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Question: Mavericks (Mac OS X 10.9) binary Bioconductor packages available for BioC 2.14
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gravatar for Dan Tenenbaum
3.1 years ago by
Dan Tenenbaum ♦♦ 8.1k
United States
Dan Tenenbaum ♦♦ 8.1k wrote:
Hi all, Bioconductor 2.14 (release) packages are now available for the Mavericks (Mac OS X 10.9) build of R. If you install this version of R, you can install Mavericks packages by typing: source("http://bioconductor.org/biocLite.R") ...and then using biocLite() to install the package(s) you want; for example: biocLite("BiocGenerics") There are still a few packages that aren't building on Mavericks. We have been in touch with their maintainers in most cases and hope that they'll be building soon. If you are the maintainer of one of these packages, feel free to contact us on bioc-devel if you need help getting your package to build. Most of the issues have to do with the fact that this version of R uses clang/clang++ instead of gcc/g++ to compile C/C++ code. If you need to use a package that's not yet available on Mavericks, you can continue to use the Snow Leopard build of R; it will work fine on Mavericks. Mavericks binaries for BioC-devel (3.0) will be available in the coming weeks. Dan
ADD COMMENTlink modified 3.1 years ago by Tom Harrop10 • written 3.1 years ago by Dan Tenenbaum ♦♦ 8.1k
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gravatar for Tom Harrop
3.1 years ago by
Tom Harrop10
Tom Harrop10 wrote:
Hi Dan, Thanks a lot for the update. I can’t get DESeq2 to load after installing it on my Mavericks build. biocLite(‘DESeq2’) runs without error, but library(‘DESeq2’) returns the error: > Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck > = vI[[j]]) : > there is no package called ‘annotate’ > Error: package or namespace load failed for ‘DESeq2’ biocLite(‘annotate’) or install.packages(‘annotate’) both return: > Warning message: > package ‘annotate’ is not available (for R version 3.1.0) I’ve tried a couple of different CRAN mirrors without luck. Is annotate one of the packages that still needs to be updated for Mavericks? Thanks, Tom sessionInfo() > R version 3.1.0 (2014-04-10) > Platform: x86_64-apple-darwin13.1.0 (64-bit) > locale: > [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8 > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods > [8] base > other attached packages: > [1] RcppArmadillo_0.4.200.0 Rcpp_0.11.1 GenomicRanges_1.16.3 > [4] GenomeInfoDb_1.0.2 IRanges_1.22.6 BiocGenerics_0.10.0 > [7] BiocInstaller_1.14.2 > loaded via a namespace (and not attached): > [1] Biobase_2.24.0 RColorBrewer_1.0-5 stats4_3.1.0 tools_3.1.0 > > [5] XVector_0.4.0 On 6 May 2014 00:37, Dan Tenenbaum <dtenenba@fhcrc.org> wrote: > Hi all, > > Bioconductor 2.14 (release) packages are now available for the Mavericks > (Mac OS X 10.9) build of R. > > If you install this version of R, you can install Mavericks packages by > typing: > > source("http://bioconductor.org/biocLite.R") > > ...and then using biocLite() to install the package(s) you want; for > example: > > biocLite("BiocGenerics") > > There are still a few packages that aren't building on Mavericks. We have > been in touch > with their maintainers in most cases and hope that they'll be building > soon. If you are > the maintainer of one of these packages, feel free to contact us on > bioc-devel if you > need help getting your package to build. > Most of the issues have to do with the fact that this version of R uses > clang/clang++ > instead of gcc/g++ to compile C/C++ code. > > If you need to use a package that's not yet available on Mavericks, you > can continue > to use the Snow Leopard build of R; it will work fine on Mavericks. > > Mavericks binaries for BioC-devel (3.0) will be available in the coming > weeks. > > Dan > > _______________________________________________ > 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 COMMENTlink written 3.1 years ago by Tom Harrop10
