- 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
