Re: [Bioc-devel] Unexpected behaviour with Assays and Vector classes
Developers, On 11/16/2015 11:39 PM, Hervé Pagès wrote: Hi Aaron, On 11/16/2015 09:39 AM, Hervé Pagès wrote: [...] Anyway, you convinced me that we should not try to follow too closely the names model for how we treat metadata columns. If nobody objects, I'll change the behavior of the various "replaceROWS" methods in the S4Vectors stack and make sure that they all transfer the metadata columns from 'value' to 'x'. This is done in S4Vectors 0.9.9 and IRanges 2.5.6 in devel, and in S4Vectors 0.8.3 and IRanges 2.4.2 in release. Just a heads-up that while making these changes to IRanges, I broke subsetting of DNAStringSet objects (and other XStringSet derivatives). So please refrain from updating IRanges today. This is now fixed in IRanges 2.4.3 (release) and 2.5.7 (devel) but the fix won't become available via biocLite() before tomorrow. Sorry for the inconvenience, H. -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fredhutch.org Phone: (206) 667-5791 Fax:(206) 667-1319 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] A bioconductor package archive?
Hi Gabe, On 11/18/2015 09:50 AM, Gabe Becker wrote: Hi all, Unless I'm missing something, there is no archive of prior source packages for Bioconductor, in the vein of CRAN's Web Archive. It has generally been accepted, I think, that if you need a version of a package - e.g., for precise reproducibility - you can go to the still-existing release repository for that Bioc release, or to the svn. The difficulty arises in determining where in the svn to look when the old-release repo has a later version of the package. In my switchr package I take the first commit with the requested version. This is generally correct, but it isn't always (for example, I recently found it does not work with IRanges version 1.20.5). Without a rule to automate the search process that will work generally, the svn repository while in principle guaranteeing that a particular previous package can be re-created, does not provide this in practice. I know that going backwards and backfilling an archive of previous Bioconductor package versions is not feasible, but would it be possible to start populating an archive now moving forward - with the expectation that they would be preserved indefinitely - to prevent this in the future? Automated tagging of package releases within the SVN would probably also work. I definitely want to add this tagging. I'm planning to do some work in December to support incremental builds so we'll be able to switch between "full build/check of everything" mode and "build/check modified packages + packages that depend on them only" mode. I'll need to have the SVN tag in the DESCRIPTION file for this. Will add it soon. I'll let others speak for the bioconductor package archive. Cheers, H. Best, ~G Gabriel Becker, Ph.D Associate Scientist Bioinformatics and Computational Biology Genentech Research [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fredhutch.org Phone: (206) 667-5791 Fax:(206) 667-1319 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Troubles using R/Bioc-devel with Mac OS X El Capitan 10.11.1
Just to mark that as solved: Seems as I've just been at the wrong place on the wrong time (by using R-devel r69640 downloaded yesterday). When compiling from the most recent R-devel_2015-11-17_r69648.tar.gz available from cran, I neither encountered the biocLite problem under linux nor the gfortran version issue with acepack under Mac OS X El Capitan. Thx for helping on that! Ludwig > (Sorry for the top-post). > > Yes, your R-devel issues on linux are due to Michael's commits. I believe > this has been addressed, but in the commit r69641; you were building > against r69640, so one commit too early! I guess you downloaded a tar.gz > file, and these 'snapshots' are created nightly. For more recent versions > you'll need either to wait or to use svn, along the lines of > > mkdir -p ~/src/; cd ~/src > svn co https://svn.r-project.org/R/trunk R-devel > R-devel/tools/rsync-recommended > mkdir -p ~/bin/R-devel; cd ~/bin/R-devel > ~/src/R-devel/configure > make -j > > From: Ludwig Geistlinger [ludwig.geistlin...