----- Original Message ----- > From: "Tom Harrop" <twharrop3 at="" gmail.com=""> > Cc: "bioc-devel" <bioc-devel at="" r-project.org="">, "Bioconductor mailing list" <bioconductor at="" r-project.org=""> > Sent: Tuesday, May 6, 2014 1:25:57 AM > Subject: Re: [BioC] Mavericks (Mac OS X 10.9) binary Bioconductor packages available for BioC 2.14 > > Hi Dan, > > Thanks a lot for the update. > > I can?t get DESeq2 to load after installing it on my Mavericks build. > > biocLite(?DESeq2?) runs without error, but library(?DESeq2?) returns > the > error: > > > Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), > > versionCheck > > = vI[[j]]) : > > there is no package called ?annotate? > > Error: package or namespace load failed for ?DESeq2? > > biocLite(?annotate?) or install.packages(?annotate?) both return: > > > Warning message: > > package ?annotate? is not available (for R version 3.1.0) > > I?ve tried a couple of different CRAN mirrors without luck. Is > annotate one > of the packages that still needs to be updated for Mavericks? > Yes, you can tell by going to the annotate landing page (http://www.bioconductor.org/packages/2.14/bioc/html/annotate.html) and seeing whether a Mavericks package is listed under Package Downloads at the bottom. I don't think there's a problem with the code in the package; rather, it has issues because its examples try to contact flaky web services. I'll see if we can do something to make this package available. Thanks, Dan > Thanks, > > Tom > > > sessionInfo() > > R version 3.1.0 (2014-04-10) > > Platform: x86_64-apple-darwin13.1.0 (64-bit) > > locale: > > [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8 > > attached base packages: > > [1] parallel stats graphics grDevices utils datasets > > methods > > [8] base > > other attached packages: > > [1] RcppArmadillo_0.4.200.0 Rcpp_0.11.1 > > GenomicRanges_1.16.3 > > [4] GenomeInfoDb_1.0.2 IRanges_1.22.6 > > BiocGenerics_0.10.0 > > [7] BiocInstaller_1.14.2 > > loaded via a namespace (and not attached): > > [1] Biobase_2.24.0 RColorBrewer_1.0-5 stats4_3.1.0 > > tools_3.1.0 > > > > [5] XVector_0.4.0 > > > > On 6 May 2014 00:37, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> wrote: > > > Hi all, > > > > Bioconductor 2.14 (release) packages are now available for the > > Mavericks > > (Mac OS X 10.9) build of R. > > > > If you install this version of R, you can install Mavericks > > packages by > > typing: > > > > source("http://bioconductor.org/biocLite.R") > > > > ...and then using biocLite() to install the package(s) you want; > > for > > example: > > > > biocLite("BiocGenerics") > > > > There are still a few packages that aren't building on Mavericks. > > We have > > been in touch > > with their maintainers in most cases and hope that they'll be > > building > > soon. If you are > > the maintainer of one of these packages, feel free to contact us on > > bioc-devel if you > > need help getting your package to build. > > Most of the issues have to do with the fact that this version of R > > uses > > clang/clang++ > > instead of gcc/g++ to compile C/C++ code. > > > > If you need to use a package that's not yet available on Mavericks, > > you > > can continue > > to use the Snow Leopard build of R; it will work fine on Mavericks. > > > > Mavericks binaries for BioC-devel (3.0) will be available in the > > coming > > weeks. > > > > Dan > > > > _______________________________________________ > > 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
ADD REPLYlink written 3.1 years ago by Dan Tenenbaum ♦♦ 8.1k
