1. http://code.google.com/p/pdb-tools/
2. Interface analysis module for biopython
>> protein interface 尚未發表
>> protein DNA : Biskit ~~
3. protein-protein docking
>> zdock
>> hddock
2011年6月10日 星期五
mac port 安裝 統計 R
經由 port 去安裝 R statistical package .
R 的版本 2.13
1. 先搜尋 port search R and statistic (statistics 多個 s 就找不到 )
>> R @2.13.0 (math, science)
>> R is GNU S - an interpreted language for statistical computing
2. sh-3.2# port install R @2.13.0
PS.安裝時要 fetching perl 5.12 ？？
processing detail
---> Computing dependencies for tiff
---> Fetching tiff
---> Attempting to fetch tiff-3.9.5.tar.gz from ftp://ftp.tw.FreeBSD.org/pub/FreeBSD/ports/distfiles/
---> Attempting to fetch tiff-3.9.5.tar.gz from ftp://ftp.tw.FreeBSD.org/pub/FreeBSD/ports/local-distfiles/
---> Attempting to fetch tiff-3.9.5.tar.gz from ftp://ftp.jp.FreeBSD.org/pub/FreeBSD/ports/distfiles/
---> Attempting to fetch tiff-3.9.5.tar.gz from ftp://ftp.jp.FreeBSD.org/pub/FreeBSD/ports/local-distfiles/
---> Attempting to fetch tiff-3.9.5.tar.gz from ftp://ftp.FreeBSD.org/pub/FreeBSD/ports/distfiles/
---> Attempting to fetch tiff-3.9.5.tar.gz from ftp://ftp.FreeBSD.org/pub/FreeBSD/ports/local-distfiles/
---> Attempting to fetch tiff-3.9.5.tar.gz from ftp://ftp.remotesensing.org/pub/libtiff/
---> Verifying checksum(s) for tiff
---> Extracting tiff
---> Configuring tiff
---> Building tiff
---> Staging tiff into destroot
---> Computing dependencies for tiff
---> Installing tiff @3.9.5_0
---> Deactivating tiff @3.9.4_0
---> Cleaning tiff
---> Activating tiff @3.9.5_0
---> Cleaning tiff
---> Computing dependencies for R
---> Dependencies to be installed: glib2 autoconf help2man p5-locale-gettext perl5 perl5.12 m4 automake libtool icu pango cairo libpixman libpng xorg-xcb-util xorg-libXmu xorg-libXt xorg-libsm xorg-libice
---> Fetching perl5.12
---> Attempting to fetch perl-5.12.3.tar.bz2 from http://www.cpan.org/src/5.0/
---> Verifying checksum(s) for perl5.12
---> Extracting perl5.12
---> Applying patches to perl5.12
---> Configuring perl5.12
---> Building perl5.12
---> Staging perl5.12 into destroot
---> Installing perl5.12 @5.12.3_1
---> Activating perl5.12 @5.12.3_1
---> Cleaning perl5.12
---> Fetching perl5
---> Verifying checksum(s) for perl5
---> Extracting perl5
---> Configuring perl5
---> Building perl5
---> Staging perl5 into destroot
---> Installing perl5 @5.12.3_1+perl5_12
---> Activating perl5 @5.12.3_1+perl5_12
---> Cleaning perl5
---> Fetching p5-locale-gettext
---> Attempting to fetch gettext-1.05.tar.gz from ftp://ftp.cpan.org/pub/CPAN/modules/by-module/Locale
---> Verifying checksum(s) for p5-locale-gettext
---> Extracting p5-locale-gettext
---> Applying patches to p5-locale-gettext
---> Configuring p5-locale-gettext
---> Building p5-locale-gettext
---> Staging p5-locale-gettext into destroot
---> Installing p5-locale-gettext @1.05_5
---> Activating p5-locale-gettext @1.05_5
---> Cleaning p5-locale-gettext
---> Fetching help2man
---> Attempting to fetch help2man-1.39.3.tar.gz from ftp://ftp.dti.ad.jp/pub/GNU/help2man
