R与BioConductor包的安装与非官方镜像的使用.pptx

RInstallationandadministrationHowtocreateanduseaR BioConductormirror WangChongzhi Asia PacificAnimalResearchwangchongzhi 2 RProjectContributors R R inStatisticsDepartmentoftheUniversityofAuckland Theco creatorofR UniversityofAucklandAssociateProfessorofStatisticsDr RossIhaka wasawardedtheCatalystLifetimeAchievementinOpenSourceAwardatthe2010NewZealandOpenSourceAwards InitiationofRproject 3 RDevelopmentCoreTeam RProjectContributors DouglasBatesJohnChambersPeterDalgaardSethFalconRobertGentlemanKurtHornikStefanoIacusRossIhakaFriedrichLeischUweLiggesThomasLumleyMartinMaechlerDuncanMurdochPaulMurrellMartynPlummerBrianRipleyDeepayanSarkarDuncanTempleLangLukeTierneySimonUrbanekplusHeinerSchwarteuptoOctober1999andGuidoMasarottouptoJune2003 ResearchProjectslme4 linear generalizedlinearandnonlinearmixedmodelsinR Matrix classesandmethodsforsparseanddensematricesinR R anOpenSourceimplementationoftheSlanguageBioconductor softwareforbioinformatics BellLabshostedthisone dayworkshopinrecognitionofJohn scontributionsandleadershipinstatisticalcomputing2 SoftwareforDataAnalysis ProgrammingwithR3 Object orientedprogramminginR 78 OnMethodsofAsymptoticApproximationtoMultivariateDistributions 4 theinvaluablehelpindonatingcode bugfixesanddocumentation RProjectContributors ValerioAimale ThomasBaier RogerBivand BenBolker DavidBrahm G ranBrostr m PatrickBurns VinceCarey SaikatDebRoy BrianD Urso LyndonDrake DirkEddelbuettel JohnFox PaulGilbert TorstenHothorn RobertKing KjetilKjernsmo PhilippeLambert JandeLeeuw JimLindsey PatrickLindsey CatherineLoader GordonMaclean JohnMaindonald DavidMeyer JensOehlsch gel SteveOncley RichardO Keefe HubertPalme Jos C Pinheiro AnthonyRossini JonathanRougier G ntherSawitzki BillSimpson GordonSmyth AdrianTrapletti TerryTherneau BillVenables GregoryR Warnes AndreasWeingessel MortenWelinder SimonWood andAchimZeileis RFoundationMembers SupportersBenefactors Institutions DonorsSupportingMembersOrdinaryMembers 5 6 What sR Risalanguageandenvironmentforstatisticalcomputingandgraphics RcanbeconsideredasadifferentimplementationofS Rprovidesawidevarietyofstatisticalandgraphicaltechniques Rishighlyextensible RisavailableasFreeSoftwareunderGNUGPL Risanintegratedsuiteofsoftwarefacilitiesfordatamanipulation calculationandgraphicaldisplay C C andFortrancodecanbelinkedandcalledatruntime ManyusersthinkofRasastatisticssystem RhasitsownLaTeX likedocumentationformat 7 R源程序 R社区 R核心团队 R刊物 R书籍 R会议 R关联项目 Bioconductor Forge RGraphGallery R主页UserGroups 中文社区 统计之都 国际 useR 中国 COS ChatOpenShare 上百种 包括统计编程 统计模型 数据分析 统计图示 以及forBioinformatics TheRJournal Volume4 2 June2012 20位 牛津大学 AT T实验室等 累计更新了95个版本1997年959K 2013年 24M 8 ObtainingR Sources binariesanddocumentationforRcanbeobtainedviaCRAN the ComprehensiveRArchiveNetwork http cran r project org CRANisanetworkofftpandwebservers PleaseusetheCRANmirrornearesttoyou DownloadRforLinuxDownloadRfor Mac OSXDownloadRforWindows Precompiledbinarydistributionsofthebasesystem SourceCodeforallPlatforms Thelatestrelease 2013 04 03 MaskedMarvel R 3 0 0 tar gzSourcesofRalphaandbetareleasesDailysnapshotsofcurrentpatchedanddevelopmentversionsSourcecodeofolderversions 