[BioC] Affy 1.5.8 functions not working on Mac OS X 10.3
stefano iacus
stefano.iacus at unimi.it
Wed Jan 26 00:16:15 CET 2005
On Jan 25, 2005, at 11:35 PM, Robert Gentleman wrote:
> So Stefano seems to have identified your problem. You either need to
> get precompiled OS X binaries, or install enough of the developer
> tools to compile the source packages from Bioconductor. The problems
> that you are having seem to be due to the fact that many functions did
> not build correctly since you don't have a C compiler.
>
> The Aqua version of R that you have installed should have some sort of
> menu item that you can use to get the packages, and I think you need
> to use that. I'm afraid I don't use it myself, so I don't know just
> how it works.
>
again the R for Mac OS X Faq.
BTW: Menu bar : Packages & Data -> Package Installer
and then you select the option for BioC binaries the 1.5.0 suite of
BioC is there.
stefano
> Robert
>
> On Jan 25, 2005, at 1:43 PM, Chad Wayne wrote:
>
>> My entire session follows. The previous .RData session was performed
>> on another computer while I was learning the basics of R and affy.
>> Prior to loading "timecourse.Rdata", I started X11 and changed the
>> working directory to the proper working directory with my data in it.
>>
>> > load("/xxx/xxx/ArrayAnalysis/timecourse.RData")
>> > ls()
>> [1] "PMA.Calls" "Pearson.cor" "adjp" "coc.phenodata"
>> [5] "deg" "eset" "mynova.full" "procs"
>> [9] "raw" "raw.pvalue" "res" "timecourse"
>> [13] "x"
>> > library(affy)
>> Loading required package: Biobase
>> Loading required package: tools
>> Loading required package: reposTools
>>
>> ## Note here that everything loaded just fine, as far as I can tell.
>> Knowing that these next two functions haven't worked for me, I used
>> them first.
>>
>> > pData(eset)
>> Error: couldn't find function "pData"
>> > ReadAffy(widget=T)
>> Loading required package: tkWidgets
>> Loading required package: widgetTools
>> Loading required package: tcltk
>> Loading required package: DynDoc
>> Error in AllButCelsForReadAffy(..., filenames = filenames, widget =
>> widget, :
>> couldn't find function "read.phenoData"
>>
>> ## When I performed ReadAffy(widget=T), the widget did function
>> normally. I selected the .cel files I wanted use (the ones that made
>> up the eset above) and then after selecting them, the error message
>> popped up.
>>
>> > packageDescription("affy", field="Version")
>> [1] "1.5.8"
>> > version
>> _
>> platform powerpc-apple-darwin6.8
>> arch powerpc
>> os darwin6.8
>> system powerpc, darwin6.8
>> status
>> major 2
>> minor 0.1
>> year 2004
>> month 11
>> day 15
>> language R
>>
>> ## This search demonstrates the packages that are active at this
>> point in the session.
>>
>> > search()
>> [1] ".GlobalEnv" "package:tkWidgets" "package:DynDoc"
>> [4] "package:widgetTools" "package:tcltk" "package:affy"
>> [7] "package:reposTools" "package:Biobase" "package:tools"
>> [10] "package:methods" "package:stats" "package:graphics"
>> [13] "package:grDevices" "package:utils" "package:datasets"
>> [16] "Autoloads" "package:base"
>>
>> ## I wanted to demonstrate the functions and files associated with
>> affy in my library. There are 116 of them.