@bio.ifi.lmu.de] > Sent: Wednesday, November 18, 2015 10:14 AM > To: Morgan, Martin > Subject: RE: [Bioc-devel] Troubles using R/Bioc-devel with Mac OS X El > Capitan 10.11.1 > > Dear Martin, > it should be possible to use gfortran-5.2 via editing the R_HOME/etc/Makeconf or ~/.R/Makevars. > > I will of course try that - it's not about taking your suggestion lightly, > just trying out what is working for me. > >> Also, if you are installing R-devel (implied by use of Bioc 3.3), there >> are some recent commits (from Michael Lawrence, involving method >> dispatch) >> that might be causing problems; you'll definitely want the head of svn >> trunk rather than a snapshot. > > Is this refering to linux issue, I reported? And what is the meaning of > your suggestions here? Should I wait for Michael Lawrence commits to take > place? > >> Creating a new generic function for as.data.frame in package >> BiocGenerics >> Error in setGeneric("as.vector", signature = "x") : >> as.vector dispatches internally; methods can be defined, but the >> generic function is implicit, and cannot be changed. >> Error : unable to load R code in package BiocGenerics > > > > Thx, > Ludwig > > >> The suggestion on R-SIG-mac in the thread I cited is that homebrew is >> not >> the right way to go. This is from very established members of the >> R-community (Simon Urbanek, Brian Ripley), and I would not treat it >> lightly. >> >> Also, if you are installing R-devel (implied by use of Bioc 3.3), there >> are some recent commits (from Michael Lawrence, involving method >> dispatch) >> that might be causing problems; you'll definitely want the head of svn >> trunk rather than a snapshot. >> >> Martin >> >> From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Ludwig >> Geistlinger [ludwig.geistlin...@bio.ifi.lmu.de] >> Sent: Wednesday, November 18, 2015 8:46 AM >> To: bioc-devel@r-project.org >> Subject: Re: [Bioc-devel] Troubles using R/Bioc-devel with Mac OS X El >> Capitan 10.11.1 >> >> While I am following Jo's suggestions on installing gcc via homebrew on >> my >> mac laptop (is it normal that the "make bootstrap" command takes >20 min >> already?), I am in parallel trying to make R/Bioc-devel working on our >> institutional linux machines. >> >> I was able to configure/make R-devel here, however when running >> biocLite() >> I am encountering (I wonder whether this should be a new thread!?): >> >>> source("http://bioconductor.org/biocLite.R";) >> Bioconductor version 3.3 (BiocInstaller 1.21.1), ?biocLite for help >>> biocLite() >> BioC_mirror: https://bioconductor.org >> Using Bioconductor 3.3 (BiocInstaller 1.21.1), R Under development >> (unstable) >> (2015-11-16 r69640). >> Installing package(s) Biobase, IRanges, AnnotationDbi >> also installing the dependencies BiocGenerics, S4Vectors >> >> trying URL >> 'https://bioconductor.org/packages/3.3/bioc/src/contrib/BiocGenerics_0.17.1.tar.gz' >> Content type 'unknown' length 38319 bytes (37 KB) >> == >> downloaded 37 KB >> >> trying URL >> 'https://bioconductor.org/packages/3.3/bioc/src/contrib/S4Vectors_0.9.9.tar.gz' >> Content type 'unknown' length 204430 bytes (199 KB) >> == >> downloaded 199 KB >> >> trying URL >> 'https://bioconductor.org/packages/3.3/bioc/src/contrib/Biobase_2.31.0.tar.gz' >> Content type 'unknown' length 1671264 bytes (1.6 MB) >> == >> downloaded 1.6 MB >> >> trying URL >> 'https://bioconductor.org/packages/3.3/bioc/src/contrib/IRanges_2.5.5.tar.gz' >> Content type 'unknown' length 490192 bytes (478 KB) >> == >> downloaded 478 KB >> >> trying URL >> 'https://bioconductor.org/packages/3.3/bioc/src/contrib/AnnotationDbi_1.33.1.tar.gz' >> Content
[Bioc-devel] A bioconductor package archive?
