[BioC] error running makeProbePackage

Wed May 16 22:19:08 CEST 2012

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