[BioC] Problems when access elements in mogene10stprobeset.db
Peng Yu
pengyu.ut at gmail.com
Fri Aug 7 03:42:56 CEST 2009
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
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>>>>>
>>>>>
>>>>
>>>
>>> _______________________________________________
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>>>
>>
>> --
>> 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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