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Package 146/234 | Hostname | OS | Arch | BUILD | CHECK | BUILD BIN |
oligo 1.2.1 Benilton Carvalho Last Changed Date: 2007-10-07 09:22:50 -0700 Last Changed Rev: 27832 | lamb1 | Linux (SUSE 10.1) | x86_64 | OK | OK | |
wellington | Linux (SUSE 9.2) | i686 | OK | [ OK ] | ||
liverpool | Windows Server 2003 R2 (32-bit) | x64 | OK | OK | OK | |
pitt | Mac OS X (10.4.10) | i386 | OK | OK | OK |
Package: oligo |
Version: 1.2.1 |
Command: /loc/biocbuild/bbs-2.1-bioc/R/bin/R CMD check oligo_1.2.1.tar.gz |
RetCode: 0 |
Time: 943.0 seconds |
Status: OK |
CheckDir: oligo.Rcheck |
Warnings: 0 |
* checking for working latex ... OK * using log directory '/extra/loc/biocbuild/bbs-2.1-bioc/meat/oligo.Rcheck' * using R version 2.6.0 (2007-10-03) * checking for file 'oligo/DESCRIPTION' ... OK * this is package 'oligo' version '1.2.1' * 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 for sufficient/correct file permissions ... 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 *source* package 'oligo' ... ** libs gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/local/include -I"/loc/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c basecontent.c -o basecontent.o gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/local/include -I"/loc/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c baseProfile.c -o baseProfile.o gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/local/include -I"/loc/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c rma2.c -o rma2.o gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/local/include -I"/loc/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c rma_background2.c -o rma_background2.o gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/local/include -I"/loc/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c rma_common.c -o rma_common.o gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/local/include -I"/loc/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c trimmed.c -o trimmed.o gcc -std=gnu99 -shared -L/usr/local/lib -o oligo.so basecontent.o baseProfile.o rma2.o rma_background2.o rma_common.o trimmed.o -L/loc/biocbuild/bbs-2.1-bioc/R/lib -lR ** R ** inst ** preparing package 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 ** help >>> Building/Updating help pages for package 'oligo' Formats: text html latex example DBPDInfo-class text html latex example FeatureSet-class text html latex example FeatureSetExtensions-class text html latex example Index-methods text html latex example IntensityMatrix-methods text html latex example MAplot-methods text html latex PDInfo-class text html latex example PDInfo-methods text html latex example Sequences-methods text html latex example SnpCallSet-methods text html latex example SnpCopyNumberSet-methods text html latex example SnpQSet-class text html latex example SnpQSet-methods text html latex example SnpSetExtensions-class text html latex example basecontent text html latex example boxplot text html latex example chromosome text html latex example crlmm text html latex example featureIndex text html latex example featureNames-methods text html latex genomeBuild text html latex example getPlatformDesign text html latex example hist text html latex example image text html latex example internals text html latex example justSNPRMA text html latex example kind text html latex example list.celfiles text html latex example manufacturer text html latex example nProbes text html latex example ncol text html latex example oligo-package text html latex example platform text html latex example platformDesign-class text html latex example plotDensity text html latex example pmAllele text html latex example pmPosition text html latex example pmStrand text html latex example probeNames text html latex example read.celfiles text html latex example read.xysfiles text html latex example rma text html latex example sequenceDesignMatrix text html latex example snprma text html latex example snprmaSummaries text html latex example ** building package indices ... * DONE (oligo)