9 InstallingRunderUnix alikes tar xfR x y z tar gz orgzip dcR x y z tar gz tar xf ChooseadirectorytoinstalltheRtreeandunpackingthesources configure prefix where you want R to gomakemakecheckmakeinstallprefix path to here Issuethefollowingcommands makeinstall tests bin RCMDmakecheck devel bin RCMDmakecheck all TestinganInstallation 10 InvokingRfromcmdline R options outfile AttheWindowscommand line Rterm exeispreferredtoR cmdlineonUNIXorWindowstostartthemainRprogram RCMDBATCH argsarg1arg2 foo R Rscriptfoo Rarg1arg2 ScriptingwithR R HOME etc RenvironR HOME etc Rprofile site thedefaultsettings writeexecutablescriptfileslike path to Rscript 11 Rpackages CRANTaskViews 12 Rpackages CRANTaskViews 13 What sBioconductor toolsfortheanalysisandcomprehensionofhigh throughputgenomicdata usestheRstatisticalprogramminglanguage andisopensourceandopendevelopment tworeleaseseachyear 671packages andanactiveusercommunity availableasanAmazonMachineImage AMI Alargenumberofmeta datapackagesprovidepathway organism microarrayandotherannotations ThefunctionalscopeincludestheanalysisofDNAmicroarray sequence flow SNP andotherdata TheBioconductorprojectstartedin2001andisoverseenbyacoreteam basedprimarilyattheFredHutchinsonCancerResearchCenter andbyothermemberscomingfromUSandinternationalinstitutions 14 GoalsoftheBioconductor ThebroadgoalsoftheBioconductorprojectare Toprovidewidespreadaccesstoabroadrangeofpowerfulstatisticalandgraphicalmethodsfortheanalysisofgenomicdata Tofacilitatetheinclusionofbiologicalmetadataintheanalysisofgenomicdata e g literaturedatafromPubMed annotationdatafromEntrezgenes Toprovideacommonsoftwareplatformthatenablestherapiddevelopmentanddeploymentofextensible scalable andinteroperablesoftware Tofurtherscientificunderstandingbyproducinghigh qualitydocumentationandreproducibleresearch Totrainresearchersoncomputationalandstatisticalmethodsfortheanalysisofgenomicdata 15 Training relatedetc Bioconductorprovidestrainingincomputationalandstatisticalmethodsfortheanalysisofgenomicdata 20122011201020092008200720062005200420032002RelatedprojectsBioJavaBioPerlBioPythonRgalaxy InstallBioconductorPackageswithaccesstointernetsource http bioconductor org biocLite R biocLite installcorepackagesbiocLite c GenomicFeatures AnnotationDbi installspecificpackages 16 17 GeneralViewtoRPackages Add onpackagesinRbasecompilerdatasetsgrDevicesgraphicsgridmethodsparallelsplinesstatstat4tcltktoolsutilsAdd onpackagesfromCRANrecommendedpackagesKernSmoothMASSMatrixbootclassclustercodetoolsforeignlatticemgcvnlmennetrpartspatialsurvivalSeetheCRANcontributedpackagespageformoreinformationAdd onpackagesfromBioconductorOtheradd onpackagesadd onpackagesuserself defined 18 defaultRpackages getOption defaultPackages 1 datasets utils grDevices graphics stats methods plus ofcourse base ThiscanbechangedbyR DEFAULT PACKAGES e g in Rprofile SettingR DEFAULT PACKAGES NULLensuresthatonlypackagebaseisloaded reducethesetforspeedwhenscriptingalsousedtocustomizeR e g forclassuse 19 Managinglibraries RpackagesareinstalledintolibrariesUserscanhaveoneormorelibraries