Question: fRMA package
0
gravatar for Li Liu
6.2 years ago by
Li Liu100
Canada
Li Liu100 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’ > 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]]
• 907 views
ADD COMMENTlink modified 6.2 years ago by Dan Tenenbaum8.2k • written 6.2 years ago by Li Liu100
Answer: fRMA package
0
gravatar for Dan Tenenbaum
6.2 years ago by
Dan Tenenbaum8.2k
United States
Dan Tenenbaum8.2k wrote:
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
ADD COMMENTlink written 6.2 years ago by Dan Tenenbaum8.2k
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? 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 [[alternative HTML version deleted]]
ADD REPLYlink written 6.2 years ago by Li Liu100
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
ADD REPLYlink written 6.2 years ago by Dan Tenenbaum8.2k
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/con trib/3.0/frma_1.12.0.zip' Content type 'application/zip' length 262021 bytes (255 Kb) opened URL downloaded 255 Kb package áÏrma?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 áÉenomicRanges?Error: package or namespace load failed for áÏrma? > 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 [[alternative HTML version deleted]]
ADD REPLYlink written 6.2 years ago by Li Liu100
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/contri b/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
ADD REPLYlink written 6.2 years ago by Dan Tenenbaum8.2k
Answer: fRMA package
0
gravatar for Dan Tenenbaum
6.2 years ago by
Dan Tenenbaum8.2k
United States
Dan Tenenbaum8.2k wrote:
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
ADD COMMENTlink written 6.2 years ago by Dan Tenenbaum8.2k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 213 users visited in the last hour