>>
>> > ls("package:affy")
>> [1] "$.AffyBatch"
>> [2] "AffyRNAdeg"
>> [3] "AllButCelsForReadAffy"
>> [4] "MAplot"
>> [5] "Mbox"
>> [6] "ReadAffy"
>> [7] "affy.scalevalue.exprSet"
>> [8] "avdiff"
>> [9] "barplot"
>> [10] "barplot.ProbeSet"
>> [11] "bg.adjust"
>> [12] "bg.correct"
>> [13] "bg.correct.mas"
>> [14] "bg.correct.none"
>> [15] "bg.correct.rma"
>> [16] "bg.correct.rma2"
>> [17] "bg.parameters"
>> [18] "bgcorrect.methods"
>> [19] "boxplot"
>> [20] "cdfFromBioC"
>> [21] "cdfFromData"
>> [22] "cdfFromEnvironment"
>> [23] "cdfFromLibPath"
>> [24] "cdfName"
>> [25] "cleancdfname"
>> [26] "close"
>> [27] "colnames"
>> [28] "computeExprSet"
>> [29] "debug.affy123"
>> [30] "express.summary.stat"
>> [31] "express.summary.stat.methods"
>> [32] "expresso"
>> [33] "expressoWidget"
>> [34] "fit.li.wong"
>> [35] "generateExprSet.methods"
>> [36] "generateExprVal.method.avgdiff"
>> [37] "generateExprVal.method.liwong"
>> [38] "generateExprVal.method.mas"
>> [39] "generateExprVal.method.medianpolish"
>> [40] "generateExprVal.method.playerout"
>> [41] "getCdfInfo"
>> [42] "hist"
>> [43] "hlog"
>> [44] "image"
>> [45] "indexProbes"
>> [46] "indices2xy"
>> [47] "intensity"
>> [48] "intensity<-"
>> [49] "just.rma"
>> [50] "justRMA"
>> [51] "li.wong"
>> [52] "list.celfiles"
>> [53] "loess.normalize"
>> [54] "ma.plot"
>> [55] "maffy.normalize"
>> [56] "maffy.subset"
>> [57] "mas5"
>> [58] "mas5.detection"
>> [59] "mas5calls"
>> [60] "mas5calls.AffyBatch"
>> [61] "mas5calls.ProbeSet"
>> [62] "medianpolish"
>> [63] "merge.AffyBatch"
>> [64] "mm"
>> [65] "mm<-"
>> [66] "mmindex"
>> [67] "multiloess"
>> [68] "mva.pairs"
>> [69] "ncol"
>> [70] "normalize"
>> [71] "normalize.AffyBatch.constant"
>> [72] "normalize.AffyBatch.contrasts"
>> [73] "normalize.AffyBatch.invariantset"
>> [74] "normalize.AffyBatch.loess"
>> [75] "normalize.AffyBatch.methods"
>> [76] "normalize.AffyBatch.qspline"
>> [77] "normalize.AffyBatch.quantiles"
>> [78] "normalize.AffyBatch.quantiles.robust"
>> [79] "normalize.constant"
>> [80] "normalize.invariantset"
>> [81] "normalize.loess"
>> [82] "normalize.methods"
>> [83] "normalize.qspline"
>> [84] "normalize.quantiles"
>> [85] "normalize.quantiles.robust"
>> [86] "nrow"
>> [87] "open"
>> [88] "pairs.AffyBatch"
>> [89] "playerout.costfunction"
>> [90] "plot.ProbeSet"
>> [91] "plotAffyRNAdeg"
>> [92] "plotDensity"
>> [93] "plotDensity.AffyBatch"
>> [94] "plotLocation"
>> [95] "pm"
>> [96] "pm<-"
>> [97] "pmcorrect.mas"
>> [98] "pmcorrect.methods"
>> [99] "pmcorrect.pmonly"
>> [100] "pmcorrect.subtractmm"
>> [101] "pmindex"
>> [102] "ppset.ttest"
>> [103] "ppsetApply"
>> [104] "probeNames"
>> [105] "probes"
>> [106] "probeset"
>> [107] "read.affybatch"
>> [108] "read.probematrix"
>> [109] "rma"
>> [110] "simplemultiLoess"
>> [111] "summaryAffyRNAdeg"
>> [112] "tukey.biweight"
>> [113] "tukeybiweight"
>> [114] "update"
>> [115] "whatcdf"
>> [116] "xy2indices"
>>
>> ## I next performed the capabilities function. The only thing not
>> available to me was GNOME
>>
>> > capabilities()
>> jpeg png tcltk X11 GNOME libz http/ftp
>> sockets
>> TRUE TRUE TRUE TRUE FALSE TRUE TRUE
>> TRUE
>> libxml fifo cledit IEEE754 bzip2 PCRE
>> TRUE TRUE TRUE TRUE TRUE TRUE
>>
>> ## I finally checked the library path for the R.framework. This is
>> what I expected. I also physically checked the file heirarchy to make
>> sure that in "library" there were files for R to use. There are.
