[BioC] batch vs interactive behavior of reposTools()

Sat Dec 18 04:39:48 CET 2004

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 at 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,type="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