R version 2.13.0 (2011-04-13) Copyright (C) 2011 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: x86_64-pc-linux-gnu (64-bit) R est un logiciel libre livré sans AUCUNE GARANTIE. Vous pouvez le redistribuer sous certaines conditions. Tapez 'license()' ou 'licence()' pour plus de détails. R est un projet collaboratif avec de nombreux contributeurs. Tapez 'contributors()' pour plus d'information et 'citation()' pour la façon de le citer dans les publications. Tapez 'demo()' pour des démonstrations, 'help()' pour l'aide en ligne ou 'help.start()' pour obtenir l'aide au format HTML. Tapez 'q()' pour quitter R. > date() [1] "Thu Sep 22 16:13:30 2011" > ################################################### > ### chunk number 2: provi1 > ################################################### > #line 157 "/bge/penel/verif_pedadoc/pedadoc/fichestd/tdr11//tdr11.rnw" > getwd() [1] "/bge/penel/verif_fiches_2" > w <- 1:25 > w [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 > > > ################################################### > ### chunk number 3: provi2 > ################################################### > #line 173 "/bge/penel/verif_pedadoc/pedadoc/fichestd/tdr11//tdr11.rnw" > library() Packages dans la bibliothèque '/usr/remote/R_LIBS_ALTERNAT' : deSolve General solvers for initial value problems of ordinary differential equations (ODE), partial differential equations (PDE), differential algebraic equations (DAE), and delay differential equations (DDE). diversitree diversitree: comparative phylogenetic tests of diversification raster Geographic analysis and modeling with raster data rjags Bayesian graphical models using MCMC subplex Subplex optimization algorithm Packages dans la bibliothèque '/usr/remote/R_LIBS' : ade4 Analysis of Ecological Data : Exploratory and Euclidean methods in Environmental sciences ade4TkGUI ade4 Tcl/Tk Graphical User Interface adehabitat Analysis of habitat selection by animals adehabitatHR Home range Estimation adehabitatHS Analysis of habitat selection by animals adehabitatLT Analysis of animal movements adehabitatMA Tools to Deal with Raster Maps 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 akima Interpolation of irregularly spaced data annaffy Annotation tools for Affymetrix biological metadata annotate Annotation for microarrays AnnotationDbi Annotation Database Interface ape Analyses of Phylogenetics and Evolution Biobase Biobase: Base functions for Bioconductor biomaRt Interface to BioMart databases (e.g. Ensembl, COSMIC ,Wormbase and Gramene) Biostrings String objects representing biological sequences, and matching algorithms bitops Functions for Bitwise operations BSgenome Infrastructure for Biostrings-based genome data packages car Companion to Applied Regression Category Category Analysis caTools Tools: moving window statistics, GIF, Base64, ROC AUC, etc. cghseg Joint segmentation, calling and normalization of multiple CGH profiles CircStats Circular Statistics, from "Topics in circular Statistics" (2001) cluster Cluster Analysis Extended Rousseeuw et al. coda Output analysis and diagnostics for MCMC DBI R Database Interface DEGseq Identify Differentially Expressed Genes from RNA-seq data deldir Delaunay Triangulation and Dirichlet (Voronoi) Tessellation. DESeq Digital gene expresion analysis based on the negative binomial distribution digest Create cryptographic hash digests of R objects DynDoc Dynamic document tools edgeR Empirical analysis of digital gene expression data in R fields Tools for spatial data fitdistrplus Help to fit of a parametric distribution to non-censored or censored data foreign Read Data Stored by Minitab, S, SAS, SPSS, Stata, Systat, dBase, ... gam Generalized Additive Models gcrma Background Adjustment Using Sequence Information gdata Various R programming tools for data manipulation gee Generalized Estimation Equation solver genefilter genefilter: methods for filtering genes from microarray experiments geneplotter Graphics related functions for Bioconductor GenomeGraphs Plotting genomic information from Ensembl genomeIntervals Operations on genomic intervals GenomicFeatures Support package for genomic annotations GenomicRanges