>>
>> > .libPaths()
>> [1] "/Library/Frameworks/R.framework/Resources/library"
>>
>>
>> ## If I type in eset, rather than getting an expression set matrix
>> (?), I get the full list of the gene IDs + log values of the samples
>> (45K+ rows)
>>
>> > eset
>> list()
>> attr(,"exprs")
>> 0h-1.cel 0h-2.cel 16h-1.cel 16h-2.cel
>> 1415670_at 10.783245 10.696067 11.372607 11.203421
>> 1415671_at 10.655126 10.972694 11.253215 11.287455
>> ... etc.
>>
>> ## Also wanted to look at the attributes of the phenodata from the
>> previous session to see whether the session was corrupted.
>>
>> > coc.phenodata
>> list()
>> attr(,"pData")
>> time.after.hCG
>> 0h-1.cel 0
>> 0h-2.cel 0
>> 16h-1.cel 16
>> 16h-2.cel 16
>> 8h-1.cel 8
>> 8h-2.cel 8
>> attr(,"varLabels")
>> attr(,"varLabels")$"time after hCG"
>> [1] ""
>>
>> attr(,"class")
>> [1] "phenoData"
>> attr(,"class")attr(,"package")
>> [1] "Biobase"
>>
>> ## Here we see another function error such that affy (BioC?) can't
>> find the proper cdf file to compare the data against.
>>
>> > raw
>> Error in cdfFromBioC(cdfname, cur$where, verbose) :
>> couldn't find function "testBioCConnection"
>> AffyBatch object
>> size of arrays=1002x1002 features (47068 kb)
>> cdf=Mouse430_2 (??? affyids)
>> Error: couldn't find function "exprs"
>> In addition: Warning message:
>> missing cdf environment ! in: show(list())
>> Error in ncol(exprs(x)) : Unable to find the argument "x" in
>> selecting a method for function "ncol"
>>
>> ## End of session.
>>
>> I suspect that there must be something wrong with either the install
>> or that the calls used by affy became corrupt either at the source or
>> during the install. I should offer one caveat here. I have
>> experienced this problem with affy ever since I first installed it
>> two weeks ago. I have attempted to do re-installs of the affy package
>> and clean installs of R. Nothing has remedied this issue. And when I
>> say clean install, I mean I have crawled through the system and
>> deleted everything from the libraries to the install .pkg that OsX
>> likes to hide. I also deleted preferences. I also check system level
>> and user level libraries to ensure I got everything that was
>> installed prior to the clean install.
>>
>> If I try to do a reinstall over the current package I get the
>> following session:
>>
>> trying URL `http://www.bioconductor.org/src/contrib/PACKAGES'
>> Content type `text/plain' length 46409 bytes
>> opened URL
>> ==================================================
>> downloaded 45Kb
>>
>> trying URL `http://www.bioconductor.org/src/contrib/PACKAGES'
>> Content type `text/plain' length 46409 bytes
>> opened URL
>> ==================================================
>> downloaded 45Kb
>>
>> trying URL `http://www.bioconductor.org/src/contrib/affy_1.5.8.tar.gz'
>> Content type `application/x-tar' length 1076622 bytes
>> opened URL
>> ==================================================
>> downloaded 1051Kb
>>
>> * Installing *source* package 'affy' ...
>> creating cache ./config.cache
>> checking how to run the C preprocessor... /lib/cpp
>> checking for main in -lz... no
>> updating cache ./config.cache
>> creating ./config.status
>> creating src/Makevars
>> ** libs
>> /Library/Frameworks/R.framework/Resources/bin/SHLIB: line 1: make:
>> command not found
>> ** Removing
>> '/Library/Frameworks/R.framework/Versions/2.0.1/Resources/library/
>> affy'
>> ** Restoring previous
>> '/Library/Frameworks/R.framework/Versions/2.0.1/Resources/library/
>> affy'
>> ERROR: compilation failed for package 'affy'
>>
>> >
>> Delete downloaded files (y/N)? y ##I deleted the file
>> this time, but have and haven't at other times.
