oligo 1.12.2
Benilton Carvalho
| Snapshot Date: 2010-10-04 11:22:20 -0700 (Mon, 04 Oct 2010) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_6/madman/Rpacks/oligo | | Last Changed Rev: 48736 / Revision: 49923 | | Last Changed Date: 2010-08-10 03:10:00 -0700 (Tue, 10 Aug 2010) |
| wilson1 | Linux (openSUSE 11.1) / x86_64 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | OK |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | [ OK ] | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* checking for working pdflatex ... OK
* using log directory 'D:/biocbld/bbs-2.6-bioc/meat/oligo.Rcheck'
* using R version 2.11.1 (2010-05-31)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'oligo/DESCRIPTION' ... OK
* this is package 'oligo' version '1.12.2'
* 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 package can be unloaded cleanly ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... 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
alleleSetFrom: no visible global function definition for 'finalizer<-'
ffSubset: no visible global function definition for 'vmode'
fitAffySnpMixture2: no visible global function definition for 'ff'
fitAffySnpMixture2: no visible global function definition for
'ffvecapply'
fitAffySnpMixture2: no visible binding for global variable 'i1'
fitAffySnpMixture2: no visible binding for global variable 'i2'
rmaBgCorrectLDSmaster: no visible global function definition for
'clone'
smartReadCEL: no visible global function definition for 'filename'
smartReadXYS: no visible global function definition for 'filename'
snpGenderCall: no visible global function definition for 'is.ff'
snprma2: no visible global function definition for 'finalizer<-'
normalizeToTarget,ff_matrix: no visible global function definition for
'clone'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... 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
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK
* install options are ' --no-html'
* installing *source* package 'oligo' ...
** libs
making DLL ...
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/preprocessCore/include" -O2 -Wall -std=gnu99 -c ParserXYS.c -o ParserXYS.o
ParserXYS.c: In function 'read_one_xys':
ParserXYS.c:105: warning: unused variable 'token'
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/preprocessCore/include" -O2 -Wall -std=gnu99 -c baseProfile.c -o baseProfile.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/preprocessCore/include" -O2 -Wall -std=gnu99 -c basecontent.c -o basecontent.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/preprocessCore/include" -O2 -Wall -std=gnu99 -c chipbackground.c -o chipbackground.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/preprocessCore/include" -O2 -Wall -std=gnu99 -c rma2.c -o rma2.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/preprocessCore/include" -O2 -Wall -std=gnu99 -c rma_common.c -o rma_common.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/preprocessCore/include" -O2 -Wall -std=gnu99 -c trimmed.c -o trimmed.o
x86_64-w64-mingw32-gcc -shared -s -static-libgcc -o oligo.dll tmp.def ParserXYS.o baseProfile.o basecontent.o chipbackground.o rma2.o rma_common.o trimmed.o -lRzlib -LD:/biocbld/bbs-2.6-bioc/R/bin -lR
installing to D:/biocbld/bbs-2.6-bioc/meat/oligo.Rcheck/oligo/libs/x64
... done
** R
** inst
** preparing package for lazy loading
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
================================================================================
Welcome to oligoClasses version 1.10.0
================================================================================
Large dataset support for 'oligo/crlmm': Disabled
- Load 'ff'
================================================================================
Parallel computing support for 'oligo/crlmm': Disabled
- Load 'ff'
- Load 'snow'
- Use options(cluster=makeCluster(...))
================================================================================
in method for 'backgroundCorrect' with signature '"ff_matrix"': no definition for class "ff_matrix"
in method for 'normalize' with signature '"ff_matrix"': no definition for class "ff_matrix"
in method for 'normalizeToTarget' with signature '"ff_matrix"': no definition for class "ff_matrix"
in method for 'summarize' with signature '"ff_matrix"': no definition for class "ff_matrix"
Creating a new generic function for "boxplot" in "oligo"
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
================================================================================
Welcome to oligo version 1.12.2
================================================================================
* DONE (oligo)