Representation and manipulation of genomic intervals Genominator Analyze, manage and store genomic data geoR Analysis of geostatistical data GO.db A set of annotation maps describing the entire Gene Ontology GOstats Tools for manipulating GO and microarrays. goTools Functions for Gene Ontology database gpclib General Polygon Clipping Library for R gplots Various R programming tools for plotting data graph graph: A package to handle graph data structures GSEABase Gene set enrichment data structures and methods gtools Various R programming tools hgu95av2.db Affymetrix Human Genome U95 Set annotation data (chip hgu95av2) Hmisc Harrell Miscellaneous hwriter HTML Writer - Outputs R objects in HTML format igraph Network analysis and visualization impute impute: Imputation for microarray data intervals Tools for working with points and intervals IRanges Infrastructure for manipulating intervals on sequences KEGG.db A set of annotation maps for KEGG lattice Lattice Graphics limma Linear Models for Microarray Data locfit Local Regression, Likelihood and Density Estimation. made4 Multivariate analysis of microarray data using ADE4 mapproj Map Projections maps Draw Geographical Maps maptools Tools for reading and handling spatial objects marray Exploratory analysis for two-color spotted microarray data MASS Main Package of Venables and Ripley's MASS mclust Model-Based Clustering / Normal Mixture Modeling misc3d Miscellaneous 3D Plots multtest Resampling-based multiple hypothesis testing nlme Linear and Nonlinear Mixed Effects Models nnet Feed-forward Neural Networks and Multinomial Log-Linear Models nws R functions for NetWorkSpaces and Sleigh org.Hs.eg.db Genome wide annotation for Human PBSmapping PBS Mapping 2.59 pixmap Bitmap Images (``Pixel Maps'') preprocessCore A collection of pre-processing functions qvalue Q-value estimation for false discovery rate control RandomFields Simulation and Analysis of Random Fields RArcInfo Functions to import data from Arc/Info V7.x binary coverages raster Geographic analysis and modeling with raster data RBGL An interface to the BOOST graph library RBioinf RBioinf RColorBrewer ColorBrewer palettes RCurl General network (HTTP/FTP/...) client interface for R rgdal Bindings for the Geospatial Data Abstraction Library rgeos Interface to Geometry Engine - Open Source (GEOS) rgl 3D visualization device system (OpenGL) rjags Bayesian graphical models using MCMC rlecuyer R interface to RNG with multiple streams R.methodsS3 Utility function for defining S3 methods Rmpi Interface (Wrapper) to MPI (Message-Passing Interface) RNAseq Count summarization and normalization pipeline for Next Generation Sequencing data. R.oo R object-oriented programming with or without references rpanel Simple interactive controls for R using the tcltk library. Rsamtools Import aligned BAM file format sequences into R / Bioconductor rsprng R interface to SPRNG (Scalable Parallel Random Number Generators) RSQLite SQLite interface for R rtracklayer R interface to genome browsers and their annotation tracks R.utils Various programming utilities samr SAM: Significance Analysis of Microarrays scatterplot3d 3D Scatter Plot segmented Segmented relationships in regression models seqinr Biological Sequences Retrieval and Analysis ShortRead Base classes and methods for high-throughput short-read sequencing data. simpleaffy Very simple high level analysis of Affymetrix data sm Smoothing methods for nonparametric regression and density estimation snow Simple Network of Workstations sp classes and methods for spatial data spam SPArse Matrix SparseM Sparse Linear Algebra spatstat Spatial Point Pattern analysis, model-fitting, simulation, tests spdep Spatial dependence: weighting schemes, statistics and models splancs Spatial and Space-Time Point Pattern Analysis sp.old ** No title available ** survival Survival analysis, including penalised likelihood. tkrplot TK Rplot vegan Community Ecology Package vsn Variance stabilization and calibration for microarray data waveslim Basic wavelet routines for one-, two- and three-dimensional signal processing wavethresh Software to perform wavelet statistics and transforms. XML