Question: batch vs interactive behavior of reposTools()
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gravatar for Marion Hakanson
14.6 years ago by
Marion Hakanson50 wrote:
Folks, I'm working up an automated build script to install bioconductor-1.5 and its dependencies in our R-2.0.1 installation, and have run across something puzzling. The platform is Sun SPARC/Solaris-9, R-2.0.1 compiled with Sun Studio-8 compilers. I'm not certain if this is a problem with reposTools() (as opposed to something with R itself), and am hoping for some outside help. What I've noticed is that when I invoke R from a shell script, with R's stdin from a file, or from a pipe, install.packages2() cannot find the dependency packages which are part of the regular R library, even though "library()" shows all the standard packages present. If I invoke R "normally," with stdin as a tty, then install.packages2() works perfectly, finding the pre-installed R library packages just fine. Note that it's only the finding of dependencies that is failing. A brief Google search turned up nothing helpful to me, nor did a quick search of this mailing list's archives. Has anyone else seen this type of behavior? I've attached a transcript of a failing session. Thanks and regards, -- Marion Hakanson <hakansom@ohsu.edu> -------------- next part -------------- Script started on Fri Dec 17 19:12:46 2004 $ mkdir /var/tmp/templib $ /mounts/apps/r-project-20/bin/R CMD INSTALL --library=/var/tmp/templib /export/marion_mounts/tmp/biocrepos/reposTools_1.5.2.tar.gz * Installing *source* package 'reposTools' ... ** R ** data ** inst ** save image [1] TRUE Loading required package: tools [1] "replisting" [1] "replisting" [1] "repURL" Creating a new generic function for "summary" in "reposTools" [1] "summary" [1] "repReleaseLevel" [1] "repReleaseLevel" [1] "show" [1] "replisting" [1] "repURL" [1] "numSubReps" [1] "numSubReps" [1] "repdatadesc" [1] "repdatadesc" [1] "repdatadesc" [1] "summary" [1] "depends" [1] "depends" [1] "suggests" [1] "suggests" [1] "imports" [1] "imports" [1] "keywords" [1] "keywords" [1] "show" [1] "ReposList" [1] "repList" [1] "repList" [1] "repList<-" [1] "repList<-" [1] "numReps" [1] "numReps" [1] "getRepEntry" [1] "getRepEntry" [1] "repPkgs" [1] "repPkgs" [1] "repPkgInfoList" [1] "repPkgInfoList" [1] "repNames" [1] "repNames" [1] "repURLs" [1] "repURLs" [1] "show" [1] "ReposEntry" [1] "repType" [1] "repName" [1] "reposThemes" [1] "reposThemes" [1] "repType" [1] "replisting" [1] "repdatadesc" [1] "repName" [1] "repURL" [1] "repdataframe" [1] "repdataframe" [1] "numSubReps" [1] "getSubRep" [1] "getSubRep" [1] "getSubRepList" [1] "getSubRepList" [1] "depends" [1] "suggests" [1] "imports" [1] "keywords" [1] "hasFiles" [1] "hasFiles" [1] "pkgRVersion" [1] "pkgRVersion" [1] "repPkgs" [1] "repObjects" [1] "repObjects" [1] "repPkgInfos" [1] "repPkgInfos" [1] "downloadFile" [1] "downloadFile" [1] "repReleaseLevel" [1] "summary" [1] "show" [1] "pkgListing" [1] "pkgList" [1] "pkgList" [1] "repList" [1] "repListing" [1] "repListing" [1] "getRepEntry" [1] "getRepURL" [1] "getRepURL" [1] "packages" [1] "packages" [1] "pkgVersionList" [1] "pkgVersionList" [1] "summary" [1] "show" [1] "reposTheme" [1] "repThemeName" [1] "repThemeName" [1] "repThemePkgs" [1] "repThemePkgs" [1] "repThemeDesc" [1] "repThemeDesc" [1] "repThemeRepos" [1] "repThemeRepos" [1] "show" [1] "VersionNumber" [1] "stringRep" [1] "major" [1] "minor" [1] "revision" [1] "stringRep" [1] "major" [1] "minor" [1] "revision" [1] "show" [1] "as.character" [1] "pkgInfo" [1] "pkgName" [1] "pkgVersion" [1] "pkgRelLevel" [1] "pkgPath" [1] "pkgContains" [1] "pkgRelLevel" [1] "pkgName" [1] "pkgVersion" [1] "pkgPath" [1] "pkgContains" [1] "==" [1] "show" [1] "localPkg" [1] "Package" [1] "Package" [1] "PkgVersion" [1] "PkgVersion" [1] "Keywords" [1] "Keywords" [1] "Depends" [1] "Depends" [1] "Suggests