[BioC] Problems when access elements in mogene10stprobeset.db
Peng Yu
pengyu.ut at gmail.com
Fri Aug 7 18:14:39 CEST 2009
Can somebody help me figure out what is wrong for my case?
Regards,
Peng
On Thu, Aug 6, 2009 at 8:42 PM, Peng Yu<pengyu.ut at gmail.com> wrote:
> BTW, I also have this alias on my system.
>
> $ which R
> alias R='R-2.9.1 --no-save --no-restore'
>
>
> On Thu, Aug 6, 2009 at 8:26 PM, Peng Yu<pengyu.ut at gmail.com> wrote:
>> Hi Hervé,
>>
>> I even can not run the second command ('showMethods'). The following
>> is the screen copy. Could you talk a look what is wrong?
>>
>> Regards,
>> Peng
>>
>>
>> =================start here
>> $ R --no-init-file
>>
>> R version 2.9.1 (2009-06-26)
>> Copyright (C) 2009 The R Foundation for Statistical Computing
>> 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.
>>
>> Natural language support but running in an English locale
>>
>> 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 an HTML browser interface to help.
>> Type 'q()' to quit R.
>>
>>> library(mogene10stprobeset.db)
>> Loading required package: AnnotationDbi
>> Loading required package: Biobase
>>
>> Welcome to Bioconductor
>>
>> Vignettes contain introductory material. To view, type
>> 'openVignette()'. To cite Bioconductor, see
>> 'citation("Biobase")' and for packages 'citation(pkgname)'.
>>
>> Loading required package: DBI
>>> showMethods("colnames")
>> Error in .showMethodsTable(fdef, includeDefs, inherited, classes = classes, :
>> trying to get slot "signature" from an object of a basic class
>> ("NULL") with no slots
>>> sessionInfo()
>> R version 2.9.1 (2009-06-26)
>> x86_64-unknown-linux-gnu
>>
>> locale:
>> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>>
>> other attached packages:
>> [1] mogene10stprobeset.db_2.0.2 RSQLite_0.7-1
>> [3] DBI_0.2-4 AnnotationDbi_1.6.1
>> [5] Biobase_2.4.1
>>
>> loaded via a namespace (and not attached):
>> [1] affy_1.22.1 affyio_1.12.0 makecdfenv_1.22.0
>> [4] preprocessCore_1.6.0
>>
>> ===================end here
>>
>> ===================start here again
>> $ R --no-init-file
>>
>> R version 2.9.1 (2009-06-26)
>> Copyright (C) 2009 The R Foundation for Statistical Computing
>> 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.
>>
>> Natural language support but running in an English locale
>>
>> 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 an HTML browser interface to help.
>> Type 'q()' to quit R.
>>
>>> sessionInfo()
>> R version 2.9.1 (2009-06-26)
>> x86_64-unknown-linux-gnu
>>
>> locale:
>> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>> ==========================end here
>>
>> 2009/8/6 Hervé Pagès <hpages at fhcrc.org>:
>>> Hi Peng,
>>>
>>> Like Marc, I cannot reproduce this either. I've run your script with
>>> Rscript and also interactively. I have exactly the same version of
>>> everything as you *except* that you end up with more stuff loaded in
>>> your session:
>>>
>>> YOU HAVE
>>> --------
>>> other attached packages:
>>> [1] mogene10stprobeset.db_2.0.2 RSQLite_0.7-1
>>> [3] DBI_0.2-4 AnnotationDbi_1.6.1
>>> [5] makecdfenv_1.22.0 affyio_1.12.0
>>> [7] affy_1.22.1 Biobase_2.4.1
>>> loaded via a namespace (and not attached):
>>> [1] preprocessCore_1.6.0
>>>
>>> I HAVE
>>> ------
>>> other attached packages:
>>> [1] mogene10stprobeset.db_2.0.2 RSQLite_0.7-1
>>> [3] DBI_0.2-4 AnnotationDbi_1.6.1
>>> [5] Biobase_2.4.1
>>>
>>> How can you end up with those extra packages? Even if I cannot
>>> explain how the presence of these packages could be related to
>>> the error you get, there is something weird here that you need
>>> to investigate.
