Bioc packages not working with R2.15.2?
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Yongde Bao ▴ 170
@yongde-bao-244
Last seen 10.2 years ago
Hi All, I recently updated my R to 2.15.2 and reloaded the bioc packages. Then I started to have troubles making use of a number of packages, not the least with OLIGO which I have been using frequently before this updating. Can someone in the know lend a helping hand on this. Below is the error message > library(oligo) Loading required package: oligoClasses Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/Users/yb8d/Library/R/2.15/library/bit/libs/x86_64/bit.so': dlopen(/Users/yb8d/Library/R/2.15/library/bit/libs/x86_64/bit.so, 6): Library not loaded: /Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libR.dylib Referenced from: /Users/yb8d/Library/R/2.15/library/bit/libs/x86_64/bit.so Reason: image not found Error: package ‘oligoClasses’ could not be loaded Then when I tried to load RSQLite I got this error: > biocLite("RSQLite") BioC_mirror: http://bioconductor.org Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15. Installing package(s) 'RSQLite' Warning: unable to access index for repository http://software.rc.fas.harvard.edu/mirrors/R/src/contrib Warning: unable to access index for repository http://software.rc.fas.harvard.edu/mirrors/R/bin/macosx/leopard/contri b/2.15 Warning: unable to access index for repository http://software.rc.fas.harvard.edu/mirrors/R/bin/macosx/leopard/contri b/2.15 Warning message: package ‘RSQLite’ is not available (for R version 2.15.2) And my sessionInfo: R version 2.15.2 (2012-10-26) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.8.3 ALL_1.4.13 RColorBrewer_1.0-2 lattice_0.20-10 limma_3.14.1 affyPLM_1.34.0 preprocessCore_1.20.0 [8] gcrma_2.30.0 affydata_1.11.17 affy_1.36.0 Biobase_2.18.0 BiocGenerics_0.4.0 R.utils_1.7.5 R.oo_1.8.0 [15] R.methodsS3_1.2.1 loaded via a namespace (and not attached): [1] affyio_1.26.0 Biostrings_2.26.2 DBI_0.2-5 GenomicRanges_1.10.5 grid_2.15.2 IRanges_1.16.4 parallel_2.15.2 [8] splines_2.15.2 stats4_2.15.2 tools_2.15.2 xtable_1.5-6 zlibbioc_1.4.0 Best, Yongde -- Yongde Bao Dept. of Microbiology, Immunology, and Cancer Biology UVA [[alternative HTML version deleted]]
Cancer oligo Cancer oligo • 2.0k views
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@benilton-carvalho-1375
Last seen 4.7 years ago
Brazil/Campinas/UNICAMP
Looks like there is some mix & matching going on? (mentioning this because it seems intriguing - for me - the fact that you're running R-2.15.2, but the error also refers to R.framework/Versions/2.13) Note that the package that is failing is 'bit' (which is not a BioC package), so reinstall it (the failure is because R cannot find the 64-bit image of that package) and its friends (the ff package). Also allow BiocInstaller to update your existing packages. Although they're not a BioC packages, you can use biocLite() for the task: > biocLite(c('bit', 'ff')) BioC_mirror: http://bioconductor.org Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15. Installing package(s) 'bit' 'ff' trying URL ' http://cran.fhcrc.org/bin/macosx/leopard/contrib/2.15/bit_1.1-9.tgz' Content type 'application/x-gzip' length 223228 bytes (217 Kb) opened URL ================================================== downloaded 217 Kb trying URL ' http://cran.fhcrc.org/bin/macosx/leopard/contrib/2.15/ff_2.2-10.tgz' Content type 'application/x-gzip' length 1629830 bytes (1.6 Mb) opened URL ================================================== downloaded 1.6 Mb Regarding the error with the installation of RSQLite, I can't reproduce the issue: > biocLite("RSQLite") BioC_mirror: http://bioconductor.org Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15. Installing package(s) 'RSQLite' trying URL ' http://cran.fhcrc.org/bin/macosx/leopard/contrib/2.15/RSQLite_0.11.2.t