----- Original Message ----- > From: "Dan Tenenbaum" <dtenenba at="" fhcrc.org=""> > To: "Tom Harrop" <twharrop3 at="" gmail.com=""> > Cc: "bioc-devel" <bioc-devel at="" r-project.org="">, "Bioconductor mailing list" <bioconductor at="" r-project.org=""> > Sent: Tuesday, May 6, 2014 7:33:01 AM > Subject: Re: [Bioc-devel] [BioC] Mavericks (Mac OS X 10.9) binary Bioconductor packages available for BioC 2.14 > > > > ----- Original Message ----- > > From: "Tom Harrop" <twharrop3 at="" gmail.com=""> > > Cc: "bioc-devel" <bioc-devel at="" r-project.org="">, "Bioconductor mailing > > list" <bioconductor at="" r-project.org=""> > > Sent: Tuesday, May 6, 2014 1:25:57 AM > > Subject: Re: [BioC] Mavericks (Mac OS X 10.9) binary Bioconductor > > packages available for BioC 2.14 > > > > Hi Dan, > > > > Thanks a lot for the update. > > > > I can?t get DESeq2 to load after installing it on my Mavericks > > build. > > > > biocLite(?DESeq2?) runs without error, but library(?DESeq2?) > > returns > > the > > error: > > > > > Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), > > > versionCheck > > > = vI[[j]]) : > > > there is no package called ?annotate? > > > Error: package or namespace load failed for ?DESeq2? > > > > biocLite(?annotate?) or install.packages(?annotate?) both return: > > > > > Warning message: > > > package ?annotate? is not available (for R version 3.1.0) > > > > I?ve tried a couple of different CRAN mirrors without luck. Is > > annotate one > > of the packages that still needs to be updated for Mavericks? > > > > Yes, you can tell by going to the annotate landing page > (http://www.bioconductor.org/packages/2.14/bioc/html/annotate.html) > and seeing whether a Mavericks package is listed under Package > Downloads at the bottom. > > I don't think there's a problem with the code in the package; rather, > it has issues because its examples try to contact flaky web > services. I'll see if we can do something to make this package > available. > annotate should now be available for Mavericks, via biocLite("annotate") Thanks, Dan > Thanks, > Dan > > > > Thanks, > > > > Tom > > > > > > sessionInfo() > > > R version 3.1.0 (2014-04-10) > > > Platform: x86_64-apple-darwin13.1.0 (64-bit) > > > locale: > > > [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8 > > > attached base packages: > > > [1] parallel stats graphics grDevices utils datasets > > > methods > > > [8] base > > > other attached packages: > > > [1] RcppArmadillo_0.4.200.0 Rcpp_0.11.1 > > > GenomicRanges_1.16.3 > > > [4] GenomeInfoDb_1.0.2 IRanges_1.22.6 > > > BiocGenerics_0.10.0 > > > [7] BiocInstaller_1.14.2 > > > loaded via a namespace (and not attached): > > > [1] Biobase_2.24.0 RColorBrewer_1.0-5 stats4_3.1.0 > > > tools_3.1.0 > > > > > > [5] XVector_0.4.0 > > > > > > > > On 6 May 2014 00:37, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> wrote: > > > > > Hi all, > > > > > > Bioconductor 2.14 (release) packages are now available for the > > > Mavericks > > > (Mac OS X 10.9) build of R. > > > > > > If you install this version of R, you can install Mavericks > > > packages by > > > typing: > > > > > > source("http://bioconductor.org/biocLite.R") > > > > > > ...and then using biocLite() to install the package(s) you want; > > > for > > > example: > > > > > > biocLite("BiocGenerics") > > > > > > There are still a few packages that aren't building on Mavericks. > > > We have > > > been in touch > > > with their maintainers in most cases and hope that they'll be > > > building > > > soon. If you are > > > the maintainer of one of these packages, feel free to contact us > > > on > > > bioc-devel if you > > > need help getting your package to build. > > > Most of the issues have to do with the fact that this version of > > > R > > > uses > > > clang/clang++ > > > instead of gcc/g++ to compile C/C++ code. > > > > > > If you need to use a package that's not yet available on > > > Mavericks, > > > you > > > can continue > > > to use the Snow Leopard build of R; it will work fine on > > > Mavericks. > > > > > > Mavericks binaries for BioC-devel (3.0) will be available in the > > > coming > > > weeks. > > > > > > Dan > > > > > > _______________________________________________ > > > 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 > > _______________________________________________ > Bioc-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel >
ADD REPLYlink written 3.1 years ago by Dan Tenenbaum ♦♦ 8.1k
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