>>>
>>> Do you see those extra packages when you run
>>> Rscript --no-init-file mogeneID.R
>>>
>>> Do you get this error when you run the script interactively?
>>> What's your sessionInfo() right after you've started R-2.9.1
>>> interactively and loaded mogene10stprobeset.db? Should be the same
>>> as mine.
>>>
>>> It looks like the colnames method for Bimap objects is returning NULL.
>>> Or like there is no colnames method for Bimap objects anymore. In that
>>> case, calling colnames on the object will also return NULL.
>>>
>>> Can you please run the following code step by step and see if you get
>>> the same output as I do:
>>>
>>>> library(mogene10stprobeset.db)
>>>> showMethods("colnames")
>>> Function: colnames (package base)
>>> x="AnnDbBimap"
>>> x="ANY"
>>> x="FlatBimap"
>>>
>>>> all_probes<-ls(mogene10stprobesetENTREZID)
>>>> set.seed(0xa1beef)
>>>> probes <-sample(all_probes, 5)
>>>> print(probes)
>>> [1] "10377734" "10527109" "10489285" "10353981" "10371859"
>>>
>>>> x <- mogene10stprobesetENTREZID
>>>> colnames(x)
>>> [1] "probe_id" "gene_id"
>>>
>>>> keys(x) <- probes
>>>> colnames(x)
>>> [1] "probe_id" "gene_id"
>>>
>>>> Rattribnames(x) <- NULL
>>>> colnames(x)
>>> [1] "probe_id" "gene_id"
>>>
>>>> y <- AnnotationDbi:::flatten(x, fromKeys.only=TRUE)
>>>> class(y)
>>> [1] "FlatBimap"
>>> attr(,"package")
>>> [1] "AnnotationDbi"
>>>
>>>> colnames(y)
>>> [1] "probe_id" "gene_id"
>>>
>>>> Rattribnames(y) <- NULL
>>>> colnames(y)
>>> [1] "probe_id" "gene_id"
>>>
>>> Thanks!
>>> H.
>>>
>>>
>>>> sessionInfo()
>>> R version 2.9.1 (2009-06-26)
>>> x86_64-unknown-linux-gnu
>>>
>>> locale:
>>> LC_CTYPE=en_CA.UTF-8;LC_NUMERIC=C;LC_TIME=en_CA.UTF-8;LC_COLLATE=en_CA.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_CA.UTF-8;LC_PAPER=en_CA.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_CA.UTF-8;LC_IDENTIFICATION=C
>>>
>>> attached base packages:
>>> [1] stats graphics grDevices utils datasets methods base
>>>
>>> other attached packages:
>>> [1] mogene10stprobeset.db_2.0.2 RSQLite_0.7-1
>>> [3] DBI_0.2-4 AnnotationDbi_1.6.1
>>> [5] Biobase_2.4.1
>>>
>>>
>>> Peng Yu wrote:
>>>>
>>>> Hi,
>>>>
>>>> I run the following command, which still give me the same error.
>>>>
>>>> Rscript --no-init-file mogeneID.R
>>>>
>>>> Can somebody let me know how to figure out what the problems are? Is
>>>> there any hiden BioC information that may be shown to pinpoint the
>>>> problems?
>>>>
>>>> Regards,
>>>> Peng
>>>>
>>>> On Thu, Aug 6, 2009 at 4:41 PM, Marc Carlson<mcarlson at fhcrc.org> wrote:
>>>>>
>>>>> Hi Peng,
>>>>>
>>>>> I have run the following;
>>>>>
>>>>> library(mogene10stprobeset.db)
>>>>> sessionInfo()
>>>>> all_probes<-ls(mogene10stprobesetENTREZID)
>>>>> set.seed(0xa1beef)
>>>>> probes <-sample(all_probes, 5)
>>>>> print(probes)
>>>>> mogene10stprobesetENTREZID[[probes[1]]]
>>>>>
>>>>>
>>>>> And it runs fine for me. So I don't think there is anything wrong with
>>>>> your R script, unless there is more than you have shown us here. The
>>>>> one thing I noticed was that my version of R was slightly newer than
>>>>> yours. But a problem like you report here should have alerted a lot
>>>>> more people if it were caused by R.