>>
>> >
>>
>> It is at this point, I toss up my hands and beg for help. Sorry for
>> the length of this I wanted to be as thorough as possible could. I
>> really do appreciate the help.
>>
>> Chad.
>>
>> On Jan 25, 2005, at 1:57 PM, Robert Gentleman wrote:
>>
>>>
>>> On Jan 25, 2005, at 9:35 AM, Chad Wayne wrote:
>>>
>>>> I appreciate you taking the time to answer my questions.
>>>>
>>>>>
>>>>> On Jan 24, 2005, at 12:55 PM, Chad Wayne wrote:
>>>>>
>>>>>> It was recommended that I post this problem to the mailing list.
>>>>>> I am unable to get affy to work, e.g. the library loads into R,
>>>>>> but the functions don't seem to work. I was hoping someone may
>>>>>> have seen this problem before and may have a solution. I am
>>>>>> working in the correct working directory.
>>>>>>
>>>>>> I am using version v2.0.1 of R with the default Bioconductor
>>>>>> package installed. Current package of Affy is 1.5.8. I am using
>>>>>> Mac OS X 10.3.7 and running X11 (X11 1.0 - XFree86 4.3.0). This
>>>>>> is a shared environment and all packages were installed in the
>>>>>> top library, not in the User library.
>>>>>>
>>>>>> On prompt:
>>>>>> > load("/nnn/nnn/nnn/timecourse.RData")
>>>>>
>>>>>> > library(affy)
>>>>>> Loading required package: Biobase
>>>>>> Loading required package: tools
>>>>>> Loading required package: reposTools
>>>>>
>>>>> So, if you go
>>>>> search()
>>>>> at this point you should get something like:
>>>>> > search()
>>>>> [1] ".GlobalEnv" "package:affy" "package:reposTools"
>>>>> [4] "package:Biobase" "package:tools" "package:methods"
>>>>> [7] "package:stats" "package:graphics" "package:grDevices"
>>>>> [10] "package:utils" "package:datasets" "Autoloads"
>>>>> [13] "package:base"
>>>>>
>>>>> The important things are for affy and Biobase to be there (at
>>>>> least given what you are saying below)
>>>>>
>>>>
>>>> I loaded affy and did the search as you suggested:
>>>>
>>>> > library(affy)
>>>> Loading required package: Biobase
>>>> Loading required package: tools
>>>> Loading required package: reposTools
>>>> > search()
>>>> [1] ".GlobalEnv" "package:affy" "package:reposTools"
>>>> [4] "package:Biobase" "package:tools" "package:methods"
>>>> [7] "package:stats" "package:graphics" "package:grDevices"
>>>> [10] "package:utils" "package:datasets" "Autoloads"
>>>> [13] "package:base"
>>>>
>>>> Appears to be there along with biobase.
>>>>
>>>>
>>>>>> > ReadAffy(widget=T)
>>>>>> Error: couldn't find function "ReadAffy"
>>>>>> > ReadAffy()
>>>>>> Error: couldn't find function "ReadAffy"
>>>>>> > pData(eset)
>>>>>> Error: couldn't find function "pData"
>>>>>>
>>>>>
>>>>>
>>>>> You can also try something like
>>>>> ls("package:affy")
>>>>>
>>>>> which should show about 116 things (mostly functions) and one
>>>>> should be ReadAffy.
>>>>>
>>>>
>>>> I also performed the ls("package:affy") and retrieved 116 items. I
>>>> attempted again to try the ReadAffy function and it failed.
>>>>
>>>
>>> Hmm, this seems really odd. So a whole bunch of questions in the
>>> hopes that one of them sheds some light on what your problem is.
>>> Basically, if the library is attached and the function is listed, it
>>> is there (or ought to be). Please show the entire transcript of you
>>> session (in answering the questions below, not just the part you
>>> want to) [possibly skipping to the end, as I now suspect that you do
>>> not have enough system software installed - we should think about
>>> how to find that out more automatically]
>>>
>>> If you just type ReadAffy, what happens?
>>> what if you type the name of one of the other functions (in any of
>>> the packages)?
>>> what is .libPaths() reporting?
>>>
>>>
>>>>> If not, then the installation is not correct. Are you sure they
>>>>> have global read permission etc on the R library directory and all
>>>>> contents? Have you checked to see if there are any files
>>>>> in those directories?