---> Attempting to fetch help2man-1.39.3.tar.gz from http://mirror.facebook.net/gnu/gnu/help2man
---> Attempting to fetch help2man-1.39.3.tar.gz from http://distfiles.macports.org/help2man
---> Verifying checksum(s) for help2man
---> Extracting help2man
---> Configuring help2man
---> Building help2man
---> Staging help2man into destroot
---> Installing help2man @1.39.3_0
---> Activating help2man @1.39.3_0
---> Cleaning help2man
---> Fetching m4
---> Attempting to fetch m4-1.4.16.tar.bz2 from ftp://ftp.dti.ad.jp/pub/GNU/m4
---> Attempting to fetch m4-1.4.16.tar.bz2 from http://mirror.facebook.net/gnu/gnu/m4
---> Attempting to fetch m4-1.4.16.tar.bz2 from http://distfiles.macports.org/m4
---> Verifying checksum(s) for m4
---> Extracting m4
---> Configuring m4
---> Building m4
---> Staging m4 into destroot
---> Installing m4 @1.4.16_0
---> Activating m4 @1.4.16_0
---> Cleaning m4
---> Fetching autoconf
---> Attempting to fetch autoconf-2.68.tar.bz2 from ftp://ftp.dti.ad.jp/pub/GNU/autoconf
---> Verifying checksum(s) for autoconf
---> Extracting autoconf
---> Configuring autoconf
---> Building autoconf
---> Staging autoconf into destroot
---> Installing autoconf @2.68_2
---> Activating autoconf @2.68_2
---> Cleaning autoconf
---> Fetching automake
---> Attempting to fetch automake-1.11.1.tar.bz2 from ftp://ftp.dti.ad.jp/pub/GNU/automake
---> Verifying checksum(s) for automake
---> Extracting automake
---> Configuring automake
---> Building automake
---> Staging automake into destroot
---> Installing automake @1.11.1_0
---> Activating automake @1.11.1_0
---> Cleaning automake
---> Fetching libtool
---> Attempting to fetch libtool-2.4.tar.gz from ftp://ftp.dti.ad.jp/pub/GNU/libtool
---> Verifying checksum(s) for libtool
---> Extracting libtool
---> Configuring libtool
---> Building libtool
---> Staging libtool into destroot
---> Installing libtool @2.4_0
---> Activating libtool @2.4_0
---> Cleaning libtool
---> Fetching glib2
---> Attempting to fetch glib-2.28.8.tar.bz2 from http://ftp.nara.wide.ad.jp/pub/X11/GNOME/sources/glib/2.28/
---> Verifying checksum(s) for glib2
---> Extracting glib2
---> Applying patches to glib2
---> Configuring glib2
---> Building glib2
---> Staging glib2 into destroot
---> Installing glib2 @2.28.8_0
---> Activating glib2 @2.28.8_0
---> Cleaning glib2
---> Fetching icu
---> Attempting to fetch icu4c-4_6_1-src.tgz from http://distfiles.macports.org/icu
---> Verifying checksum(s) for icu
---> Extracting icu
---> Applying patches to icu
---> Configuring icu
---> Building icu
---> Staging icu into destroot
---> Installing icu @4.6.1_0
---> Activating icu @4.6.1_0
---> Cleaning icu
---> Fetching libpixman
---> Attempting to fetch pixman-0.22.0.tar.bz2 from http://distfiles.macports.org/libpixman
---> Verifying checksum(s) for libpixman
---> Extracting libpixman
---> Configuring libpixman
---> Building libpixman
---> Staging libpixman into destroot
---> Installing libpixman @0.22.0_0
---> Activating libpixman @0.22.0_0
---> Cleaning libpixman
---> Fetching libpng
---> Attempting to fetch libpng-1.4.7.tar.bz2 from http://nchc.dl.sourceforge.net/libpng
