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 |
* 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
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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>>> 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 chm
IntensityMatrix-methods text html latex chm
MAplot-methods text html latex chm
PDInfo-class text html latex example chm
PDInfo-methods text html latex chm
Sequences-methods text html latex chm
SnpQSet-class text html latex example chm
SnpQSet-methods text html latex chm
SnpSetExtensions-class text html latex example chm
basecontent text html latex example chm
boxplot text html latex chm
chromosome text html latex chm
crlmm text html latex example chm
featureIndex text html latex chm
featureNames-methods text html latex chm
genomeBuild text html latex chm
getCrlmmSummaries text html latex chm
getPlatformDesign text html latex chm
hist text html latex chm
image text html latex chm
internals text html latex chm
justSNPRMA text html latex example chm
kind text html latex chm
list.celfiles text html latex chm
manufacturer text html latex chm
nProbes text html latex chm
ncol text html latex chm
oligo-package text html latex example chm
platform text html latex chm
platformDesign-class text html latex example chm
plotDensity text html latex chm
pmAllele text html latex chm
pmPosition text html latex chm
pmStrand text html latex chm
probeNames text html latex chm
read.celfiles text html latex chm
read.xysfiles text html latex chm
readSummaries text html latex chm
rma text html latex chm
sequenceDesignMatrix text html latex chm
snprma text html latex chm
snprmaSummaries text html latex chm
Microsoft HTML Help Compiler 4.74.8702
Compiling e:\biocbld\bbs-2.2-bioc\meat\oligo.Rcheck\00_pkg_src\oligo\chm\oligo.chm
Compile time: 0 minutes, 0 seconds
46 Topics
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Created e:\biocbld\bbs-2.2-bioc\meat\oligo.Rcheck\00_pkg_src\oligo\chm\oligo.chm, 44,184 bytes
Compression decreased file by 96,946 bytes.
adding MD5 sums
* DONE (oligo)