normallyspecifiedbytheenvironmentvariableR LIBS USER SeedefaultvalueviaSys getenv R LIBS USER BothR LIBS USERandR LIBS SITEcanspecifymultiplelibrarypaths separatedbycolons semicolonsonWindows 20 Installingpackages Packagesmaybedistributedinsourceformorcompiledbinaryform Installingsourcepackagesrequirescompilersandrelatedtools Binarypackagesareplatform specific RCMDINSTALLpath pkg version tar gzspecifyimplicitlyorexplicitlythelibrarytowhichthepackageistobeinstalled RCMDINSTALL llibpath pkg version tar gzwherelibgivesthepathtothelibrarytreetoinstallto Installingpackages 1 Unix likeonly 21 Installingpackages Formostusersitsufficestocall install packages pkgname oritsGUIequivalentiftheintentionistoinstallaCRANpackageandinternetaccessisavailable RCMDINSTALL l path to librarypkg1pkg2 lcanbeomitted shownby libPaths useRCMDINSTALL helptoseethelistofoptionsavailable Installingpackages 2 internetavailable 22 Installingpackages InstallingCRANpackagesfromwithinR1 settheoptionCRANtoyournearestCRANmirror chooseCRANmirror graphics FLASE 2 downloadandinstallpackagespkg1andpkg2by install packages c pkg1 pkg2 Theessentialdependenciesofthespecifiedpackageswillalsobefetched 2 1 fetchapackageandallthoseitdependson inanyway thatarenotalreadyinstalled like install packages Rcmdr dependencies TRUE Installingpackages 3 internetavailable 23 Installingpackages choosethepackagerepositoriestobeused setRepositories graphics FALSE 1 CRAN2 BioCsoftware3 BioCannotation4 BioCexperiment5 BioCextra6 Omegahat7 R Forge8 setRepositories addURLs c CRANbgi ftp 10 0 0 10 cran graphics FALSE Installingpackages 4 setpackagerepositories 24 Installingpackages options BioC mirror http 10 30 0 223 bioconductor setRepositories graphics FALSE 1 CRAN2 BioCsoftware3 BioCannotation4 BioCexperiment5 BioCextra6 Omegahat7 R Forge8 Enteroneormorenumbersseparatedbyspaces oranemptylinetocancel1 2然后常规install packages即可 BioC的四项都用BioC mirror Installingpackages 5 BioConductorpackages 选择BioC的项 比如software 这里输入2 win和Linux不一样 25 Usepackages Youcan load theinstalledpackagepkgbylibrary pkg Youcanthenfindoutwhichfunctionsitprovidesbytypingoneoflibrary help pkg help package pkg Youcanunloadtheloadedpackagepkgbydetach package pkg unload TRUE 26 Update removepackages update packagesremove packages 27 28 CRANMirror PHPacceptsonlyuptotwomirrorspercountry wethinktheremaybeneedtotreatChinadifferentfrom say Luxembourg TheCRANmastersiteatWUWien Austria canbefoundattheURLshttp cran r project orgftp cran r project org pub R rsync cran r project org CRANAllyouhavetodoisrecursivelymirrorthecompletetreetoyourwebserveronaregularbasis atleasttwiceaweek betterevery1 2days butnotmorethantwiceaday 29 30 BioconductorMirror TheBioconductorpackagerepositoriesmaybemirroredwithrsync Ifyouwouldliketobecomeamirrorforpackageanddatapackagerepositories pleaseusethecommandsbelow IfyouwanttomirrortheBioconductor2 12repos thecurrentreleaseversion pleaseusethefollowingcommands AllBioconductor2 12reposrsync zrtlv deletebioconductor org 2 12 dest bioc 2 12Bioconductor2 12Softwarereporsync zrtlv deletebioconductor org 2 12 bioc dest bioc 2 12 bioc 31 32 Withnoaccesstointernet 3811hadmirr