---> Verifying checksum(s) for libpng
---> Extracting libpng
---> Configuring libpng
---> Building libpng
---> Staging libpng into destroot
---> Installing libpng @1.4.7_0
---> Activating libpng @1.4.7_0
---> Cleaning libpng
---> Fetching xorg-xcb-util
---> Attempting to fetch xcb-util-0.3.8.tar.bz2 from http://distfiles.macports.org/xorg-xcb-util
---> Verifying checksum(s) for xorg-xcb-util
---> Extracting xorg-xcb-util
---> Configuring xorg-xcb-util
---> Building xorg-xcb-util
---> Staging xorg-xcb-util into destroot
---> Installing xorg-xcb-util @0.3.8_0
---> Activating xorg-xcb-util @0.3.8_0
---> Cleaning xorg-xcb-util
---> Fetching cairo
---> Attempting to fetch cairo-1.10.2.tar.gz from http://distfiles.macports.org/cairo
---> Verifying checksum(s) for cairo
---> Extracting cairo
---> Configuring cairo
---> Building cairo
---> Staging cairo into destroot
---> Installing cairo @1.10.2_3+x11
---> Activating cairo @1.10.2_3+x11
---> Cleaning cairo
---> Fetching pango
---> Attempting to fetch pango-1.28.4.tar.bz2 from http://ftp.nara.wide.ad.jp/pub/X11/GNOME/sources/pango/1.28
---> Verifying checksum(s) for pango
---> Extracting pango
---> Applying patches to pango
---> Configuring pango
---> Building pango
---> Staging pango into destroot
---> Installing pango @1.28.4_0+x11
---> Activating pango @1.28.4_0+x11
---> Cleaning pango
---> Fetching xorg-libice
---> Attempting to fetch libICE-1.0.7.tar.bz2 from http://distfiles.macports.org/xorg-libice
---> Verifying checksum(s) for xorg-libice
---> Extracting xorg-libice
---> Configuring xorg-libice
---> Building xorg-libice
---> Staging xorg-libice into destroot
---> Installing xorg-libice @1.0.7_0
---> Activating xorg-libice @1.0.7_0
---> Cleaning xorg-libice
---> Fetching xorg-libsm
---> Attempting to fetch libSM-1.2.0.tar.bz2 from http://distfiles.macports.org/xorg-libsm
---> Verifying checksum(s) for xorg-libsm
---> Extracting xorg-libsm
---> Configuring xorg-libsm
---> Building xorg-libsm
---> Staging xorg-libsm into destroot
---> Installing xorg-libsm @1.2.0_0
---> Activating xorg-libsm @1.2.0_0
---> Cleaning xorg-libsm
---> Fetching xorg-libXt
---> Attempting to fetch libXt-1.1.1.tar.bz2 from http://distfiles.macports.org/xorg-libXt
---> Verifying checksum(s) for xorg-libXt
---> Extracting xorg-libXt
---> Configuring xorg-libXt
---> Building xorg-libXt
---> Staging xorg-libXt into destroot
---> Installing xorg-libXt @1.1.1_0
---> Activating xorg-libXt @1.1.1_0
---> Cleaning xorg-libXt
---> Fetching xorg-libXmu
---> Attempting to fetch libXmu-1.1.0.tar.bz2 from http://distfiles.macports.org/xorg-libXmu
---> Verifying checksum(s) for xorg-libXmu
---> Extracting xorg-libXmu
---> Configuring xorg-libXmu
---> Building xorg-libXmu
---> Staging xorg-libXmu into destroot
---> Installing xorg-libXmu @1.1.0_0
---> Activating xorg-libXmu @1.1.0_0
---> Cleaning xorg-libXmu
---> Fetching R
---> Attempting to fetch R-2.13.0.tar.gz from http://distfiles.macports.org/R
---> Verifying checksum(s) for R
---> Extracting R
---> Configuring R
---> Building R
---> Staging R into destroot