gz' Content type 'application/x-gzip' length 2219524 bytes (2.1 Mb) opened URL ================================================== downloaded 2.1 Mb > sessionInfo() R version 2.15.2 RC (2012-10-25 r61014) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.8.3 loaded via a namespace (and not attached): [1] tools_2.15.2 On 16 November 2012 15:12, YBao <yb8d@virginia.edu> wrote: > Hi All, > > I recently updated my R to 2.15.2 and reloaded the bioc packages. Then I > started to have troubles making use of a number of packages, not the least > with OLIGO which I have been using frequently before this updating. Can > someone in the know lend a helping hand on this. Below is the error message > > > library(oligo) > Loading required package: oligoClasses > Error in dyn.load(file, DLLpath = DLLpath, ...) : > unable to load shared object > '/Users/yb8d/Library/R/2.15/library/bit/libs/x86_64/bit.so': > dlopen(/Users/yb8d/Library/R/2.15/library/bit/libs/x86_64/bit.so, 6): > Library not loaded: > /Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libR.dylib > Referenced from: > /Users/yb8d/Library/R/2.15/library/bit/libs/x86_64/bit.so > Reason: image not found > Error: package ‘oligoClasses’ could not be loaded > > Then when I tried to load RSQLite I got this error: > > biocLite("RSQLite") > BioC_mirror: http://bioconductor.org > Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15. > Installing package(s) 'RSQLite' > Warning: unable to access index for repository > http://software.rc.fas.harvard.edu/mirrors/R/src/contrib > Warning: unable to access index for repository > > http://software.rc.fas.harvard.edu/mirrors/R/bin/macosx/leopard/cont rib/2.15 > Warning: unable to access index for repository > > http://software.rc.fas.harvard.edu/mirrors/R/bin/macosx/leopard/cont rib/2.15 > Warning message: > package ‘RSQLite’ is not available (for R version 2.15.2) > > And my sessionInfo: > R version 2.15.2 (2012-10-26) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] BiocInstaller_1.8.3 ALL_1.4.13 RColorBrewer_1.0-2 > lattice_0.20-10 limma_3.14.1 affyPLM_1.34.0 > preprocessCore_1.20.0 > [8] gcrma_2.30.0 affydata_1.11.17 affy_1.36.0 > Biobase_2.18.0 BiocGenerics_0.4.0 R.utils_1.7.5 > R.oo_1.8.0 > [15] R.methodsS3_1.2.1 > > loaded via a namespace (and not attached): > [1] affyio_1.26.0 Biostrings_2.26.2 DBI_0.2-5 > GenomicRanges_1.10.5 grid_2.15.2 IRanges_1.16.4 > parallel_2.15.2 > [8] splines_2.15.2 stats4_2.15.2 tools_2.15.2 > xtable_1.5-6 zlibbioc_1.4.0 > > Best, > > Yongde > > > -- > Yongde Bao > Dept. of Microbiology, Immunology, > and Cancer Biology > UVA > > [[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]]
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On Fri, Nov 16, 2012 at 8:28 AM, Benilton Carvalho <beniltoncarvalho at="" gmail.com=""> wrote: > Looks like there is some mix & matching going on? (mentioning this because > it seems intriguing - for me - the fact that you're running R-2.15.2, but > the error also refers to R.framework/Versions/2.13) > > Note that the package that is failing is 'bit' (which is not a BioC > package), so reinstall it (the failure is because R cannot find the 64-bit > image of that package) and its friends (the ff package). Also allow > BiocInstaller to update your existing packages. Although they're not a BioC > packages, you can use biocLite() for the task: > >> biocLite(c('bit', 'ff')) > BioC_mirror: http://bioconductor.org > Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15. > Installing package(s) 'bit' 'ff' > trying URL ' > http://cran.fhcrc.org/bin/macosx/leopard/contrib/2.15/bit_1.1-9.tgz' > Content type 'application/x-gzip' length 223228 bytes (217 Kb) > opened URL > ================================================== > downloaded 217 Kb > > trying URL ' > http://cran.fhcrc.org/bin/macosx/leopard/contrib/2.15/ff_2.2-10.tgz' > Content