[BioC] Problems when access elements in mogene10stprobeset.db
Martin Morgan
mtmorgan at fhcrc.org
Fri Aug 7 19:10:31 CEST 2009
Marc Carlson wrote:
> Hi Peng,
>
> We know that it is not the R code you showed us or the packages that
> they depend on because that code has been verified to work several ways
> by multiple different people. But there is something strange going on
> because your sessionInfo() shows 3 packages loading that are not loaded
> when anyone else runs your code. Loading these packages does not
> reproduce the problem either, but the fact that your system is loading
> them when they are not needed suggests that there must be something is
> going on that we don't know about... And you are using --no-restore and
> --no-init-file, so they should not be loading up from a previous R
> session. So I can't help but wonder if perhaps you might have left some
> of the code that you are running out of the previous message by
> mistake? Also have you tried --vanilla to just eliminate every possible
> outside influence on your R session?
also invoking your R directly, not relying on aliases
/path/to/R --vanilla
Check that .libPaths() contains only a single path, and that this points
to a directory containing just properly installed packages. Then
trouble-shooting on your end to confirm that packages loaded one by one
do not cause unusual behavior e.g., that
library(AnnotationDbi)
showMethods('colnames')
returns as Herve said. Of course it is difficult to know what is
'unusual' but the possibilities are not readily diagnosed 'from our end'.
And since you had earlier issues with out-of-date packages perhaps
confirming that you have exclusively used biocLite() to install new
packages, and update.packages(repos=biocinstallRepos()) to update
packages, as described on
http://bioconductor.org/docs/install/
Finally it would be a short task to start with a fresh R installation
and confirm that a clean installation is in fact successful.
Martin
>
>
> Marc
>
>
>
> Peng Yu wrote:
>> 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
>>>>>> 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
>>>>>>
>>>>>>
>>>>> --
>>>>> 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
>>>>>
>>>>>
>> _______________________________________________
>> 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
>>
>>
>
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--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
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