>>>>>
>>>>
>>>> Do I need to go to terminal to change the permissions or is there a
>>>> nice simple way to check permissions and change them accordingly if
>>>> that is the problem. Sorry that this appears so dense, but I
>>>> haven't quite got the hang of the unix side of OsX yet.
>>>>
>>>
>>> I doubt I was right about that; but there is nothing special going
>>> on on OS X, you do need a lot of stuff installed though - and that
>>> might be your problem.
>>>
>>> try this:
>>> > capabilities()
>>> jpeg png tcltk X11 http/ftp sockets libxml
>>> fifo
>>> TRUE TRUE TRUE TRUE TRUE TRUE TRUE
>>> TRUE
>>> cledit IEEE754 iconv
>>> TRUE TRUE TRUE
>>>
>>> And in particular you are going to need X11 and tcltk (and you want
>>> most of the others). The R FAQ for OS X provides explicit details on
>>> how to do this.
>>>
>>> Robert
>>>
>>>
>>>> Thanks again,
>>>>
>>>> Chad.
>>>>
>>>>> Robert
>>>>>
>>>>>> I've also attempted to "start from scratch" from the original
>>>>>> .cel files and get the same type of error message that the
>>>>>> function couldn't be found.
>>>>>>
>>>>>> I have checked to ensure that affy is installed and loaded, and
>>>>>> based on the Package Manager, it is .
>>>>>>
>>>>>>
>>>>>> I've also tried using limma (v1.8.10), and had no problems, other
>>>>>> than I can't read in the eset.
>>>>>>
>>>>>> > packageDescription("limma", field="Version")
>>>>>> [1] "1.8.10"
>>>>>> > packageDescription("affy", field="Version")
>>>>>> [1] "1.5.8"
>>>>>> > version
>>>>>> _
>>>>>> platform powerpc-apple-darwin6.8
>>>>>> arch powerpc
>>>>>> os darwin6.8
>>>>>> system powerpc, darwin6.8
>>>>>> status
>>>>>> major 2
>>>>>> minor 0.1
>>>>>> year 2004
>>>>>> month 11
>>>>>> day 15
>>>>>> language R
>>>>>>
>>>>>>
>>>>>> Thanks for the assistance.
>>>>>>
>>>>>> Chad Wayne
>>>>>>
>>>>>> Chad M. Wayne, Ph. D.
>>>>>> Baylor College of Medicine
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioconductor mailing list
>>>>>> Bioconductor at stat.math.ethz.ch
>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>>>
>>>>>>
>>>>> +------------------------------------------------------------------
>>>>> ---------------------+
>>>>> | Robert Gentleman phone: (206) 667-7700
>>>>> |
>>>>> | Head, Program in Computational Biology fax: (206) 667-1319 |
>>>>> | Division of Public Health Sciences office: M2-B865
>>>>> |
>>>>> | Fred Hutchinson Cancer Research Center
>>>>> |
>>>>> | email: rgentlem at fhcrc.org
>>>>> |
>>>>> +------------------------------------------------------------------
>>>>> ---------------------+
>>>>>
>>>>>
>>>>
>>>>
>>> +--------------------------------------------------------------------
>>> -------------------+
>>> | Robert Gentleman phone: (206) 667-7700
>>> |
>>> | Head, Program in Computational Biology fax: (206) 667-1319 |
>>> | Division of Public Health Sciences office: M2-B865
>>> |
>>> | Fred Hutchinson Cancer Research Center
>>> |
>>> | email: rgentlem at fhcrc.org
>>> |
>>> +--------------------------------------------------------------------
>>> -------------------+
>>>
>>>
>>
>>
> +----------------------------------------------------------------------
> -----------------+
> | Robert Gentleman phone: (206) 667-7700
> |
> | Head, Program in Computational Biology fax: (206) 667-1319 |
> | Division of Public Health Sciences office: M2-B865
> |
> | Fred Hutchinson Cancer Research Center
> |
> | email: rgentlem at fhcrc.org
> |
> +----------------------------------------------------------------------
> -----------------+
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
>
More information about the Bioconductor
mailing list