Hi all, Unless I'm missing something, there is no archive of prior source packages for Bioconductor, in the vein of CRAN's Web Archive. It has generally been accepted, I think, that if you need a version of a package - e.g., for precise reproducibility - you can go to the still-existing release repository for that Bioc release, or to the svn. The difficulty arises in determining where in the svn to look when the old-release repo has a later version of the package. In my switchr package I take the first commit with the requested version. This is generally correct, but it isn't always (for example, I recently found it does not work with IRanges version 1.20.5). Without a rule to automate the search process that will work generally, the svn repository while in principle guaranteeing that a particular previous package can be re-created, does not provide this in practice. I know that going backwards and backfilling an archive of previous Bioconductor package versions is not feasible, but would it be possible to start populating an archive now moving forward - with the expectation that they would be preserved indefinitely - to prevent this in the future? Automated tagging of package releases within the SVN would probably also work. Best, ~G Gabriel Becker, Ph.D Associate Scientist Bioinformatics and Computational Biology Genentech Research [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Troubles using R/Bioc-devel with Mac OS X El Capitan 10.11.1
The suggestion on R-SIG-mac in the thread I cited is that homebrew is not the right way to go. This is from very established members of the R-community (Simon Urbanek, Brian Ripley), and I would not treat it lightly. Also, if you are installing R-devel (implied by use of Bioc 3.3), there are some recent commits (from Michael Lawrence, involving method dispatch) that might be causing problems; you'll definitely want the head of svn trunk rather than a snapshot. Martin From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Ludwig Geistlinger [ludwig.geistlin...@bio.ifi.lmu.de] Sent: Wednesday, November 18, 2015 8:46 AM To: bioc-devel@r-project.org Subject: Re: [Bioc-devel] Troubles using R/Bioc-devel with Mac OS X El Capitan 10.11.1 While I am following Jo's suggestions on installing gcc via homebrew on my mac laptop (is it normal that the "make bootstrap" command takes >20 min already?), I am in parallel trying to make R/Bioc-devel working on our institutional linux machines. I was able to configure/make R-devel here, however when running biocLite() I am encountering (I wonder whether this should be a new thread!?): > source("http://bioconductor.org/biocLite.R";) Bioconductor version 3.3 (BiocInstaller 1.21.1), ?biocLite for help > biocLite() BioC_mirror: https://bioconductor.org Using Bioconductor 3.3 (BiocInstaller 1.21.1), R Under development (unstable) (2015-11-16 r69640). Installing package(s) ‘Biobase’, ‘IRanges’, ‘AnnotationDbi’ also installing the dependencies ‘BiocGenerics’, ‘S4Vectors’ trying URL 'https://bioconductor.org/packages/3.3/bioc/src/contrib/BiocGenerics_0.17.1.tar.gz' Content type 'unknown' length 38319 bytes (37 KB) == downloaded 37 KB trying URL 'https://bioconductor.org/packages/3.3/bioc/src/contrib/S4Vectors_0.9.9.tar.gz' Content type 'unknown' length 204430 bytes (199 KB) == downloaded 199 KB trying URL 'https://bioconductor.org/packages/3.3/bioc/src/contrib/Biobase_2.31.0.tar.gz' Content type 'unknown' length 1671264 bytes (1.6 MB) == downloaded 1.6 MB trying URL 'https://bioconductor.org/packages/3.3/bioc/src/contrib/IRanges_2.5.5.tar.gz' Content type 'unknown' length 490192 bytes (478 KB) == downloaded 478 KB trying URL 'https://bioconductor.org/packages/3.3/bioc/src/contrib/AnnotationDbi_1.33.1.tar.gz' Content type 'unknown' length 4268223 bytes (4.1 MB) == downloaded 4.1 MB * installing *source* package ‘BiocGenerics’ ... ** R ** inst ** preparing package for lazy loading Creating a new generic function for ‘append’ in package ‘BiocGenerics’ Creating a new generic function for ‘as.data.frame’ in package ‘BiocGenerics’ Error in setGeneric("as.vector", signature = "x") : ‘as.vector’ dispatches internally; methods can be defined, but the generic function is implicit, and cannot be changed. Error : unable to load R code in package ‘BiocGenerics’ ERROR: lazy loading failed for package ‘BiocGenerics’ * removing ‘/home/users/geistlinger/R/R-devel/library/BiocGenerics’ ERROR: dependency ‘BiocGenerics’ is not available for package ‘S4Vectors’ * removing ‘/home/users/geistlinger/R/R-devel/library/S4Vectors’ ERROR: dependency ‘BiocGenerics’ is not available for package ‘Biobase’ * removing ‘/home/users/geistlinger/R/R-devel/library/Biobase’ ERROR: dependencies ‘BiocGenerics’, ‘S4Vectors’ are not available for package ‘IRanges’ * removing ‘/home/users/geistlinger/R/R-devel/library/IRanges’ ERROR: dependencies ‘BiocGenerics’, ‘Biobase’, ‘IRanges’, ‘S4Vectors’ are not available for package ‘AnnotationDbi’ * removing ‘/home/users/geistlinger/R/R-devel/library/AnnotationDbi’ The downloaded source packages are in ‘/tmp/Rtmpx7szqQ/downloaded_packages’ Updating HTML index of packages in '.Library' Making 'packages.html' ... done Warning messages: 1: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘BiocGenerics’ had non-zero exit status 2: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘S4Vectors’ had non-zero exit status 3: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘Biobase’ had non-zero exit status 4: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘IRanges’ had non-zero exit status 5: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘AnnotationDbi’ had non-zero exit status Any suggestions here as well? Thanks! > sessionInfo() R Under development (unstable) (2015-11-16 r69640) Platform: x86_64-pc-linux-gnu (64-bit) Running under: SUSE Linux Enterprise Desktop 12 locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=C LC_COLLATE=C [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8 [7] L
Re: [Bioc-devel] Troubles using R/Bioc-devel with Mac OS X El Capitan 10.11.1
For your Linux problem: You might have build R differently from what you had in the past, e.g. static vs dynamic. Try to explicitly re-install those failed dependences and see if you any further. If so, you might wanna remove all your installed packages and start over with a fresh package library setup. Just an idea Henrik On Nov 18, 2015 05:47, "Ludwig Geistlinger" < ludwig.geistlin...@bio.ifi.lmu.de> wrote: > While I am following Jo's suggestions on installing gcc via homebrew on my > mac laptop (is it normal that the "make bootstrap" command takes >20 min > already?), I am in parallel trying to make R/Bioc-devel working on our > institutional linux machines. > > I was able to configure/make R-devel here, however when running biocLite() > I am encountering (I wonder whether this should be a new thread!?): > > > source("http://bioconductor.org/biocLite.R";) > Bioconductor version 3.3 (BiocInstaller 1.21.1), ?biocLite for help > > biocLite() > BioC_mirror: https://bioconductor.org > Using Bioconductor 3.3 (BiocInstaller 1.21.1), R Under development > (unstable) > (2015-11-16 r69640). > Installing package(s) ‘Biobase’, ‘IRanges’, ‘AnnotationDbi’ > also installing the dependencies ‘BiocGenerics’, ‘S4Vectors’ > > trying URL > ' > https://bioconductor.org/packages/3.3/bioc/src/contrib/BiocGenerics_0.17.1.tar.gz > ' > Content type 'unknown' length 38319 bytes (37 KB) > == > downloaded 37 KB > > trying URL > ' > https://bioconductor.org/packages/3.3/bioc/src/contrib/S4Vectors_0.9.9.tar.gz > ' > Content type 'unknown' length 204430 bytes (199 KB) > == > downloaded 199 KB > > trying URL > ' > https://bioconductor.org/packages/3.3/bioc/src/contrib/Biobase_2.31.0.tar.gz > ' > Content type 'unknown' length 1671264 bytes (1.6 MB) > == > downloaded 1.6 MB > > trying URL > ' > https://bioconductor.org/packages/3.3/bioc/src/contrib/IRanges_2.5.5.tar.gz > ' > Content type 'unknown' length 490192 bytes (478 KB) > == > downloaded 478 KB > > trying URL > ' > https://bioconductor.org/packages/3.3/bioc/src/contrib/AnnotationDbi_1.33.1.tar.gz > ' > Content type 'unknown' length 4268223 bytes (4.1 MB) > == > downloaded 4.1 MB > > * installing *source* package ‘BiocGenerics’ ... > ** R > ** inst > ** preparing package for lazy loading > Creating a new generic function for ‘append’ in package ‘BiocGenerics’ > Creating a new generic function for ‘as.data.frame’ in package > ‘BiocGenerics’ > Error in setGeneric("as.vector", signature = "x") : > ‘as.vector’ dispatches internally; methods can be defined, but the > generic function is implicit, and cannot be changed. > Error : unable to load R code in package ‘BiocGenerics’ > ERROR: lazy loading failed for package ‘BiocGenerics’ > * removing ‘/home/users/geistlinger/R/R-devel/library/BiocGenerics’ > ERROR: dependency ‘BiocGenerics’ is not available for package ‘S4Vectors’ > * removing ‘/home/users/geistlinger/R/R-devel/library/S4Vectors’ > ERROR: dependency ‘BiocGenerics’ is not available for package ‘Biobase’ > * removing ‘/home/users/geistlinger/R/R-devel/library/Biobase’ > ERROR: dependencies ‘BiocGenerics’, ‘S4Vectors’ are not available for > package ‘IRanges’ > * removing ‘/home/users/geistlinger/R/R-devel/library/IRanges’ > ERROR: dependencies ‘BiocGenerics’, ‘Biobase’, ‘IRanges’, ‘S4Vectors’ are > not available for package ‘AnnotationDbi’ > * removing ‘/home/users/geistlinger/R/R-devel/library/AnnotationDbi’ > > The downloaded source packages are in > ‘/tmp/Rtmpx7szqQ/downloaded_packages’ > Updating HTML index of packages in '.Library' > Making 'packages.html' ... done > Warning messages: > 1: In install.packages(pkgs = doing, lib = lib, ...) : > installation of package ‘BiocGenerics’ had non-zero exit status > 2: In install.packages(pkgs = doing, lib = lib, ...) : > installation of package ‘S4Vectors’ had non-zero exit status > 3: In install.packages(pkgs = doing, lib = lib, ...) : > installation of package ‘Biobase’ had non-zero exit status > 4: In install.packages(pkgs = doing, lib = lib, ...) : > installation of package ‘IRanges’ had non-zero exit status > 5: In install.packages(pkgs = doing, lib = lib, ...) : > installation of package ‘AnnotationDbi’ had non-zero exit status > > > Any suggestions here as well? Thanks! > > > > sessionInfo() > R Under development (unstable) (2015-11-16 r69640) > Platform: x86_64-pc-linux-gnu (64-bit) > Running under: SUSE Linux Enterprise Desktop 12 > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=C LC_COLLATE=C > [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packag
Re: [Bioc-devel] Troubles using R/Bioc-devel with Mac OS X El Capitan 10.11.1
Could be that gcc via homebrew takes a while… especially if it is compiling that stuff from source… > On 18 Nov 2015, at 14:46, Ludwig Geistlinger > wrote: > > While I am following Jo's suggestions on installing gcc via homebrew on my > mac laptop (is it normal that the "make bootstrap" command takes >20 min > already?), I am in parallel trying to make R/Bioc-devel working on our > institutional linux machines. > > I was able to configure/make R-devel here, however when running biocLite() > I am encountering (I wonder whether this should be a new thread!?): > >> source("http://bioconductor.org/biocLite.R";) > Bioconductor version 3.3 (BiocInstaller 1.21.1), ?biocLite for help >> biocLite() > BioC_mirror: https://bioconductor.org > Using Bioconductor 3.3 (BiocInstaller 1.21.1), R Under development (unstable) > (2015-11-16 r69640). > Installing package(s) 'Biobase', 'IRanges', 'AnnotationDbi' > also installing the dependencies 'BiocGenerics', 'S4Vectors' > > trying URL > 'https://bioconductor.org/packages/3.3/bioc/src/contrib/BiocGenerics_0.17.1.tar.gz' > Content type 'unknown' length 38319 bytes (37 KB) > == > downloaded 37 KB > > trying URL > 'https://bioconductor.org/packages/3.3/bioc/src/contrib/S4Vectors_0.9.9.tar.gz' > Content type 'unknown' length 204430 bytes (199 KB) > == > downloaded 199 KB > > trying URL > 'https://bioconductor.org/packages/3.3/bioc/src/contrib/Biobase_2.31.0.tar.gz' > Content type 'unknown' length 1671264 bytes (1.6 MB) > == > downloaded 1.6 MB > > trying URL > 