[BioC] fRMA package
Dan Tenenbaum
dtenenba at fhcrc.org
Wed Aug 7 15:43:23 CEST 2013
On Wed, Aug 7, 2013 at 5:23 AM, Li Liu <liliu_1 at hotmail.com> wrote:
> Hi Dan,
>
> Thank you very much. I installed the GenomicRanges but it still has the
> error.
>
> Li
>
>
>> source("http://bioconductor.org/biocLite.R")
> Bioconductor version 2.12 (BiocInstaller 1.10.3), ?biocLite for help
>> biocLite("GenomicRanges")
> BioC_mirror: http://bioconductor.org
> Using Bioconductor version 2.12 (BiocInstaller 1.10.3), R version 3.0.1.
> Installing package(s) 'GenomicRanges'
> trying URL
> 'http://bioconductor.org/packages/2.12/bioc/bin/windows/contrib/3.0/GenomicRanges_1.12.4.zip'
> Content type 'application/zip' length 3306511 bytes (3.2 Mb)
> opened URL
> downloaded 3.2 Mb
>
> package 慓enomicRanges?successfully unpacked and MD5 sums checked
>
> The downloaded binary packages are in
> C:\Users\lucy\AppData\Local\Temp\RtmpSoVWuQ\downloaded_packages
> Warning message:
> installed directory not writable, cannot update packages 'class',
> 'foreign', 'MASS', 'mgcv', 'nlme', 'nnet', 'spatial'
>> 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\RtmpSoVWuQ\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 慽terators?Error: package or namespace load
Now it is saying it needs the package "iterators" installed. So:
biocLite("iterators")
library(fRMA)
Dan
> failed for 慺rma?
>
>> 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
> [8] base
>
> other attached packages:
> [1] BiocInstaller_1.10.3 Biobase_2.20.1 BiocGenerics_0.6.0
>
> loaded via a namespace (and not attached):
> [1] affxparser_1.32.3 affy_1.38.1 affyio_1.28.0
> [4] bit_1.1-10 ff_2.2-11 GenomicRanges_1.12.4
> [7] IRanges_1.18.2 MASS_7.3-26 preprocessCore_1.22.0
> [10] stats4_3.0.1 tools_3.0.1 zlibbioc_1.6.0
>
>
>
>
>
>
>
>> Date: Tue, 6 Aug 2013 19:31:27 -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 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]]
>> >> >> >
>> >> >> >
>> >> >> > _______________________________________________
>> >> >> > 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
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