[BioC] error running makeProbePackage
James W. MacDonald
jmacdon at uw.edu
Wed May 16 23:01:37 CEST 2012
OK, after running that, what do you get from
traceback()
and what do you get if you type
getProbeDataAffy
Paste both, please.
Best,
Jim
On 5/16/2012 4:42 PM, Zhang, Jian wrote:
>> makeProbePackage( arraytype="gngnf1ba",datafile="C:/testAffyILM/GPL1074.probe_tab",
> + outdir="C:/testAffyILM",maintainer ="Jian Zhang<jianz at amgen.com>", version ="0.0.1",
> + species="Homo_sapiens", check = FALSE, force=TRUE)
> Importing the data.
> Error in as.environment(pos) : using 'as.environment(NULL)' is defunct
>
> Jian
>
> -----Original Message-----
> From: James W. MacDonald [mailto:jmacdon at uw.edu]
> Sent: Wednesday, May 16, 2012 1:40 PM
> To: Zhang, Jian
> Cc: Bioconductor at r-project.org
> Subject: Re: [BioC] error running makeProbePackage
>
> OK, run the code that you were using to create the package, and then
> paste the output.
>
> Best,
>
> Jim
>
>
>
> On 5/16/2012 4:32 PM, Zhang, Jian wrote:
>> Here you go:
>>
>> R version 2.15.0 (2012-03-30)
>> Platform: i386-pc-mingw32/i386 (32-bit)
>>
>> locale:
>> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
>> [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
>> [5] LC_TIME=English_United States.1252
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>>
>> other attached packages:
>> [1] gngnf1bacdf_1.14.0 affy_1.34.0 AnnotationDbi_1.18.0 Biobase_2.16.0 BiocGenerics_0.2.0
>>
>> loaded via a namespace (and not attached):
>> [1] affyio_1.24.0 BiocInstaller_1.4.4 DBI_0.2-5 IRanges_1.14.3
>> [5] preprocessCore_1.18.0 RSQLite_0.11.1 stats4_2.15.0 tools_2.15.0
>> [9] zlibbioc_1.2.0
>>
>> Jian
>> -----Original Message-----
>> From: James W. MacDonald [mailto:jmacdon at uw.edu]
>> Sent: Wednesday, May 16, 2012 1:30 PM
>> To: Zhang, Jian
>> Cc: Bioconductor at r-project.org
>> Subject: Re: [BioC] error running makeProbePackage
>>
>> You forgot to
>>
>> library(AnnotationDbi)
>>
>> first.
>>
>> Jim
>>
>>
>>
>> On 5/16/2012 4:28 PM, Zhang, Jian wrote:
>>> Jim,
>>>
>>> Sorry about the mess up with the responses. I did not mean to take it off the list, just wasn't aware how to use the list.
>>> This was the first time I was using any list like this. My sincere apologies.
>>>
>>> Here I try again for what you asked:
>>>
>>> R version 2.15.0 (2012-03-30)
>>> Platform: i386-pc-mingw32/i386 (32-bit)
>>>
>>> locale:
>>> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
>>> [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
>>> [5] LC_TIME=English_United States.1252
>>>
>>> attached base packages:
>>> [1] stats graphics grDevices utils datasets methods base
>>>
>>> Jian
>>>
>>> -----Original Message-----
>>> From: James W. MacDonald [mailto:jmacdon at uw.edu]
>>> Sent: Wednesday, May 16, 2012 1:19 PM
>>> To: Zhang, Jian
>>> Cc: Bioconductor at r-project.org
>>> Subject: Re: [BioC] error running makeProbePackage
>>>
>>> Hi Jian,
>>>
>>> First off, please don't take things off-list. We like to think of the
>>> list archives as a searchable resource, and if you take things off-list
>>> it diminishes that goal.
