Changes between Version 6 and Version 7 of jazz/09-05-19

Timestamp:

May 19, 2009, 3:14:40 PM (16 years ago)

Author:

jazz

Comment:

--

jazz/09-05-19

@@ -20 +20 @@
 /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
+}}}
 
 == Virtualization ==