[BioC] fRMA package

[Dan Tenenbaum]

On Tue, Aug 6, 2013 at 6:55 PM, Li Liu <liliu_1 at hotmail.com> wrote:
> HI Dan,
>
> The following is what I run in R studio and the sessionInfo() output in
> window 7. Thanks.
>
> Li
>
>> source("http://bioconductor.org/biocLite.R")
>> biocLite("frma")
> BioC_mirror: http://bioconductor.org
> Using Bioconductor version 2.12 (BiocInstaller 1.10.3), R version 3.0.1.
> Installing package(s) 'frma'
> trying URL
> 'http://bioconductor.org/packages/2.12/bioc/bin/windows/contrib/3.0/frma_1.12.0.zip'
> Content type 'application/zip' length 262021 bytes (255 Kb)
> opened URL
> downloaded 255 Kb
>
> package 慺rma?successfully unpacked and MD5 sums checked
>
> The downloaded binary packages are in
> C:\Users\lucy\AppData\Local\Temp\Rtmpw3cXZ7\downloaded_packages
> Warning message:
> installed directory not writable, cannot update packages 'class', 'foreign',
> 'MASS',
>   'mgcv', 'nlme', 'nnet', 'spatial'
>
>> library(frma)
> Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
>   there is no package called 慓enomicRanges?Error: package or namespace load
> failed for 慺rma?
>

This error is telling you that you need to install GenomicRanges, so:

biocLite("GenomicRanges")

Then try:

library(fRMA)

again.

Dan


>> sessionInfo()
> R version 3.0.1 (2013-05-16)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=English_Canada.1252  LC_CTYPE=English_Canada.1252
> [3] LC_MONETARY=English_Canada.1252 LC_NUMERIC=C
> [5] LC_TIME=English_Canada.1252
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods
> base
>
> other attached packages:
> [1] affy_1.38.1          Biobase_2.20.1       BiocGenerics_0.6.0
> BiocInstaller_1.10.3
>
> loaded via a namespace (and not attached):
> [1] affxparser_1.32.3     affyio_1.28.0         IRanges_1.18.2
> [4] MASS_7.3-26           preprocessCore_1.22.0 stats4_3.0.1
> [7] tools_3.0.1           zlibbioc_1.6.0
>
>
>
>
>
>
>> Date: Tue, 6 Aug 2013 15:59:16 -0700
>
>> Subject: Re: [BioC] fRMA package
>> From: dtenenba at fhcrc.org
>> To: liliu_1 at hotmail.com
>> CC: dtenenba at fhcrc.org; bioconductor at r-project.org; rafa at jhu.edu
>
>>
>> On Tue, Aug 6, 2013 at 3:56 PM, Li Liu <liliu_1 at hotmail.com> wrote:
>> > Hi Dan,
>> >
>> > Thank you for the information. I tried to install the package in another
>> > computer with windows 7 but it still doesn't work. Is there any other
>> > idea?
>> >
>>
>> Can you send the exact commands you tried and R's response? Also the
>> output of sessionInfo().
>>
>> Thanks,
>> Dan
>>
>>
>> > Thanks.
>> >
>> > Li
>> >
>> >> Date: Tue, 6 Aug 2013 11:36:53 -0700
>> >> Subject: Re: [BioC] fRMA package
>> >> From: dtenenba at fhcrc.org
>> >> To: liliu_1 at hotmail.com
>> >> CC: bioconductor at r-project.org; rafa at jhu.edu
>> >>
>> >> On Tue, Aug 6, 2013 at 10:52 AM, Li Liu <liliu_1 at hotmail.com> wrote:
>> >> > Hi,
>> >> >
>> >> > I want to use the rRMA package in the Bioconductor. I can install the
>> >> > package successfully but when I run the library there is and error.
>> >> > Is there
>> >> > anybody who can help? Thanks.
>> >> >
>> >> > Li
>> >> >
>> >> >
>> >> >> biocLite("frma")
>> >> > BioC_mirror: http://bioconductor.org
>> >> > Using Bioconductor version 2.12 (BiocInstaller 1.10.3), R version
>> >> > 3.0.1.
>> >> > Installing package(s) 'frma'
>> >> > trying URL
>> >> >
>> >> > 'http://bioconductor.org/packages/2.12/bioc/bin/windows/contrib/3.0/frma_1.12.0.zip'
>> >> > Content type 'application/zip' length 262021 bytes (255 Kb)
>> >> > opened URL
>> >> > downloaded 255 Kb
>> >> >
>> >> > package ‘frma’ successfully unpacked and MD5 sums checked
>> >> >
>> >> > The downloaded binary packages are in
>> >> > C:\Documents and Settings\li\Local
>> >> > Settings\Temp\RtmpYpJMpj\downloaded_packages
>> >> >
>> >> >> library(frma)
>> >> > Error in inDL(x, as.logical(local), as.logical(now), ...) :
>> >> > unable to load shared object 'C:/Program
>> >> > Files/R/R-3.0.1/library/affxparser/libs/i386/affxparser.dll':
>> >> > LoadLibrary failure: The specified procedure could not be found.
>> >> >
>> >> > Error: package or namespace load failed for ‘frma’
>> >> >
>> >>
>> >> Are you on windows XP? If I recall correctly, the problem is that
>> >> affxparser does not always work on Windows XP. More information here:
>> >>
>> >> https://stat.ethz.ch/pipermail/bioconductor/2013-March/051760.html
>> >>
>> >> Dan
>> >>
>> >>
>> >> >> sessionInfo()
>> >> > R version 3.0.1 (2013-05-16)
>> >> > Platform: i386-w64-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] parallel stats graphics grDevices utils datasets methods base
>> >> >
>> >> > other attached packages:
>> >> > [1] BiocInstaller_1.10.3 affy_1.38.1 Biobase_2.20.1
>> >> > BiocGenerics_0.6.0
>> >> >
>> >> > loaded via a namespace (and not attached):
>> >> > [1] affyio_1.28.0 MASS_7.3-28 preprocessCore_1.22.0
>> >> > [4] tools_3.0.1 zlibbioc_1.6.0
>> >> >
>> >> >
>> >> > [[alternative HTML version deleted]]
>> >> >
>> >> >
>> >> > _______________________________________________
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