>>>>>
>>>>> Marc
>>>>>
>>>>>
>>>>>
>>>>> Peng Yu wrote:
>>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> Below this email is the R script and the output that I got after
>>>>>> running the script. Can somebody take a look help me figure out why I
>>>>>> get an error message? I followed in the instructions in
>>>>>> AnnotationDbi.pdf.
>>>>>>
>>>>>> Regards,
>>>>>> Peng
>>>>>>
>>>>>> $ cat mogeneID.R
>>>>>> library(mogene10stprobeset.db)
>>>>>> sessionInfo()
>>>>>> all_probes<-ls(mogene10stprobesetENTREZID)
>>>>>> set.seed(0xa1beef)
>>>>>> probes <-sample(all_probes, 5)
>>>>>> print(probes)
>>>>>> mogene10stprobesetENTREZID[[probes[1]]]
>>>>>>
>>>>>> $ Rscript mogeneID.R
>>>>>> Loading required package: methods
>>>>>> Loading required package: Biobase
>>>>>> Loading required package: utils
>>>>>>
>>>>>> Welcome to Bioconductor
>>>>>>
>>>>>> Vignettes contain introductory material. To view, type
>>>>>> 'openVignette()'. To cite Bioconductor, see
>>>>>> 'citation("Biobase")' and for packages 'citation(pkgname)'.
>>>>>>
>>>>>> Loading required package: affy
>>>>>> Loading required package: affyio
>>>>>> Loading required package: AnnotationDbi
>>>>>> Loading required package: DBI
>>>>>> R version 2.9.1 (2009-06-26)
>>>>>> x86_64-unknown-linux-gnu
>>>>>>
>>>>>> locale:
>>>>>>
>>>>>> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>>>>>>
>>>>>> attached base packages:
>>>>>> [1] stats graphics grDevices datasets utils methods base
>>>>>>
>>>>>> other attached packages:
>>>>>> [1] mogene10stprobeset.db_2.0.2 RSQLite_0.7-1
>>>>>> [3] DBI_0.2-4 AnnotationDbi_1.6.1
>>>>>> [5] makecdfenv_1.22.0 affyio_1.12.0
>>>>>> [7] affy_1.22.1 Biobase_2.4.1
>>>>>>
>>>>>> loaded via a namespace (and not attached):
>>>>>> [1] preprocessCore_1.6.0
>>>>>> [1] "10377734" "10527109" "10489285" "10353981" "10371859"
>>>>>> Error in names(colnames) <- colmetanames(x) :
>>>>>> attempt to set an attribute on NULL
>>>>>> Calls: [[ ... as.list -> as.list -> .tagCol -> tagname -> tagname
>>>>>> Execution halted
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioconductor mailing list
>>>>>> Bioconductor at stat.math.ethz.ch
>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>>> Search the archives:
>>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>>>
>>>>>>
>>>>>
>>>>
>>>> _______________________________________________
>>>> Bioconductor mailing list
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>>>> Search the archives:
>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>
>>>
>>> --
>>> Hervé Pagès
>>>
>>> Program in Computational Biology
>>> Division of Public Health Sciences
>>> Fred Hutchinson Cancer Research Center
>>> 1100 Fairview Ave. N, M2-B876
>>> P.O. Box 19024
>>> Seattle, WA 98109-1024
>>>
>>> E-mail: hpages at fhcrc.org
>>> Phone: (206) 667-5791
>>> Fax: (206) 667-1319
>>>
>>
>
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