[BioC] error running makeProbePackage
James W. MacDonald
jmacdon at uw.edu
Wed May 16 22:39:38 CEST 2012
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]]
>>>>
>>>> _______________________________________________
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>>> --
>>> 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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