bioconductorパッケージのインストール



Bioconducltor(microarrayデータの解析を端緒にバイオインフォマティクス関係の統計書解析ツールを集めた大きなパッケージ。Rベースで作られている。公式サイト: Welcome to Bioconductor — bioconductor.org 。レファレンス:Bioconductor: open software development for comput...[Genome Biol. 2004] - PubMed Result

Rのパッケージのインストールは、(通常)、インストール済みのGUI画面のツールバーからPackagesを選び、Install Packagesメニューをたどることで、インストール先の指定、インストールパッケージの指定をすることで実現される。bioconductorは、ほかのパッケージと同様のインストールになるような記述があるが、どうもそうなっていないようで、上述のbioconductorサイトへアクセスして取得するのを通例とするようだ。

具体的には、上記サイトにあるとおり、

  • Rを立ち上げた状態で
  • コンソールに
    • コマンド1

source("http://www.bioconductor.org/biocLite.R")

リターン

    • コマンド2

biocLite()

リターン

と実行する。そうすると、かなり長時間ダウンロードプログラムが実行され、以下の経過表示がなされた後(2005年8月29日現在)、インストールが終了する。

> source("http://www.bioconductor.org/biocLite.R")
> biocLite()

Running bioCLite version 0.1 with R version 2.1.0

Running biocinstall version 1.2 with R version 2.1.0
also installing the dependencies 'GO', 'KEGG'

trying URL 'http://www.bioconductor.org/packages/data/annotation/stable/bin/windows/contrib/2.1/GO_1.8.2.zip'
Content type 'application/zip' length 12676072 bytes
opened URL
downloaded 12378Kb

trying URL 'http://www.bioconductor.org/packages/data/annotation/stable/bin/windows/contrib/2.1/KEGG_1.8.1.zip'
Content type 'application/zip' length 233148 bytes
opened URL
downloaded 227Kb

trying URL 'http://www.bioconductor.org/packages/bioc/stable/bin/windows/contrib/2.1/affy_1.6.7.zip'
Content type 'application/zip' length 1438528 bytes
opened URL
downloaded 1404Kb

trying URL 'http://www.bioconductor.org/packages/bioc/stable/bin/windows/contrib/2.1/affydata_1.4.1.zip'
Content type 'application/zip' length 9867339 bytes
opened URL
downloaded 9636Kb

trying URL 'http://www.bioconductor.org/packages/bioc/stable/bin/windows/contrib/2.1/affyPLM_1.3.3.zip'
Content type 'application/zip' length 3912506 bytes
opened URL
downloaded 3820Kb

trying URL 'http://www.bioconductor.org/packages/bioc/stable/bin/windows/contrib/2.1/annaffy_1.0.18.zip'
Content type 'application/zip' length 344446 bytes
opened URL
downloaded 336Kb

trying URL 'http://www.bioconductor.org/packages/bioc/stable/bin/windows/contrib/2.1/annotate_1.5.16.zip'
Content type 'application/zip' length 1724934 bytes
opened URL
downloaded 1684Kb

trying URL 'http://www.bioconductor.org/packages/bioc/stable/bin/windows/contrib/2.1/Biobase_1.5.12.zip'
Content type 'application/zip' length 623915 bytes
opened URL
downloaded 609Kb

trying URL 'http://www.bioconductor.org/packages/bioc/stable/bin/windows/contrib/2.1/Biostrings_1.1.1.zip'
Content type 'application/zip' length 217247 bytes
opened URL
downloaded 212Kb

trying URL 'http://www.bioconductor.org/packages/bioc/stable/bin/windows/contrib/2.1/DynDoc_1.5.5.zip'
Content type 'application/zip' length 91752 bytes
opened URL
downloaded 89Kb

trying URL 'http://www.bioconductor.org/packages/bioc/stable/bin/windows/contrib/2.1/gcrma_1.1.4.zip'
Content type 'application/zip' length 131819 bytes
opened URL
downloaded 128Kb