---> Installing R @2.13.0_0+gcc44+recommended
---> Activating R @2.13.0_0+gcc44+recommended
---> Cleaning R
R 的版本 2.13
1. 先搜尋 port search R and statistic (statistics 多個 s 就找不到 )
>> R @2.13.0 (math, science)
>> R is GNU S - an interpreted language for statistical computing
2. sh-3.2# port install R @2.13.0
PS.安裝時要 fetching perl 5.12 ？？
processing detail
---> Computing dependencies for tiff
---> Fetching tiff
---> Attempting to fetch tiff-3.9.5.tar.gz from ftp://ftp.tw.FreeBSD.org/pub/FreeBSD/ports/distfiles/
---> Attempting to fetch tiff-3.9.5.tar.gz from ftp://ftp.tw.FreeBSD.org/pub/FreeBSD/ports/local-distfiles/
---> Attempting to fetch tiff-3.9.5.tar.gz from ftp://ftp.jp.FreeBSD.org/pub/FreeBSD/ports/distfiles/
---> Attempting to fetch tiff-3.9.5.tar.gz from ftp://ftp.jp.FreeBSD.org/pub/FreeBSD/ports/local-distfiles/
---> Attempting to fetch tiff-3.9.5.tar.gz from ftp://ftp.FreeBSD.org/pub/FreeBSD/ports/distfiles/
---> Attempting to fetch tiff-3.9.5.tar.gz from ftp://ftp.FreeBSD.org/pub/FreeBSD/ports/local-distfiles/
---> Attempting to fetch tiff-3.9.5.tar.gz from ftp://ftp.remotesensing.org/pub/libtiff/
---> Verifying checksum(s) for tiff
---> Extracting tiff
---> Configuring tiff
---> Building tiff
---> Staging tiff into destroot
---> Computing dependencies for tiff
---> Installing tiff @3.9.5_0
---> Deactivating tiff @3.9.4_0
---> Cleaning tiff
---> Activating tiff @3.9.5_0
---> Cleaning tiff
---> Computing dependencies for R
---> Dependencies to be installed: glib2 autoconf help2man p5-locale-gettext perl5 perl5.12 m4 automake libtool icu pango cairo libpixman libpng xorg-xcb-util xorg-libXmu xorg-libXt xorg-libsm xorg-libice
---> Fetching perl5.12
---> Attempting to fetch perl-5.12.3.tar.bz2 from http://www.cpan.org/src/5.0/
---> Verifying checksum(s) for perl5.12
---> Extracting perl5.12
---> Applying patches to perl5.12
---> Configuring perl5.12
---> Building perl5.12
---> Staging perl5.12 into destroot
---> Installing perl5.12 @5.12.3_1
---> Activating perl5.12 @5.12.3_1
---> Cleaning perl5.12
---> Fetching perl5
---> Verifying checksum(s) for perl5
---> Extracting perl5
---> Configuring perl5
---> Building perl5
---> Staging perl5 into destroot
---> Installing perl5 @5.12.3_1+perl5_12
---> Activating perl5 @5.12.3_1+perl5_12
---> Cleaning perl5
---> Fetching p5-locale-gettext
---> Attempting to fetch gettext-1.05.tar.gz from ftp://ftp.cpan.org/pub/CPAN/modules/by-module/Locale
---> Verifying checksum(s) for p5-locale-gettext
---> Extracting p5-locale-gettext
---> Applying patches to p5-locale-gettext
---> Configuring p5-locale-gettext
---> Building p5-locale-gettext
---> Staging p5-locale-gettext into destroot
---> Installing p5-locale-gettext @1.05_5
---> Activating p5-locale-gettext @1.05_5
---> Cleaning p5-locale-gettext
---> Fetching help2man
---> Attempting to fetch help2man-1.39.3.tar.gz from ftp://ftp.dti.ad.jp/pub/GNU/help2man
---> Attempting to fetch help2man-1.39.3.tar.gz from http://mirror.facebook.net/gnu/gnu/help2man
---> Attempting to fetch help2man-1.39.3.tar.gz from http://distfiles.macports.org/help2man
