[BioC] Affy 1.5.8 functions not working on Mac OS X 10.3
Robert Gentleman
rgentlem at fhcrc.org
Tue Jan 25 23:35:31 CET 2005
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.
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
|
+-----------------------------------------------------------------------
----------------+
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