" [1] "Suggests" [1] "Imports" [1] "Imports" [1] "Repos" [1] "Repos" [1] "Bundle" [1] "Bundle" [1] "pkgStatusList" [1] "show" [1] "statusList" [1] "statusList" [1] "statusList<-" [1] "statusList<-" [1] "matchesList" [1] "matchesList" [1] "matchesList<-" [1] "matchesList<-" [1] "packages" [1] "found" [1] "found" [1] "notFound" [1] "notFound" [1] "updated" [1] "updated" [1] "notUpdated" [1] "notUpdated" [1] "urls" [1] "urls" [1] "pkgVersions" [1] "pkgVersions" [1] "foundPkgs" [1] "foundPkgs" [1] "notFoundPkgs" [1] "notFoundPkgs" [1] "updatedPkgs" [1] "updatedPkgs" [1] "getPackage" [1] "getPackage" [1] "getFound" [1] "getFound" [1] "getUpdated" [1] "getUpdated" [1] "getUrl" [1] "getUrl" [1] "getPkgVersion" [1] "getPkgVersion" [1] "pkgStatus" [1] "package" [1] "package" [1] "found" [1] "updated" [1] "URL" [1] "URL" [1] "pkgVersion" [1] "show" ** help >>> Building/Updating help pages for package 'reposTools' Formats: text html latex example ReposEntry-class text html latex example ReposList-class text html latex example VersionNumber-class text html latex example buildPkgInfo text html latex example buildReposEntry text html latex example buildVersionNumber text html latex example checkVers text html latex example closeLocLib text html latex example download.packages2 text html latex example genRepos text html latex example genReposHtml text html latex example getDependings text html latex example getLocalPkgs text html latex example getMaxVersion text html latex example getOptReposList text html latex example getPkgVers text html latex example getReplisting text html latex example getReposEntry text html latex example getReposList text html latex example getReposOption text html latex example getRversion text html latex example initVersionNumber text html latex install.packages2 text html latex example load.locLib text html latex example loadDepends text html latex example loadRepDD text html latex example localPkg-class text html latex example note text html latex example parseThemesXML text html latex example pkgInfo-class text html latex example pkgListing-class text html latex example pkgStatus-class text html latex example pkgStatusList-class text html latex example repdatadesc-class text html latex example replisting-class text html latex example reposTheme-class text html latex example reposToolsLibPaths text html latex example repositories text html latex example resolve.depends text html latex example save.locLib text html latex example saveDfRda text html latex example splitDFstrings text html latex example syncLocalLibList text html latex example themes text html latex example unpackExtractPkgDESC text html latex example userQuery text html latex example winConvertSourceRepos text html latex example writeThemesXML text html latex example * DONE (reposTools) $ export R_LIBS=/var/tmp/templib $ cat | /mounts/apps/r-project-20/bin/R --no-save R : Copyright 2004, The R Foundation for Statistical Computing Version 2.0.1 Patched (2004-12-06), ISBN 3-900051-07-0 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for a HTML browser interface to help. Type 'q()' to quit R. > .libPaths() libPaths() [1] "/var/tmp/templib" [2] "/mounts/apps/r-project-20/lib/sparcv9/R/library" > library(reposTools) library(reposTools) Loading required package: tools > z<-getReposEntry("file:///export/marion_mounts/tmp/biocrepos") z<-getReposEntry("file:///export/marion_mounts/tmp/biocrepos") > repPkgs(z) repPkgs(z) [1] "AnnBuilder" "Biobase" "Biostrings" [4] "ChromoViz" "DEDS" "DNAcopy" [7] "DynDoc" "EBarrays" "GLAD" [10] "GO" "GOstats" "GOstats" [13] "GeneSpring" "GeneTS" "GeneTraffic" [16] "GraphAT" "HEM" "Icens" [19] "KEGGSOAP" "KEGG" "LPE" [22] "MCMCpack" "MLInterfaces" "MeasurementError.cor" [25] "MergeMaid" "OLIN" "OLINgui" [28] "PROcess" "R2HTML" "RBGL" [31] "RColorBrewer" "ROC" "RSNPper" [34] "RSvgDevice" "RdbiPgSQL" "Rdbi" [37] "Resourcerer" "Rgraphviz" "Ruuid" [40] "SAGElyzer" "SNAData" "SparseM" [43] "XML" "YEAST" "aCGH" [46] "affyPLM" "affy" "affycomp" [49] "affydata" "affylmGUI" "affypdnn" [52] "altcdfenvs" "annaffy" "annotate" [55] "arrayMagic" "arrayQuality" "aws" [58] "bim" "cclust" "convert" [61] "ctc" "daMA" "e1071" [64] "ecolitk" "edd" "exprExternal" [67] "externalVector" "factDesign" "gbm" [70] "gcrma" "genArise" "genefilter" [73] "geneplotter" "globaltest" "goCluster" [76] "goTools" "gpls" "graph" [79] "gtkDevice" "gtkWidgets" "hexbin" [82] "hgu133a" "hgu133acdf" "hgu133aprobe" [85] "hgu95acdf" "hgu95av2" "hgu95av2cdf" [88] "hgu95av2probe" "hopach" "hsahomology" [91] "hu6800" "hu6800cdf" "hu6800probe" [94] "iSPlot" "impute" "ipred" [97] "limmaGUI" "limma" "locfit" [100] "makecdfenv" "marray" "matchprobes" [103] "mclust" "mlbench" "msbase" [106] "multtest" "mvtnorm" "nnNorm" [109] "pairseqsim" "pamr" "pickgene" [112] "plasmodiumanophelescdf" "prada" "qtl" [115] "qvalue" "rae230a" "rae230aprobe" [118] "rama" "randomForest" "reposTools" [121] "rrcov" "siggenes" "simpleaffy" [124] "sma" "snow" "splicegear" [127] "stam" "statmod" "stepNorm" [130] "tkWidgets" "tkrplot" "twilight" [133] "vsn" "webbioc" "widgetInvoke" [136] "widgetTools" "xenopuslaevis" "xlahomology" [139] "xtable" "zebrafish" > install.packages2(pkgs=c("AnnBuilder"),repEntry=z,getAllDeps=TRUE,ty pe="Source") install.packages2(pkgs=c("AnnBuilder"),repEntry=z,getAllDeps=TRUE,type ="Source") Note: You did not specify a download type. Using a default value of: Source This will be fine for almost all users Note: You did not specify a download type. Using a default value of: Source This will be fine for almost all users Note: Package tools not found in any known repository. Note: You did not specify a download type. Using a default value of: Source This will be fine for almost all users Note: You did not specify a download type. Using a default value of: Source This will be fine for almost all users Note: Package methods not found in any known repository. Note: You did not specify a download type. Using a default value of: Source This will be fine for almost all users Note: Package tcltk not found in any known repository. Note: Package widgetTools not found in any known repository. Note: You did not specify a download type. Using a default value of: Source This will be fine for almost all users Note: You did not specify a download type. Using a default value of: Source This will be fine for almost all users Note: Package methods not found in any known repository. Note: You did not specify a download type. Using a default value of: Source This will be fine for almost all users Note: You did not specify a download type. Using a default value of: Source This will be fine for almost all users Note: Package methods not found in any known repository. Note: You did not specify a download type. Using a default value of: Source This will be fine for almost all users Note: Package tcltk not found in any known repository. Note: Package widgetTools not found in any known repository. Note: You did not specify a download type. Using a default value of: Source This will be fine for almost all users Note: You did not specify a download type. Using a default value of: Source This will be fine for almost all users Note: Package tools not found in any known repository. Note: Package DynDoc not found in any known repository. Note: Package tkWidgets not found in any known repository. Note: Package Biobase not found in any known repository. Note: You did not specify a download type. Using a default value of: Source This will be fine for almost all users [1] "Attempting to download XML from file:///export/marion_mounts/tmp/biocrepos" [1] "Download complete." [1] "Installing XML" ^C Execution halted $ exit script done on Fri Dec 17 19:29:00 2004
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