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/c ontrib/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 [[alternative HTML version deleted]]