'https://bioconductor.org/packages/3.3/bioc/src/contrib/IRanges_2.5.5.tar.gz' > Content type 'unknown' length 490192 bytes (478 KB) > == > downloaded 478 KB > > trying URL > 'https://bioconductor.org/packages/3.3/bioc/src/contrib/AnnotationDbi_1.33.1.tar.gz' > Content type 'unknown' length 4268223 bytes (4.1 MB) > == > downloaded 4.1 MB > > * installing *source* package 'BiocGenerics' ... > ** R > ** inst > ** preparing package for lazy loading > Creating a new generic function for 'append' in package 'BiocGenerics' > Creating a new generic function for 'as.data.frame' in package 'BiocGenerics' > Error in setGeneric("as.vector", signature = "x") : > 'as.vector' dispatches internally; methods can be defined, but the > generic function is implicit, and cannot be changed. > Error : unable to load R code in package 'BiocGenerics' > ERROR: lazy loading failed for package 'BiocGenerics' > * removing '/home/users/geistlinger/R/R-devel/library/BiocGenerics' > ERROR: dependency 'BiocGenerics' is not available for package 'S4Vectors' > * removing '/home/users/geistlinger/R/R-devel/library/S4Vectors' > ERROR: dependency 'BiocGenerics' is not available for package 'Biobase' > * removing '/home/users/geistlinger/R/R-devel/library/Biobase' > ERROR: dependencies 'BiocGenerics', 'S4Vectors' are not available for > package 'IRanges' > * removing '/home/users/geistlinger/R/R-devel/library/IRanges' > ERROR: dependencies 'BiocGenerics', 'Biobase', 'IRanges', 'S4Vectors' are > not available for package 'AnnotationDbi' > * removing '/home/users/geistlinger/R/R-devel/library/AnnotationDbi' > > The downloaded source packages are in >'/tmp/Rtmpx7szqQ/downloaded_packages' > Updating HTML index of packages in '.Library' > Making 'packages.html' ... done > Warning messages: > 1: In install.packages(pkgs = doing, lib = lib, ...) : > installation of package 'BiocGenerics' had non-zero exit status > 2: In install.packages(pkgs = doing, lib = lib, ...) : > installation of package 'S4Vectors' had non-zero exit status > 3: In install.packages(pkgs = doing, lib = lib, ...) : > installation of package 'Biobase' had non-zero exit status > 4: In install.packages(pkgs = doing, lib = lib, ...) : > installation of package 'IRanges' had non-zero exit status > 5: In install.packages(pkgs = doing, lib = lib, ...) : > installation of package 'AnnotationDbi' had non-zero exit status > > > Any suggestions here as well? Thanks! > > >> sessionInfo() > R Under development (unstable) (2015-11-16 r69640) > Platform: x86_64-pc-linux-gnu (64-bit) > Running under: SUSE Linux Enterprise Desktop 12 > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=C LC_COLLATE=C > [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] BiocInstaller_1.21.1 > > loaded via a namespace (and not attached): > [1] tools_3.3.0 > > > > > > > > > > >> Dear Ludwig, >> >> I tried to install that package and it
Re: [Bioc-devel] Troubles using R/Bioc-devel with Mac OS X El Capitan 10.11.1
While I am following Jo's suggestions on installing gcc via homebrew on my mac laptop (is it normal that the "make bootstrap" command takes >20 min already?), I am in parallel trying to make R/Bioc-devel working on our institutional linux machines. I was able to configure/make R-devel here, however when running biocLite() I am encountering (I wonder whether this should be a new thread!?): > source("http://bioconductor.org/biocLite.R";) Bioconductor version 3.3 (BiocInstaller 1.21.1), ?biocLite for help > biocLite() BioC_mirror: https://bioconductor.org Using Bioconductor 3.3 (BiocInstaller 1.21.1), R Under development (unstable) (2015-11-16 r69640). Installing package(s) Biobase, IRanges, AnnotationDbi also installing the dependencies BiocGenerics, S4Vectors trying URL 'https://bioconductor.org/packages/3.3/bioc/src/contrib/BiocGenerics_0.17.1.tar.gz' Content type 'unknown' length 38319 bytes (37 KB) == downloaded 37 KB trying URL 'https://bioconductor.org/packages/3.3/bioc/src/contrib/S4Vectors_0.9.9.tar.gz' Content type 'unknown' length 204430 bytes (199 KB) == downloaded 199 KB