Tools for parsing and generating XML within R and S-Plus. xtable Export tables to LaTeX or HTML Packages dans la bibliothèque '/bge/penel/R/x86_64-pc-linux-gnu-library/2.6' : ade4 Analysis of Ecological Data : Exploratory and Euclidean methods in Environmental sciences adehabitat Analysis of habitat selection by animals Packages dans la bibliothèque '/usr/local/lib/R/site-library' : ade4 Analysis of Ecological Data : Exploratory and Euclidean methods in Environmental sciences ade4TkGUI ade4 Tcl/Tk Graphical User Interface akima Interpolation of irregularly spaced data ape Analyses of Phylogenetics and Evolution cghseg cghseg provides functions for the segmentation of CGH data coda Output analysis and diagnostics for MCMC deldir Delaunay Triangulation and Dirichlet (Voronoi) Tessellation. gam Generalized Additive Models gee Generalized Estimation Equation solver geoR Analysis of geostatistical data ggplot2 An implementation of the Grammar of Graphics gpclib General Polygon Clipping Library for R mapproj Map Projections maps Draw Geographical Maps maptools Tools for reading and handling spatial objects Matrix Sparse and Dense Matrix Classes and Methods misc3d Miscellaneous 3D Plots PBSmapping PBS Mapping 2.59 pixmap Bitmap Images (``Pixel Maps'') plyr Tools for splitting, applying and combining data proto Prototype object-based programming RandomFields Simulation and Analysis of Random Fields RArcInfo Functions to import data from Arc/Info V7.x binary coverages RColorBrewer ColorBrewer palettes reshape Flexibly reshape data. rgl 3D visualization device system (OpenGL) rjags Bayesian graphical models using MCMC Rmpi Interface (Wrapper) to MPI (Message-Passing Interface) rpanel Simple interactive controls for R using the tcltk library. scatterplot3d 3D Scatter Plot segmented Segmented relationships in regression models seqinr Biological Sequences Retrieval and Analysis sm Smoothing methods for nonparametric regression and density estimation sp classes and methods for spatial data spam SPArse Matrix SparseM Sparse Linear Algebra spdep Spatial dependence: weighting schemes, statistics and models splancs Spatial and Space-Time Point Pattern Analysis tripack Triangulation of irregularly spaced data waveslim Basic wavelet routines for one-, two- and three-dimensional signal processing wavethresh Software to perform wavelet statistics and transforms. Packages dans la bibliothèque '/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 compiler The R Compiler Package 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 Support Functions and Datasets for Venables and Ripley's MASS Matrix Sparse and Dense Matrix Classes and Methods methods Formal Methods and Classes mgcv GAMs with GCV/AIC/REML smoothness estimation and GAMMs by 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 Message d'avis : In library() : la bibliothèque ‘/usr/lib/R/site-library’ ne contient aucun package > > > ################################################### > ### chunk number 4: dow1 eval=FALSE > ################################################### > ## #line 192 "/bge/penel/verif_pedadoc/pedadoc/fichestd/tdr11//tdr11.rnw" > ## montripack <- download.packages("tripack",destdir=getwd())[,2] > ## montripack > ## install.packages(montripack, getwd(), CRAN = NULL) > > > ################################################### > ### chunk number 5: dow2 eval=FALSE > ################################################### > ## #line 202 "/bge/penel/verif_pedadoc/pedadoc/fichestd/tdr11//tdr11.rnw" > ## library(tripack) > > > ################################################### > ### chunk number 6: dow3 eval=FALSE > ################################################### > ## #line 215 "/bge/penel/verif_pedadoc/pedadoc/fichestd/tdr11//tdr11.rnw" > ## library(tripack,lib.loc=getwd()) > > > ################################################### > ### chunk number 7: dow3bis > ################################################### > #line 219 "/bge/penel/verif_pedadoc/pedadoc/fichestd/tdr11//tdr11.rnw" > library(tripack) Erreur : le package 'tripack' a été compilé avant R 2.10.0 : veuillez réinstaller une version plus récente, s'il-vous-plait Exécution arrêtée