type 'application/x-gzip' length 1629830 bytes (1.6 Mb) > opened URL > ================================================== > downloaded 1.6 Mb > > > Regarding the error with the installation of RSQLite, I can't reproduce the > issue: > This is probably because your mirror is not up to date. Try setting it to the master as follows: options("BioC_mirror" = "http://www.bioconductor.org") Then: source("http://bioconductor.org/biocLite.R") biocLite("RSQLite") Dan >> biocLite("RSQLite") > BioC_mirror: http://bioconductor.org > Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15. > Installing package(s) 'RSQLite' > trying URL ' > http://cran.fhcrc.org/bin/macosx/leopard/contrib/2.15/RSQLite_0.11.2 .tgz' > Content type 'application/x-gzip' length 2219524 bytes (2.1 Mb) > opened URL > ================================================== > downloaded 2.1 Mb >> sessionInfo() > R version 2.15.2 RC (2012-10-25 r61014) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] BiocInstaller_1.8.3 > > loaded via a namespace (and not attached): > [1] tools_2.15.2 > > > > On 16 November 2012 15:12, YBao <yb8d at="" virginia.edu=""> wrote: > >> Hi All, >> >> I recently updated my R to 2.15.2 and reloaded the bioc packages. Then I >> started to have troubles making use of a number of packages, not the least >> with OLIGO which I have been using frequently before this updating. Can >> someone in the know lend a helping hand on this. Below is the error message >> >> > library(oligo) >> Loading required package: oligoClasses >> Error in dyn.load(file, DLLpath = DLLpath, ...) : >> unable to load shared object >> '/Users/yb8d/Library/R/2.15/library/bit/libs/x86_64/bit.so': >> dlopen(/Users/yb8d/Library/R/2.15/library/bit/libs/x86_64/bit.so, 6): >> Library not loaded: >> /Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libR.dylib >> Referenced from: >> /Users/yb8d/Library/R/2.15/library/bit/libs/x86_64/bit.so >> Reason: image not found >> Error: package ?oligoClasses? could not be loaded >> >> Then when I tried to load RSQLite I got this error: >> > biocLite("RSQLite") >> BioC_mirror: http://bioconductor.org >> Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15. >> Installing package(s) 'RSQLite' >> Warning: unable to access index for repository >> http://software.rc.fas.harvard.edu/mirrors/R/src/contrib >> Warning: unable to access index for repository >> >> http://software.rc.fas.harvard.edu/mirrors/R/bin/macosx/leopard/con trib/2.15 >> Warning: unable to access index for repository >> >> http://software.rc.fas.harvard.edu/mirrors/R/bin/macosx/leopard/con trib/2.15 >> Warning message: >> package ?RSQLite? is not available (for R version 2.15.2) >> >> And my sessionInfo: >> R version 2.15.2 (2012-10-26) >> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >> >> locale: >> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] BiocInstaller_1.8.3 ALL_1.4.13 RColorBrewer_1.0-2 >> lattice_0.20-10 limma_3.14.1 affyPLM_1.34.0 >> preprocessCore_1.20.0 >> [8] gcrma_2.30.0 affydata_1.11.17 affy_1.36.0 >> Biobase_2.18.0 BiocGenerics_0.4.0 R.utils_1.7.5 >> R.oo_1.8.0 >> [15] R.methodsS3_1.2.1 >> >> loaded via a namespace (and not attached): >> [1] affyio_1.26.0 Biostrings_2.26.2 DBI_0.2-5 >> GenomicRanges_1.10.5 grid_2.15.2 IRanges_1.16.4 >> parallel_2.15.2 >> [8] splines_2.15.2 stats4_2.15.2 tools_2.15.2 >> xtable_1.5-6 zlibbioc_1.4.0 >> >> Best, >> >> Yongde >> >> >> -- >> Yongde Bao >> Dept. of Microbiology, Immunology, >> and Cancer Biology >> UVA >> >> [[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 >> > > [[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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Thanks to all who are helping with this matter. After doing what Dan suggested I am still getting an error: > options("BioC_mirror"="http://www.bioconductor.org") > source("http://bioconductor.org/biocLite.R") > biocLite("RSQLite") BioC_mirror: http://www.bioconductor.org Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15. Installing package(s) 'RSQLite' Warning: unable to access index for repository http://software.rc.fas.harvard.edu/mirrors/R/src/contrib Warning: unable to access index for repository http://software.rc.fas.harvard.edu/mirrors/R/bin/macosx/leopard/contri b/2.15 Warning: unable to access index for repository http://software.rc.fas.harvard.edu/mirrors/R/bin/macosx/leopard/contri b/2.15 Warning message: package ‘RSQLite’ is not available (for R version 2.15.2) Earlier, I also tried what Benilton suggested and also got an error: > biocLite(c("bit", "ff")) BioC_mirror: http://www.bioconductor.org Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15. Installing package(s) 'bit' 'ff' Warning: unable to access index for repository http://software.rc.fas.harvard.edu/mirrors/R/src/contrib Warning: unable to access index for repository http://software.rc.fas.harvard.edu/mirrors/R/bin/macosx/leopard/contri b/2.15 Warning: unable to access index for repository http://software.rc.fas.harvard.edu/mirrors/R/bin/macosx/leopard/contri b/2.15 Warning message: packages ‘bit’, ‘ff’ are not available (for R version 2.15.2) Would it be advisable to clean up everything related to R and BioC then reload everything fresh? Thanks YB On Fri, Nov 16, 2012 at 11:39 AM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote: > On Fri, Nov 16, 2012 at 8:28 AM, Benilton Carvalho > <beniltoncarvalho@gmail.com> wrote: > > Looks like there is some mix & matching going on? (mentioning this > because > > it seems intriguing - for me - the fact that you're running R-2.15.2, but > > the error also refers to R.framework/Versions/2.13) > > > > Note that the package that is failing is 'bit' (which is not a BioC > > package), so reinstall it (the failure is because R cannot find the > 64-bit > > image of that package) and its friends (the ff package). Also allow > > BiocInstaller to update your existing packages. Although they're not a > BioC > > packages, you can use biocLite() for the task: > > > >> biocLite(c('bit', 'ff')) > > BioC_mirror: http://bioconductor.org > > Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15. > > Installing package(s) 'bit' 'ff' > > trying URL ' > > http://cran.fhcrc.org/bin/macosx/leopard/contrib/2.15/bit_1.1-9.tgz' > > Content type 'application/x-gzip' length 223228 bytes (217 Kb) > > opened URL > > ================================================== > > downloaded 217 Kb > > > > trying URL ' > > http://cran.fhcrc.org/bin/macosx/leopard/contrib/2.15/ff_2.2-10.tgz' > > Content type 'application/x-gzip' length 1629830 bytes (1.6 Mb) > > opened URL > > ================================================== > > downloaded 1.6 Mb > > > > > > Regarding the error with the installation of RSQLite, I can't reproduce > the > > issue: > > > > This is probably because your mirror is not up to date. Try setting it > to the master as follows: > options("BioC_mirror" = "http://www.bioconductor.org") > Then: > source("http://bioconductor.org/biocLite.R") > biocLite("RSQLite") > > Dan > > > >> biocLite("RSQLite") > > BioC_mirror: http://bioconductor.org > > Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15. > > Installing package(s) 'RSQLite' > > trying URL ' > > http://cran.fhcrc.org/bin/macosx/leopard/contrib/2.15/RSQLite_0.11 .2.tgz > ' > > Content type 'application/x-gzip' length 2219524 bytes (2.1 Mb) > > opened URL > > ================================================== > > downloaded 2.1 Mb > >> sessionInfo() > > R version 2.15.2 RC (2012-10-25 r61014) > > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > > > locale: > > [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 > > > > attached base packages: > > [1] stats graphics grDevices utils