

From: liliu_1@hotmail.com
To: dtenenba@fhcrc.org
Subject: RE: [BioC] fRMA package
Date: Wed, 7 Aug 2013 12:23:16 -0400




Hi Dan,

It works finally. Thank you very much for your nice help.

Li

> Date: Wed, 7 Aug 2013 06:43:23 -0700
> Subject: Re: [BioC] fRMA package
> From: dtenenba@fhcrc.org
> To: liliu_1@hotmail.com; bioconductor@r-project.org
> 
> On Wed, Aug 7, 2013 at 5:23 AM, Li Liu <liliu_1@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 ‘GenomicRanges?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 ‘frma?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 ‘iterators?Error: package or namespace load
> 
> 
> Now it is saying it needs the package "iterators" installed. So:
> biocLite("iterators")
> library(fRMA)
> 
> Dan
> 
> 
> > failed for ‘frma?
> >
> >> 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@fhcrc.org
> >> To: liliu_1@hotmail.com
> >> CC: bioconductor@r-project.org; rafa@jhu.edu
> >>
> >> On Tue, Aug 6, 2013 at 6:55 PM, Li Liu <liliu_1@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 ‘frma?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 ‘GenomicRanges?Error: package or namespace
> >> > load
> >> > failed for ‘frma?
> >> >
> >>
> >> 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@fhcrc.org
> >> >> To: liliu_1@hotmail.com
> >> >> CC: dtenenba@fhcrc.org; bioconductor@r-project.org; rafa@jhu.edu
> >> >
> >> >>
> >> >> On Tue, Aug 6, 2013 at 3:56 PM, Li Liu <liliu_1@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@fhcrc.org
> >> >> >> To: liliu_1@hotmail.com
> >> >> >> CC: bioconductor@r-project.org; rafa@jhu.edu
> >> >> >>
> >> >> >> On Tue, Aug 6, 2013 at 10:52 AM, Li Liu <liliu_1@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@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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