---> Verifying checksum(s) for help2man
---> Extracting help2man
---> Configuring help2man
---> Building help2man
---> Staging help2man into destroot
---> Installing help2man @1.39.3_0
---> Activating help2man @1.39.3_0
---> Cleaning help2man
---> Fetching m4
---> Attempting to fetch m4-1.4.16.tar.bz2 from ftp://ftp.dti.ad.jp/pub/GNU/m4
---> Attempting to fetch m4-1.4.16.tar.bz2 from http://mirror.facebook.net/gnu/gnu/m4
---> Attempting to fetch m4-1.4.16.tar.bz2 from http://distfiles.macports.org/m4
---> Verifying checksum(s) for m4
---> Extracting m4
---> Configuring m4
---> Building m4
---> Staging m4 into destroot
---> Installing m4 @1.4.16_0
---> Activating m4 @1.4.16_0
---> Cleaning m4
---> Fetching autoconf
---> Attempting to fetch autoconf-2.68.tar.bz2 from ftp://ftp.dti.ad.jp/pub/GNU/autoconf
---> Verifying checksum(s) for autoconf
---> Extracting autoconf
---> Configuring autoconf
---> Building autoconf
---> Staging autoconf into destroot
---> Installing autoconf @2.68_2
---> Activating autoconf @2.68_2
---> Cleaning autoconf
---> Fetching automake
---> Attempting to fetch automake-1.11.1.tar.bz2 from ftp://ftp.dti.ad.jp/pub/GNU/automake
---> Verifying checksum(s) for automake
---> Extracting automake
---> Configuring automake
---> Building automake
---> Staging automake into destroot
---> Installing automake @1.11.1_0
---> Activating automake @1.11.1_0
---> Cleaning automake
---> Fetching libtool
---> Attempting to fetch libtool-2.4.tar.gz from ftp://ftp.dti.ad.jp/pub/GNU/libtool
---> Verifying checksum(s) for libtool
---> Extracting libtool
---> Configuring libtool
---> Building libtool
---> Staging libtool into destroot
---> Installing libtool @2.4_0
---> Activating libtool @2.4_0
---> Cleaning libtool
---> Fetching glib2
---> Attempting to fetch glib-2.28.8.tar.bz2 from http://ftp.nara.wide.ad.jp/pub/X11/GNOME/sources/glib/2.28/
---> Verifying checksum(s) for glib2
---> Extracting glib2
---> Applying patches to glib2
---> Configuring glib2
---> Building glib2
---> Staging glib2 into destroot
---> Installing glib2 @2.28.8_0
---> Activating glib2 @2.28.8_0
---> Cleaning glib2
---> Fetching icu
---> Attempting to fetch icu4c-4_6_1-src.tgz from http://distfiles.macports.org/icu
---> Verifying checksum(s) for icu
---> Extracting icu
---> Applying patches to icu
---> Configuring icu
---> Building icu
---> Staging icu into destroot
---> Installing icu @4.6.1_0
---> Activating icu @4.6.1_0
---> Cleaning icu
---> Fetching libpixman
---> Attempting to fetch pixman-0.22.0.tar.bz2 from http://distfiles.macports.org/libpixman
---> Verifying checksum(s) for libpixman
---> Extracting libpixman
---> Configuring libpixman
---> Building libpixman
---> Staging libpixman into destroot
---> Installing libpixman @0.22.0_0
---> Activating libpixman @0.22.0_0
---> Cleaning libpixman
---> Fetching libpng
---> Attempting to fetch libpng-1.4.7.tar.bz2 from http://nchc.dl.sourceforge.net/libpng
---> Verifying checksum(s) for libpng
---> Extracting libpng
---> Configuring libpng
---> Building libpng
---> Staging libpng into destroot
