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/con trib/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’ > 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]]

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/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 at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

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 ?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 ?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 ?terators?Error: package or namespace load Now it is saying it needs the package "iterators" installed. So: biocLite("iterators") library(fRMA) Dan > failed for ?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 ?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 ?enomicRanges?Error: package or namespace >> > load >> > failed for ?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/con trib/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