datasets methods base > > > > other attached packages: > > [1] BiocInstaller_1.8.3 > > > > loaded via a namespace (and not attached): > > [1] tools_2.15.2 > > > > > > > > On 16 November 2012 15:12, YBao <yb8d@virginia.edu> wrote: > > > >> Hi All, > >> > >> I recently updated my R to 2.15.2 and reloaded the bioc packages. Then I > >> started to have troubles making use of a number of packages, not the > least > >> with OLIGO which I have been using frequently before this updating. Can > >> someone in the know lend a helping hand on this. Below is the error > message > >> > >> > library(oligo) > >> Loading required package: oligoClasses > >> Error in dyn.load(file, DLLpath = DLLpath, ...) : > >> unable to load shared object > >> '/Users/yb8d/Library/R/2.15/library/bit/libs/x86_64/bit.so': > >> dlopen(/Users/yb8d/Library/R/2.15/library/bit/libs/x86_64/bit.so, 6): > >> Library not loaded: > >> /Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libR.dylib > >> Referenced from: > >> /Users/yb8d/Library/R/2.15/library/bit/libs/x86_64/bit.so > >> Reason: image not found > >> Error: package ‘oligoClasses’ could not be loaded > >> > >> Then when I tried to load RSQLite I got this error: > >> > biocLite("RSQLite") > >> BioC_mirror: http://bioconductor.org > >> Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15. > >> Installing package(s) 'RSQLite' > >> Warning: unable to access index for repository > >> http://software.rc.fas.harvard.edu/mirrors/R/src/contrib > >> Warning: unable to access index for repository > >> > >> > http://software.rc.fas.harvard.edu/mirrors/R/bin/macosx/leopard/cont rib/2.15 > >> Warning: unable to access index for repository > >> > >> > http://software.rc.fas.harvard.edu/mirrors/R/bin/macosx/leopard/cont rib/2.15 > >> Warning message: > >> package ‘RSQLite’ is not available (for R version 2.15.2) > >> > >> And my sessionInfo: > >> R version 2.15.2 (2012-10-26) > >> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > >> > >> locale: > >> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > >> > >> attached base packages: > >> [1] stats graphics grDevices utils datasets methods base > >> > >> other attached packages: > >> [1] BiocInstaller_1.8.3 ALL_1.4.13 RColorBrewer_1.0-2 > >> lattice_0.20-10 limma_3.14.1 affyPLM_1.34.0 > >> preprocessCore_1.20.0 > >> [8] gcrma_2.30.0 affydata_1.11.17 affy_1.36.0 > >> Biobase_2.18.0 BiocGenerics_0.4.0 R.utils_1.7.5 > >> R.oo_1.8.0 > >> [15] R.methodsS3_1.2.1 > >> > >> loaded via a namespace (and not attached): > >> [1] affyio_1.26.0 Biostrings_2.26.2 DBI_0.2-5 > >> GenomicRanges_1.10.5 grid_2.15.2 IRanges_1.16.4 > >> parallel_2.15.2 > >> [8] splines_2.15.2 stats4_2.15.2 tools_2.15.2 > >> xtable_1.5-6 zlibbioc_1.4.0 > >> > >> Best, > >> > >> Yongde > >> > >> > >> -- > >> Yongde Bao > >> Dept. of Microbiology, Immunology, > >> and Cancer Biology > >> UVA > >> > >> [[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]] > > > > > > _______________________________________________ > > 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 > -- Yongde Bao DNA Sciences Core Dept. of Microbiology, Immunology, and Cancer Biology UVA [[alternative HTML version deleted]]
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Hi, On Fri, Nov 16, 2012 at 12:11 PM, YBao <yb8d at="" virginia.edu=""> wrote: > Thanks to all who are helping with this matter. > > After doing what Dan suggested I am still getting an error: > >> options("BioC_mirror"="http://www.bioconductor.org") >> source("http://bioconductor.org/biocLite.R") >> biocLite("RSQLite") > BioC_mirror: http://www.bioconductor.org > Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15. > Installing package(s) 'RSQLite' > Warning: unable to access index for repository > http://software.rc.fas.harvard.edu/mirrors/R/src/contrib > Warning: unable to access index for repository > http://software.rc.fas.harvard.edu/mirrors/R/bin/macosx/leopard/cont rib/2.15 > Warning: unable to access index for repository > http://software.rc.fas.harvard.edu/mirrors/R/bin/macosx/leopard/cont rib/2.15 > Warning message: > package ?RSQLite? is not available (for R version 2.15.2) This is quite strange. I just entered the same exact commands and it works for me (also running R-2.15.2 on osx). I'm a bit confused, though, why even after you set your bioc mirror, you are still trying to get your packages from `...harvard.edu`. I guess your problem lies there. > Would it be advisable to clean up everything related to R and BioC then > reload everything fresh? I suspect that's easy enough to try. The only other thing I can suggest for debugging purposes is to start R (via terminal) w/ the --vanilla switch, in case some setting/thing somewhere is tripping you up, eg. form the shel: $ R --vanilla R> options("BioC_mirror"="http://www.bioconductor.org") R> source("http://bioconductor.org/biocLite.R") R> biocLite("RSQLite") HTH, -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact
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On Fri, Nov 16, 2012 at 9:30 AM, Steve Lianoglou <mailinglist.honeypot at="" gmail.com=""> wrote: > Hi, > > On Fri, Nov 16, 2012 at 12:11 PM, YBao <yb8d at="" virginia.edu=""> wrote: >> Thanks to all who are helping with this matter. >> >> After doing what Dan suggested I am still getting an error: >> >>> options("BioC_mirror"="http://www.bioconductor.org") >>> source("http://bioconductor.org/biocLite.R") >>> biocLite("RSQLite") >> BioC_mirror: http://www.bioconductor.org >> Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15. >> Installing package(s) 'RSQLite' >> Warning: unable to access index for repository >> http://software.rc.fas.harvard.edu/mirrors/R/src/contrib >> Warning: unable to access index for repository >> http://software.rc.fas.harvard.edu/mirrors/R/bin/macosx/leopard/con trib/2.15 >> Warning: unable to access index for repository >> http://software.rc.fas.harvard.edu/mirrors/R/bin/macosx/leopard/con trib/2.15 >> Warning message: >> package ?RSQLite? is not available (for R version 2.15.2) > Sorry, I guess you need to change your CRAN mirror. Try this: chooseCRANmirror() and pick one of the ones I know is good: Switzerland or USA (WA 1). But yes, starting over would probably be good. And as suggested, using R --vanilla Dan > This is quite strange. I just entered the same exact commands and it > works for me (also running R-2.15.2 on osx). > > I'm a bit confused, though, why even after you set your bioc mirror, > you are still trying to get your packages from `...harvard.edu`. > > I guess your problem lies there. > >> Would it be advisable to clean up everything related to R and BioC then >> reload everything fresh? > > I suspect that's easy enough to try. > > The only other thing I can suggest for debugging purposes is to start > R (via terminal) w/ the --vanilla switch, in case some setting/thing > somewhere is tripping you up, eg. form the shel: > > $ R --vanilla > R> options("BioC_mirror"="http://www.bioconductor.org") > R> source("http://bioconductor.org/biocLite.R") > R> biocLite("RSQLite") > > HTH, > -steve > > -- > Steve Lianoglou > Graduate Student: Computational Systems Biology > | Memorial Sloan-Kettering Cancer Center > | Weill Medical College of Cornell University > Contact Info: http://cbio.mskcc.org/~lianos/contact