trying URL 'http://www.bioconductor.org/packages/bioc/stable/bin/windows/contrib/2.1/genefilter_1.6.3.zip'
Content type 'application/zip' length 323875 bytes
opened URL
downloaded 316Kb

trying URL 'http://www.bioconductor.org/packages/bioc/stable/bin/windows/contrib/2.1/geneplotter_1.6.1.zip'
Content type 'application/zip' length 1537720 bytes
opened URL
downloaded 1501Kb

trying URL 'http://www.bioconductor.org/packages/data/annotation/stable/bin/windows/contrib/2.1/hgu95av2_1.8.4.zip'
Content type 'application/zip' length 5989106 bytes
opened URL
downloaded 5848Kb

trying URL 'http://cran.fhcrc.org/bin/windows/contrib/2.1/limma_2.0.4.zip'
Content type 'application/zip' length 1312391 bytes
opened URL
downloaded 1281Kb

trying URL 'http://www.bioconductor.org/packages/bioc/stable/bin/windows/contrib/2.1/marray_1.6.3.zip'
Content type 'application/zip' length 4363269 bytes
opened URL
downloaded 4261Kb

trying URL 'http://www.bioconductor.org/packages/bioc/stable/bin/windows/contrib/2.1/matchprobes_1.0.22.zip'
Content type 'application/zip' length 7337852 bytes
opened URL
downloaded 7165Kb

trying URL 'http://cran.fhcrc.org/bin/windows/contrib/2.1/multtest_1.7.3.zip'
Content type 'application/zip' length 1508460 bytes
opened URL
downloaded 1473Kb

trying URL 'http://www.bioconductor.org/packages/bioc/stable/bin/windows/contrib/2.1/reposTools_1.5.19.zip'
Content type 'application/zip' length 628767 bytes
opened URL
downloaded 614Kb

trying URL 'http://www.bioconductor.org/packages/bioc/stable/bin/windows/contrib/2.1/ROC_1.1.1.zip'
Content type 'application/zip' length 133323 bytes
opened URL
downloaded 130Kb

trying URL 'http://www.bioconductor.org/packages/bioc/stable/bin/windows/contrib/2.1/vsn_1.6.3.zip'
Content type 'application/zip' length 1537894 bytes
opened URL
downloaded 1501Kb

trying URL 'http://cran.fhcrc.org/bin/windows/contrib/2.1/xtable_1.2-5.zip'
Content type 'application/zip' length 65572 bytes
opened URL
downloaded 64Kb

package 'GO' successfully unpacked and MD5 sums checked
package 'KEGG' successfully unpacked and MD5 sums checked
package 'affy' successfully unpacked and MD5 sums checked
package 'affydata' successfully unpacked and MD5 sums checked
package 'affyPLM' successfully unpacked and MD5 sums checked
package 'annaffy' successfully unpacked and MD5 sums checked
package 'annotate' successfully unpacked and MD5 sums checked
package 'Biobase' successfully unpacked and MD5 sums checked
package 'Biostrings' successfully unpacked and MD5 sums checked
package 'DynDoc' successfully unpacked and MD5 sums checked
package 'gcrma' successfully unpacked and MD5 sums checked
package 'genefilter' successfully unpacked and MD5 sums checked
package 'geneplotter' successfully unpacked and MD5 sums checked
package 'hgu95av2' successfully unpacked and MD5 sums checked
package 'limma' successfully unpacked and MD5 sums checked
package 'marray' successfully unpacked and MD5 sums checked
package 'matchprobes' successfully unpacked and MD5 sums checked
package 'multtest' successfully unpacked and MD5 sums checked
package 'reposTools' successfully unpacked and MD5 sums checked
package 'ROC' successfully unpacked and MD5 sums checked
package 'vsn' successfully unpacked and MD5 sums checked
package 'xtable' successfully unpacked and MD5 sums checked

The downloaded packages are in
C:\Documents and Settings\yamada\Local Settings\Temp\Rtmp6156\downloaded_packages
updating HTML package descriptions
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