---> Installing libpng @1.4.7_0
---> Activating libpng @1.4.7_0
---> Cleaning libpng
---> Fetching xorg-xcb-util
---> Attempting to fetch xcb-util-0.3.8.tar.bz2 from http://distfiles.macports.org/xorg-xcb-util
---> Verifying checksum(s) for xorg-xcb-util
---> Extracting xorg-xcb-util
---> Configuring xorg-xcb-util
---> Building xorg-xcb-util
---> Staging xorg-xcb-util into destroot
---> Installing xorg-xcb-util @0.3.8_0
---> Activating xorg-xcb-util @0.3.8_0
---> Cleaning xorg-xcb-util
---> Fetching cairo
---> Attempting to fetch cairo-1.10.2.tar.gz from http://distfiles.macports.org/cairo
---> Verifying checksum(s) for cairo
---> Extracting cairo
---> Configuring cairo
---> Building cairo
---> Staging cairo into destroot
---> Installing cairo @1.10.2_3+x11
---> Activating cairo @1.10.2_3+x11
---> Cleaning cairo
---> Fetching pango
---> Attempting to fetch pango-1.28.4.tar.bz2 from http://ftp.nara.wide.ad.jp/pub/X11/GNOME/sources/pango/1.28
---> Verifying checksum(s) for pango
---> Extracting pango
---> Applying patches to pango
---> Configuring pango
---> Building pango
---> Staging pango into destroot
---> Installing pango @1.28.4_0+x11
---> Activating pango @1.28.4_0+x11
---> Cleaning pango
---> Fetching xorg-libice
---> Attempting to fetch libICE-1.0.7.tar.bz2 from http://distfiles.macports.org/xorg-libice
---> Verifying checksum(s) for xorg-libice
---> Extracting xorg-libice
---> Configuring xorg-libice
---> Building xorg-libice
---> Staging xorg-libice into destroot
---> Installing xorg-libice @1.0.7_0
---> Activating xorg-libice @1.0.7_0
---> Cleaning xorg-libice
---> Fetching xorg-libsm
---> Attempting to fetch libSM-1.2.0.tar.bz2 from http://distfiles.macports.org/xorg-libsm
---> Verifying checksum(s) for xorg-libsm
---> Extracting xorg-libsm
---> Configuring xorg-libsm
---> Building xorg-libsm
---> Staging xorg-libsm into destroot
---> Installing xorg-libsm @1.2.0_0
---> Activating xorg-libsm @1.2.0_0
---> Cleaning xorg-libsm
---> Fetching xorg-libXt
---> Attempting to fetch libXt-1.1.1.tar.bz2 from http://distfiles.macports.org/xorg-libXt
---> Verifying checksum(s) for xorg-libXt
---> Extracting xorg-libXt
---> Configuring xorg-libXt
---> Building xorg-libXt
---> Staging xorg-libXt into destroot
---> Installing xorg-libXt @1.1.1_0
---> Activating xorg-libXt @1.1.1_0
---> Cleaning xorg-libXt
---> Fetching xorg-libXmu
---> Attempting to fetch libXmu-1.1.0.tar.bz2 from http://distfiles.macports.org/xorg-libXmu
---> Verifying checksum(s) for xorg-libXmu
---> Extracting xorg-libXmu
---> Configuring xorg-libXmu
---> Building xorg-libXmu
---> Staging xorg-libXmu into destroot
---> Installing xorg-libXmu @1.1.0_0
---> Activating xorg-libXmu @1.1.0_0
---> Cleaning xorg-libXmu
---> Fetching R
---> Attempting to fetch R-2.13.0.tar.gz from http://distfiles.macports.org/R
---> Verifying checksum(s) for R
---> Extracting R
---> Configuring R
---> Building R
---> Staging R into destroot
---> Installing R @2.13.0_0+gcc44+recommended
---> Activating R @2.13.0_0+gcc44+recommended
---> Cleaning R
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