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On Fri, Nov 16, 2012 at 12:11 PM, YBao <yb8d@virginia.edu> wrote: > Thanks to all who are helping with this matter. > > After doing what Dan suggested I am still getting an error: > > > options("BioC_mirror"="http://www.bioconductor.org") > > source("http://bioconductor.org/biocLite.R") > > biocLite("RSQLite") > BioC_mirror: http://www.bioconductor.org > Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15. > Installing package(s) 'RSQLite' > Warning: unable to access index for repository > http://software.rc.fas.harvard.edu/mirrors/R/src/contrib > Warning: unable to access index for repository > > http://software.rc.fas.harvard.edu/mirrors/R/bin/macosx/leopard/cont rib/2.15 > Warning: unable to access index for repository > > http://software.rc.fas.harvard.edu/mirrors/R/bin/macosx/leopard/cont rib/2.15 > Warning message: > package ‘RSQLite’ is not available (for R version 2.15.2) > > Earlier, I also tried what Benilton suggested and also got an error: > > biocLite(c("bit", "ff")) > BioC_mirror: http://www.bioconductor.org > Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15. > Installing package(s) 'bit' 'ff' > Warning: unable to access index for repository > http://software.rc.fas.harvard.edu/mirrors/R/src/contrib > Warning: unable to access index for repository > > http://software.rc.fas.harvard.edu/mirrors/R/bin/macosx/leopard/cont rib/2.15 > Warning: unable to access index for repository > > http://software.rc.fas.harvard.edu/mirrors/R/bin/macosx/leopard/cont rib/2.15 > Warning message: > packages ‘bit’, ‘ff’ are not available (for R version 2.15.2) > Looks like you are using an "unofficial" mirror? You might try chooseCRANmirror() to choose an official mirror near you. If you want to check the status of any mirrors (if you have problems), it is worth checking this page: http://cran.r-project.org/mirmon_report.html Sean > > Would it be advisable to clean up everything related to R and BioC then > reload everything fresh? > > Thanks > > YB > > > > On Fri, Nov 16, 2012 at 11:39 AM, Dan Tenenbaum <dtenenba@fhcrc.org> > wrote: > > > On Fri, Nov 16, 2012 at 8:28 AM, Benilton Carvalho > > <beniltoncarvalho@gmail.com> wrote: > > > Looks like there is some mix & matching going on? (mentioning this > > because > > > it seems intriguing - for me - the fact that you're running R-2.15.2, > but > > > the error also refers to R.framework/Versions/2.13) > > > > > > Note that the package that is failing is 'bit' (which is not a BioC > > > package), so reinstall it (the failure is because R cannot find the > > 64-bit > > > image of that package) and its friends (the ff package). Also allow > > > BiocInstaller to update your existing packages. Although they're not a > > BioC > > > packages, you can use biocLite() for the task: > > > > > >> biocLite(c('bit', 'ff')) > > > BioC_mirror: http://bioconductor.org > > > Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15. > > > Installing package(s) 'bit' 'ff' > > > trying URL ' > > > http://cran.fhcrc.org/bin/macosx/leopard/contrib/2.15/bit_1.1-9.tgz' > > > Content type 'application/x-gzip' length 223228 bytes (217 Kb) > > > opened URL > > > ================================================== > > > downloaded 217 Kb > > > > > > trying URL ' > > > http://cran.fhcrc.org/bin/macosx/leopard/contrib/2.15/ff_2.2-10.tgz' > > > Content type 'application/x-gzip' length 1629830 bytes (1.6 Mb) > > > opened URL > > > ================================================== > > > downloaded 1.6 Mb > > > > > > > > > Regarding the error with the installation of RSQLite, I can't reproduce > > the > > > issue: > > > > > > > This is probably because your mirror is not up to date. Try setting it > > to the master as follows: > > options("BioC_mirror" = "http://www.bioconductor.org") > > Then: > > source("http://bioconductor.org/biocLite.R") > > biocLite("RSQLite") > > > > Dan > > > > > > >> biocLite("RSQLite") > > > BioC_mirror: http://bioconductor.org > > > Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15. > > > Installing package(s) 'RSQLite' > > > trying URL ' > > > > http://cran.fhcrc.org/bin/macosx/leopard/contrib/2.15/RSQLite_0.11.2 .tgz > > ' > > > Content type 'application/x-gzip' length 2219524 bytes (2.1 