[BioC] Re: trouble installing "affy" package

[Debjani Bhowmick]

Hello
Sorry if the mails seem repetitive....
I have tried to go through previous mails to track if my problem of 
loading the affy package has occured before and I found this mail which 
voices exactly the same problem that I have.

This is the message I get while installing affy library:
-- 
Warning message:
There is no package called 'Biobase' in: library(package, character.only 
= TRUE, logical = TRUE, warn.conflicts = warn.conflicts,
[1] FALSE
Warning message:
There is no package called 'affy' in: library(package, character.only = 
TRUE, logical = TRUE, warn.conflicts = warn.conflicts,
[1] FALSE
Warning message:
There is no package called 'affydata' in: library(package, 
character.only = TRUE, logical = TRUE, warn.conflicts = warn.conflicts,
Error in getClass(Class, where = topenv(parent.frame())) :
	"MIAME" is not a defined class
Execution halted
ERROR: execution of package source for 'affyPLM' failed
** Removing '/mnt/people40c/bhowmick/RLib2/affyPLM'
Broken Pipe
Warning message:
Installation of package affyPLM had non-zero exit status in: 
installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) --


As suggested, I checked and found that 'Biobase' is properly installed 
and this is the output:
ls("package:Biobase")
  [1] "$.exprSet"             "$.phenoData"           "Aggregate" 

  [4] "abstract"              "addNonExisting"        "addPDF2Vig" 

  [7] "addVig2Menu"           "addVig4Unix"           "addVig4Win" 

[10] "aggenv"                "aggfun"                "annotation"
[13] "annotation<-"          "as.data.frame.exprSet" "content"
[16] "copyEnv"               "copySubstitute"        "createPackage"
[19] "description"           "description<-"         "dumpPackTxt"
[22] "env2list"              "esApply"               "expinfo"
[25] "exprs"                 "exprs2excel"           "exprs<-"
[28] "geneNames"             "geneNames<-"           "getPkgVigs"
[31] "hybridizations"        "initfun"               "iter"
[34] "list2env"              "locked"                "multiassign"
[37] "multiget"              "normControls"          "notes"
[40] "notes<-"               "openPDF"               "openVignette"
[43] "otherInfo"             "pData"                 "pData<-"
[46] "package.version"       "phenoData"             "phenoData<-"
[49] "preproc"               "read.MIAME"            "read.exprSet"
[52] "read.phenoData"        "sampleNames"           "samples"
[55] "se.exprs"              "se.exprs<-"            "setOptionPdfViewer"
[58] "split"                 "testBioCConnection"    "update2MIAME"
[61] "varLabels"             "write.exprs"

showClass("exprSet")

Slots:

Name:             exprs         se.exprs        phenoData      description
Class:       exprMatrix       exprMatrix        phenoData characterORMIAME

Name:        annotation            notes
Class:        character        character
 > showClass("MIAME")

Slots:

Name:            name            lab        contact          title
Class:      character      character      character      character

Name:        abstract            url        samples hybridizations
Class:      character      character           list           list

Name:    normControls  preprocessing          other
Class:           list           list           list

Extends: "characterORMIAME"








Wolfgang Huber wrote:
> References: <1BF3BA9E-5287-11D8-90FC-000A956845CE at duke.edu> 
> <FE8987DC-52AD-11D8-90FC-000A956845CE at duke.edu>
> 
> Hi Jeffrey,
> 
> loading Biobase, and the class definitions of AffyBatch.R are really
> essential for the functioning of the affy package. I don't think you can
> expect to get any kind of meaningful results without these. So the
> proper thing to do is to find out why Biobase doesn't install.
> 
> When you downlonad Biobase_1.XX.tar.gz file manually and try to install,
> do you get an error message, and which? What version are you using?
> 
> If you succeed to load Biobase, can you send us the output of
> 
>  > library(Biobase)
>  > ls("package:Biobase")
>  > showClass("exprSet")
>  > showClass("MIAME")
> 
> Best wishes
>   Wolfgang
> 
> 
> Jeffrey Chang wrote:
> 
>> I still don't know what the problem is, but I've hacked my way around 
>> it in a *really* ugly way.  The key seems to be in the error message:
>>
>>> Error in getClass(Class, where = topenv(parent.frame())) :
>>>          "MIAME" is not a defined class
>>
>>
I hope someone can help me with my problem...
thanks
Debjani
-- 
Debjani Bhowmick
Chairs of Statistics
Institute of Mathematics
Swiss Federal Institute of Technology(EPFL)
1015 Lausanne Switzerland
Phone: +41 21 693 5596  Fax: +41 21 693 4250
.