>>>
>>>
>>> On 5/16/2012 4:13 PM, Zhang, Jian wrote:
>>>> Jim,
>>>>
>>>> Here is the output you asked:
>>>>
>>>> Error in `?`(sessionInfo(), AFAIK) :
>>> You misunderstand me. I don't want you to cut and paste things from my
>>> response. I want you to load AnnotationDbi into an R session, then type
>>>
>>> sessionInfo()
>>>
>>> at the R prompt, then paste what you get into your response. You should
>>> get something like this:
>>>
>>> > sessionInfo()
>>> R version 2.15.0 RC (2012-03-25 r58832)
>>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>>
>>> locale:
>>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
>>> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
>>> [7] LC_PAPER=C LC_NAME=C
>>> [9] LC_ADDRESS=C LC_TELEPHONE=C
>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>>
>>> attached base packages:
>>> [1] tcltk stats graphics grDevices utils datasets methods
>>> [8] base
>>>
>>> other attached packages:
>>> [1] mogene10sttranscriptcluster.db_8.0.1 org.Mm.eg.db_2.7.1
>>> [3] mogene10stv1probe_2.10.0 BiocInstaller_1.4.4
>>> [5] maSigPro_1.28.0 DynDoc_1.34.0
>>> [7] widgetTools_1.34.0 affycoretools_1.29.7
>>> [9] KEGG.db_2.7.1 GO.db_2.7.1
>>> [11] AnnotationDbi_1.19.0 affy_1.35.1
>>> [13] Biobase_2.16.0 BiocGenerics_0.2.0
>>> [15] pd.mogene.1.0.st.v1_3.6.0 RSQLite_0.11.1
>>> [17] DBI_0.2-5 limma_3.12.0
>>> [19] oligo_1.20.3 oligoClasses_1.18.0
>>>
>>> loaded via a namespace (and not attached):
>>> [1] affxparser_1.28.0 affyio_1.24.0 annaffy_1.28.0
>>> [4] annotate_1.34.0 biomaRt_2.12.0 Biostrings_2.24.1
>>> [7] bit_1.1-8 Category_2.22.0 codetools_0.2-8
>>> [10] ff_2.2-7 foreach_1.4.0 gcrma_2.28.0
>>> [13] gdata_2.8.2 genefilter_1.38.0 GOstats_2.22.0
>>> [16] gplots_2.10.1 graph_1.34.0 grid_2.15.0
>>> [19] GSEABase_1.18.0 gtools_2.6.2 IRanges_1.14.3
>>> [22] iterators_1.0.6 lattice_0.20-6 Mfuzz_2.14.0
>>> [25] preprocessCore_1.18.0 RBGL_1.32.0 RCurl_1.91-1
>>> [28] splines_2.15.0 stats4_2.15.0 survival_2.36-14
>>> [31] tkWidgets_1.34.0 tools_2.15.0 XML_3.9-4
>>> [34] xtable_1.7-0 zlibbioc_1.2.0
>>>
>>> Best,
>>>
>>> Jim
>>>
>>>
>>>> c("no documentation of type 'list(platform = \"i386-pc-mingw32\", arch = \"i386\", os = \"mingw32\", system = \"i386, mingw32\", status = \"\", major = \"2\", minor = \"15.0\", year = \"2012\", month = \"03\", day = \"30\", `svn rev` = \"58871\", language = \"R\", version.string = \"R version 2.15.0 (2012-03-30)\", nickname = \"\")' and topic 'AFAIK' (or error in processing help)", "no documentation of type 'i386-pc-mingw32/i386 (32-bit)' and topic 'AFAIK' (or error in processing help)", "no documentation of type 'LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252' and topic 'AFAIK' (or error in processing help)",
>>>> "no documentation of type 'c(\"stats\", \"graphics\", \"grDevices\", \"utils\", \"datasets\", \"methods\", \"base\")' and topic 'AFAIK' (or error in processing help)", "no documentation of type 'list(gngnf1bacdf = list(Package = \"gngnf1bacdf\", Title = \"g
>>>>
>>>> Jian
>>>>
>>>> -----Original Message-----
>>>> From: James W. MacDonald [mailto:jmacdon at uw.edu]
>>>> Sent: Wednesday, May 16, 2012 11:51 AM
>>>> To: Zhang, Jian
>>>> Cc: bioconductor at r-project.org
>>>> Subject: Re: [BioC] error running makeProbePackage
>>>>
>>>> Hi Jian,
>>>>
>>>> On 5/16/2012 2:27 PM, Zhang, Jian wrote:
>>>>> Hi,
>>>>>
>>>>> I try to use R-1.15.0 and Bionconductor 2.10 makeProbePackage() in AnnotationDbi to make probe package for a custom microarray.
>>>>> It worked on my Windows Vista machine, but failed on my Windows 7 machine with the following message:
>>>>>
>>>>> Error in as.environment(pos) : using 'as.environment(NULL)' is defunct
>>>>>
>>>>> Does anyone have experience with this problem? Any suggestion for solution is appreciated!
>>>> What is the output of sessionInfo()? AFAIK, as.environment(NULL) hasn't
>>>> been used in a core BioC package for years - R-core deprecated and
>>>> defuncteded (new word!) that paradigmatic use of as.environment before 2006!
>>>>
>>>> Best,
>>>>
>>>> Jim
>>>>
>>>>
>>>>> Jian Zhang
>>>>>
>>>>>
>>>>> [[alternative HTML version deleted]]
>>>>>
>>>>> _______________________________________________
>>>>> Bioconductor mailing list
>>>>> Bioconductor at r-project.org
>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>> --
>>>> James W. MacDonald, M.S.
>>>> Biostatistician
>>>> University of Washington
>>>> Environmental and Occupational Health Sciences
>>>> 4225 Roosevelt Way NE, # 100
>>>> Seattle WA 98105-6099
>>>>
>>> --
>>> James W. MacDonald, M.S.
>>> Biostatistician
>>> University of Washington
>>> Environmental and Occupational Health Sciences
>>> 4225 Roosevelt Way NE, # 100
>>> Seattle WA 98105-6099
>>>
>> --
>> James W. MacDonald, M.S.
>> Biostatistician
>> University of Washington
>> Environmental and Occupational Health Sciences
>> 4225 Roosevelt Way NE, # 100
>> Seattle WA 98105-6099
>>
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>
--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099
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