Mb) > > > opened URL > > > ================================================== > > > downloaded 2.1 Mb > > >> sessionInfo() > > > R version 2.15.2 RC (2012-10-25 r61014) > > > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > > > > > locale: > > > [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 > > > > > > attached base packages: > > > [1] stats graphics grDevices utils datasets methods base > > > > > > other attached packages: > > > [1] BiocInstaller_1.8.3 > > > > > > loaded via a namespace (and not attached): > > > [1] tools_2.15.2 > > > > > > > > > > > > On 16 November 2012 15:12, YBao <yb8d@virginia.edu> wrote: > > > > > >> Hi All, > > >> > > >> I recently updated my R to 2.15.2 and reloaded the bioc packages. > Then I > > >> started to have troubles making use of a number of packages, not the > > least > > >> with OLIGO which I have been using frequently before this updating. > Can > > >> someone in the know lend a helping hand on this. Below is the error > > message > > >> > > >> > library(oligo) > > >> Loading required package: oligoClasses > > >> Error in dyn.load(file, DLLpath = DLLpath, ...) : > > >> unable to load shared object > > >> '/Users/yb8d/Library/R/2.15/library/bit/libs/x86_64/bit.so': > > >> dlopen(/Users/yb8d/Library/R/2.15/library/bit/libs/x86_64/bit.so, > 6): > > >> Library not loaded: > > >> /Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libR.dylib > > >> Referenced from: > > >> /Users/yb8d/Library/R/2.15/library/bit/libs/x86_64/bit.so > > >> Reason: image not found > > >> Error: package ‘oligoClasses’ could not be loaded > > >> > > >> Then when I tried to load RSQLite I got this error: > > >> > biocLite("RSQLite") > > >> BioC_mirror: http://bioconductor.org > > >> Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15. > > >> Installing package(s) 'RSQLite' > > >> Warning: unable to access index for repository > > >> http://software.rc.fas.harvard.edu/mirrors/R/src/contrib > > >> Warning: unable to access index for repository > > >> > > >> > > > http://software.rc.fas.harvard.edu/mirrors/R/bin/macosx/leopard/cont rib/2.15 > > >> Warning: unable to access index for repository > > >> > > >> > > > http://software.rc.fas.harvard.edu/mirrors/R/bin/macosx/leopard/cont rib/2.15 > > >> Warning message: > > >> package ‘RSQLite’ is not available (for R version 2.15.2) > > >> > > >> And my sessionInfo: > > >> R version 2.15.2 (2012-10-26) > > >> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > >> > > >> locale: > > >> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > >> > > >> attached base packages: > > >> [1] stats graphics grDevices utils datasets methods base > > >> > > >> other attached packages: > > >> [1] BiocInstaller_1.8.3 ALL_1.4.13 RColorBrewer_1.0-2 > > >> lattice_0.20-10 limma_3.14.1 affyPLM_1.34.0 > > >> preprocessCore_1.20.0 > > >> [8] gcrma_2.30.0 affydata_1.11.17 affy_1.36.0 > > >> Biobase_2.18.0 BiocGenerics_0.4.0 R.utils_1.7.5 > > >> R.oo_1.8.0 > > >> [15] R.methodsS3_1.2.1 > > >> > > >> loaded via a namespace (and not attached): > > >> [1] affyio_1.26.0 Biostrings_2.26.2 DBI_0.2-5 > > >> GenomicRanges_1.10.5 grid_2.15.2 IRanges_1.16.4 > > >> parallel_2.15.2 > > >> [8] splines_2.15.2 stats4_2.15.2 tools_2.15.2 > > >> xtable_1.5-6 zlibbioc_1.4.0 > > >> > > >> Best, > > >> > > >> Yongde > > >> > > >> > > >> -- > > >> Yongde Bao > > >> Dept. of Microbiology, Immunology, > > >> and Cancer Biology > > >> UVA > > >> > > >> [[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]] > > > > > > > > > _______________________________________________ > > > 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 > > > > > > -- > Yongde Bao > DNA Sciences Core > Dept. of Microbiology, Immunology, > and Cancer Biology > UVA > > [[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]]
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