= 2009-05-19 = * [專案] 陽明生物資訊計算叢集設定 * 上次遇到 firmware-bnx2 的問題，在 Debian Lenny 上無法正常重建網路開機環境，因此改用 Ubuntu 9.04 進行網路安裝，過程很順利。 * 硬碟 I/O 很慢的主因是有做硬體 RAID，而且持續在做 SYNC 的動作，因此只要把 RAID 卡關掉就可以比較快速地開進作業系統。 * 參考[http://wiki.lustre.org/index.php/Debian_Install Lustre on Debian]，在 Ubuntu 9.04 上編譯 Lustre 核心模組。 * [失敗] 因為 Lustre 目前官方只支援到 2.6.22，因此無法 patch 產生 2.6.28 的核心模組。 {{{ ~$ sudo apt-get update ~$ sudo apt-get install linux-patch-lustre lustre-source linux-source kernel-package ~$ cd /usr/src /usr/src$ sudo tar jxvf linux-source-2.6.28.tar.bz2 /usr/src$ cd linux-source-2.6.28/ /usr/src/linux-source-2.6.28$ sudo cp /boot/config-2.6.28-11-generic .config /usr/src/linux-source-2.6.28$ sudo make oldconfig /usr/src/linux-source-2.6.28$ sudo su /usr/src/linux-source-2.6.28# tar jxvf ../lustre.tar.bz2 /usr/src/linux-source-2.6.28# export CONCURRENCY_LEVEL=3 /usr/src/linux-source-2.6.28# make-kpkg clean /usr/src/linux-source-2.6.28# make-kpkg --rootcmd fakeroot --added-patches=lustre --initrd --append-to-version "-lustre-1.6.5.1-4" --revision=20090519 kernel_image }}} * 安裝 JDK {{{ ~$ sudo apt-get install sun-java6-jdk }}} * 安裝 R 及 Bioconductor {{{ ~$ sudo apt-get install r-base ~$ sudo R > source("http://www.bioconductor.org/biocLite.R") > biocLite() Warning messages: 1: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : dependency ‘Matrix’ is not available 2: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : installation of package 'IRanges' had non-zero exit status 3: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : installation of package 'Biostrings' had non-zero exit status }}} * 第一個錯誤是找不到 r-cran-matrix 套件，這裡用暴力法安裝所有在 apt 套件庫裡的 R 相關套件(除了 rjava 外) {{{ ~$ sudo apt-get install `apt-cache search --names-only "^r-cran" | awk '{ print $1 }' | grep -v "r-cran-rjava" ` }}} * 裝好之後，重裝一次 Bioconductor 就沒有錯誤了。 {{{ ~$ sudo apt-get install r-base ~$ sudo R > source("http://www.bioconductor.org/biocLite.R") > biocLite() > library() Packages in library '/usr/local/lib/R/site-library': affy Methods for Affymetrix Oligonucleotide Arrays affydata Affymetrix Data for Demonstration Purpose affyio Tools for parsing Affymetrix data files affyPLM Methods for fitting probe-level models affyQCReport QC Report Generation for affyBatch objects annaffy Annotation tools for Affymetrix biological metadata annotate Annotation for microarrays AnnotationDbi Annotation Database Interface Biobase Biobase: Base functions for Bioconductor Biostrings String objects representing biological sequences, and matching algorithms DynDoc Dynamic document tools gcrma Background Adjustment Using Sequence Information genefilter genefilter: methods for filtering genes from microarray experiments geneplotter Grapics related functions for Bioconductor GO.db A set of annotation maps describing the entire Gene Ontology hgu95av2.db Affymetrix Human Genome U95 Set annotation data (chip hgu95av2) IRanges Low-level containers for storing sets of integer ranges KEGG.db A set of annotation maps for KEGG limma Linear Models for Microarray Data marray Exploratory analysis for two-color spotted microarray data matchprobes Basic infrastructure for using oligonucleotide microarray reporter sequence information for preprocessing and quality assessment multtest Resampling-based multiple hypothesis testing preprocessCore A collection of pre-processing functions ROC utilities for ROC, with uarray focus RSQLite SQLite interface for R simpleaffy Very simple high level analysis of Affymetrix data vsn Variance stabilization and calibration for microarray data xtable Export tables to LaTeX or HTML Packages in library '/usr/lib/R/site-library': abind Combine multi-dimensional arrays acepack ace() and avas() for selecting