* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.3-bioc/meat/oligo.Rcheck'
* using R version 2.8.1 (2008-12-22)
* using session charset: ISO8859-1
* checking for file 'oligo/DESCRIPTION' ... OK
* this is package 'oligo' version '1.6.0'
* 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 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'
coerce,platformDesign-data.frame: no visible binding for global
variable 'x'
nProbes,AffySNPPDInfo: no visible binding for global variable 'tbl'
nProbes,AffySNPPDInfo: no visible binding for global variable
'row_count'
nProbes,ExpressionPDInfo: no visible binding for global variable 'tbl'
nProbes,ExpressionPDInfo: no visible binding for global variable
'row_count'
nProbes,TilingPDInfo: no visible binding for global variable 'tbl'
nProbes,TilingPDInfo: no visible binding for global variable
'row_count'
* 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
installing R.css in E:/biocbld/bbs-2.3-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-2.3-bioc/R/src/extra/zlib -DHAVE_ZLIB -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/preprocessCore/include" -O3 -Wall -c baseProfile.c -o baseProfile.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/src/extra/zlib -DHAVE_ZLIB -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/preprocessCore/include" -O3 -Wall -c basecontent.c -o basecontent.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/src/extra/zlib -DHAVE_ZLIB -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/preprocessCore/include" -O3 -Wall -c rma2.c -o rma2.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/src/extra/zlib -DHAVE_ZLIB -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/preprocessCore/include" -O3 -Wall -c rma_background2.c -o rma_background2.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/src/extra/zlib -DHAVE_ZLIB -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/preprocessCore/include" -O3 -Wall -c rma_common.c -o rma_common.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/src/extra/zlib -DHAVE_ZLIB -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/preprocessCore/include" -O3 -Wall -c trimmed.c -o trimmed.o
windres --preprocessor="gcc -E -xc -DRC_INVOKED" -I e:/biocbld/bbs-2.3-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-2.3-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'
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Microsoft HTML Help Compiler 4.74.8702
Compiling e:\biocbld\bbs-2.3-bioc\meat\oligo.Rcheck\00_pkg_src\oligo\chm\oligo.chm
Compile time: 0 minutes, 0 seconds
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Created e:\biocbld\bbs-2.3-bioc\meat\oligo.Rcheck\00_pkg_src\oligo\chm\oligo.chm, 44,300 bytes
Compression decreased file by 100,331 bytes.
adding MD5 sums
* DONE (oligo)