regression transformations adapt adapt -- multidimensional numerical integration bayesm Bayesian Inference for Marketing/Micro-econometrics bitops Functions for Bitwise operations cairoDevice Cairo-based cross-platform antialiased graphics device driver. car Companion to Applied Regression caTools Tools: moving window statistics, GIF, Base64, ROC AUC, etc. chron Chronological objects which can handle dates and times coda Output analysis and diagnostics for MCMC combinat combinatorics utilities date Functions for handling dates DBI R Database Interface Design Design Package eco R Package for Ecological Inference in 2x2 Tables effects Effect Displays for Linear, Generalized Linear, Multinomial-Logit, and Proportional-Odds Logit Models fArma ARMA Time Series Modelling fAsianOptions EBM and Asian Option Valuation fAssets Rmetrics - Assets Selection and Modelling fBasics Rmetrics - Markets and Basic Statistics fBonds Bonds and Interest Rate Models fCalendar Chronological and Calendarical Objects fCopulae Rmetrics - Dependence Structures with Copulas fEcofin Economic and Financial Data Sets fExoticOptions Exotic Option Valuation fExtremes Rmetrics - Extreme Financial Market Data fGarch Rmetrics - Autoregressive Conditional Heteroskedastic Modelling fImport Rmetrics - Economic and Financial Data Import fMultivar Multivariate Market Analysis fNonlinear Nonlinear and Chaotic Time Series Modelling fOptions Basics of Option Valuation fPortfolio Rmetrics - Portfolio Selection and Optimization fRegression Regression Based Decision and Prediction fSeries Financial Time Series Objects fTrading Technical Trading Analysis fUnitRoots Trends and Unit Roots fUtilities Function Utilities gdata Various R programming tools for data manipulation genetics Population Genetics getopt C-like getopt behavior. gmaps Wrapper and auxilliary functions for maps package to work with grid graphics system. gmodels Various R programming tools for model fitting gplots Various R programming tools for plotting data gregmisc Greg's Miscellaneous Functions gtools Various R programming tools haplo.stats Statistical Analysis of Haplotypes with Traits and Covariates when Linkage Phase is Ambiguous hdf5 HDF5 Hmisc Harrell Miscellaneous its Irregular Time Series jit Just-in-time compiler for the R language latticeExtra Extra Graphical Utilities Based on Lattice lme4 Linear mixed-effects models using S4 classes lmtest Testing Linear Regression Models lpSolve Interface to Lp_solve v. 5.5 to solve linear/integer programs mapdata Extra Map Databases mapproj Map Projections maps Draw Geographical Maps MatchIt MatchIt: Nonparametric Preprocessing for Parametric Casual Inference Matrix Sparse and Dense Matrix Classes and Methods MCMCpack Markov chain Monte Carlo (MCMC) Package misc3d Miscellaneous 3D Plots mnormt The multivariate normal and t distributions MNP R Package for Fitting the Multinomial Probit Model multcomp Simultaneous Inference in General Parametric Models mvtnorm Multivariate Normal and t Distributions nws R functions for NetWorkSpaces and Sleigh polspline Polynomial spline routines pscl Political Science Computational Laboratory, Stanford University psy Various procedures used in psychometry qtl Tools for analyzing QTL experiments quadprog Functions to solve Quadratic Programming Problems. qvalue Q-value estimation for false discovery rate control Rcmdr R Commander RColorBrewer ColorBrewer palettes Rcpp Rcpp R/C++ interface package relimp Relative Contribution of Effects in a Regression Model rggobi Interface between R and GGobi rgl 3D visualization device system (OpenGL) Rglpk R/GNU Linear Programming Kit Interface RGtk2 R bindings for Gtk 2.8.0 and above Rmetrics Rmetrics - Financial Engineering and Computational Finance Rmpi Interface (Wrapper) to MPI (Message-Passing Interface) RMySQL R interface to the MySQL database robustbase Basic Robust Statistics ROCR Visualizing the performance of scoring classifiers. RODBC ODBC Database Access rpvm R interface to PVM (Parallel Virtual Machine) RQuantLib R interface to the QuantLib library Rserve Binary R server rsprng R interface to SPRNG (Scalable Parallel Random Number Generators) RUnit R Unit test framework sandwich Robust Covariance Matrix Estimators sm Smoothing methods for nonparametric regression and density estimation sn The skew-normal and skew-t distributions snow Simple Network of Workstations strucchange Testing, Monitoring and Dating Structural Changes timeDate Rmetrics - Chronological and Calendarical Objects timeSeries Rmetrics - Financial Time Series Objects tkrplot TK Rplot tseries Time series analysis and computational finance urca Unit root and cointegration tests for time series data VGAM Vector Generalized Linear and Additive Models XML Tools for parsing and generating XML within R and S-Plus. Zelig Everyone's Statistical Software zoo Z's ordered observations Packages in library '/usr/lib/R/library': base The R Base Package boot Bootstrap R (S-Plus) Functions (Canty) class Functions for Classification cluster Cluster Analysis Extended Rousseeuw et al. codetools Code Analysis Tools for R datasets The R Datasets Package foreign Read Data Stored by Minitab, S, SAS, SPSS, Stata, Systat, dBase, ... graphics The R Graphics Package grDevices The R Graphics Devices and Support for Colours and Fonts grid The Grid Graphics Package KernSmooth Functions for kernel smoothing for Wand & Jones (1995) lattice Lattice Graphics MASS Main Package of Venables and Ripley's MASS methods Formal Methods and Classes mgcv GAMs with GCV smoothness estimation and GAMMs by REML/PQL nlme Linear and Nonlinear Mixed Effects Models nnet Feed-forward Neural Networks and Multinomial Log-Linear Models rpart Recursive Partitioning spatial Functions for Kriging and Point Pattern Analysis splines Regression Spline Functions and Classes stats The R Stats Package stats4 Statistical Functions using S4 Classes survival Survival analysis, including penalised likelihood. tcltk Tcl/Tk Interface tools Tools for Package Development utils The R Utils Package }}} * 額外加裝 [http://cran.r-project.org/web/packages/ape/ R ape] 套件 - [wiki:jazz/09-04-13 參考步驟] (nlme, lattice 均有新版) {{{ # apt-get install libc6-dev gfortran liblapack-dev # wget http://cran.r-project.org/src/contrib/gee_4.13-13.tar.gz # R CMD INSTALL gee_4.13-13.tar.gz # wget http://cran.r-project.org/src/contrib/nlme_3.1-91.tar.gz # R CMD INSTALL nlme_3.1-91.tar.gz # wget http://cran.r-project.org/src/contrib/lattice_0.17-25.tar.gz # R CMD INSTALL lattice_0.17-25.tar.gz # wget http://cran.r-project.org/src/contrib/ape_2.3.tar.gz # R CMD INSTALL ape_2.3.tar.gz }}} * 加裝 [http://software.intel.com/en-us/articles/non-commercial-software-development/ Intel C++ Compiler for Linux] - 先註冊要序號，然後下載 IA-32 與 IA-64 的版本。這次裝的 Ubuntu 9.04 是用 i686 32 位元版本，因此這次先裝 IA-32 版本。 == Virtualization == * [備忘] 裝 Xen 要記得裝 [http://packages.debian.org/bridge-utils bridge-utils] == Mobile Computing == * 同步機制一直是行動裝置一個極為關鍵的需求，無論是否採用雲端運算，大家還是希望可以自己保有自己的私人資料在行動裝置上。最近 Synthesis AG 釋出開放原始碼的 [http://www.synthesis.ch/indefero/index.php/p/libsynthesis/ libsynthesis] 可以讓開發者在 Linux 平台上撰寫自己的 SyncML-DS (SyncML Data Sync) 應用程式。還在 Moblin 的 [http://git.moblin.org/cgit.cgi/libsynthesis Git] 上維護了一份原始碼。-- [http://lwn.net/Articles/333059/ 相關新聞] == 生活常識 == * [http://www.cw.com.tw/article/print.jsp?id=37700 超級防蚊計劃] * [http://www.cw.com.tw/article/print.jsp?id=37690 睡不好！改善品質第1步：週末不補眠]