trying URL 'https://bioconductor.org/packages/3.3/bioc/src/contrib/Biobase_2.31.0.tar.gz' Content type 'unknown' length 1671264 bytes (1.6 MB) == downloaded 1.6 MB trying URL 'https://bioconductor.org/packages/3.3/bioc/src/contrib/IRanges_2.5.5.tar.gz' Content type 'unknown' length 490192 bytes (478 KB) == downloaded 478 KB trying URL 'https://bioconductor.org/packages/3.3/bioc/src/contrib/AnnotationDbi_1.33.1.tar.gz' Content type 'unknown' length 4268223 bytes (4.1 MB) == downloaded 4.1 MB * installing *source* package BiocGenerics ... ** R ** inst ** preparing package for lazy loading Creating a new generic function for append in package BiocGenerics Creating a new generic function for as.data.frame in package BiocGenerics Error in setGeneric("as.vector", signature = "x") : as.vector dispatches internally; methods can be defined, but the generic function is implicit, and cannot be changed. Error : unable to load R code in package BiocGenerics ERROR: lazy loading failed for package BiocGenerics * removing /home/users/geistlinger/R/R-devel/library/BiocGenerics ERROR: dependency BiocGenerics is not available for package S4Vectors * removing /home/users/geistlinger/R/R-devel/library/S4Vectors ERROR: dependency BiocGenerics is not available for package Biobase * removing /home/users/geistlinger/R/R-devel/library/Biobase ERROR: dependencies BiocGenerics, S4Vectors are not available for package IRanges * removing /home/users/geistlinger/R/R-devel/library/IRanges ERROR: dependencies BiocGenerics, Biobase, IRanges, S4Vectors are not available for package AnnotationDbi * removing /home/users/geistlinger/R/R-devel/library/AnnotationDbi The downloaded source packages are in /tmp/Rtmpx7szqQ/downloaded_packages Updating HTML index of packages in '.Library' Making 'packages.html' ... done Warning messages: 1: In install.packages(pkgs = doing, lib = lib, ...) : installation of package BiocGenerics had non-zero exit status 2: In install.packages(pkgs = doing, lib = lib, ...) : installation of package S4Vectors had non-zero exit status 3: In install.packages(pkgs = doing, lib = lib, ...) : installation of package Biobase had non-zero exit status 4: In install.packages(pkgs = doing, lib = lib, ...) : installation of package IRanges had non-zero exit status 5: In install.packages(pkgs = doing, lib = lib, ...) : installation of package AnnotationDbi had non-zero exit status Any suggestions here as well? Thanks! > sessionInfo() R Under development (unstable) (2015-11-16 r69640) Platform: x86_64-pc-linux-gnu (64-bit) Running under: SUSE Linux Enterprise Desktop 12 locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=C LC_COLLATE=C [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.21.1 loaded via a namespace (and not attached): [1] tools_3.3.0 > Dear Ludwig, > > I tried to install that package and it compiled nicely on my system with >> sessionInfo() > R Under development (unstable) (2015-10-20 r69547) > Platform: x86_64-apple-darwin15.0.0/x86_64 (64-bit) > Running under: OS X 10.11.2 (El Capitan) > > 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 atta
Re: [Bioc-devel] Troubles using R/Bioc-devel with Mac OS X El Capitan 10.11.1
Dear Ludwig, I tried to install that package and it compiled nicely on my system with > sessionInfo() R Under development (unstable) (2015-10-20 r69547) Platform: x86_64-apple-darwin15.0.0/x86_64 (64-bit) Running under: OS X 10.11.2 (El Capitan) 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_1.21.1 loaded via a namespace (and not attached): [1] tools_3.3.0 I’m installing the fortran through homebrew, actually, fortran is part of the gcc “bottle” there, thus I installed brew install gcc and I’m building and compiling R always from source with: /configure SHELL='/bin/bash' \ --prefix=$PREFIX \ r_arch=x86_64 \ --x-includes=/usr/X11/include/ \ --x-libraries=/usr/X11/lib/ \ CC="clang" \ CXX="clang++" \ OBJC="clang" \ F77="gfortran -arch x86_64" \ FC="gfortran -arch x86_64" \ --with-system-zlib \ --with-blas='-framework Accelerate' \ --with-lapack \ CPPFLAGS="-D__ACCELERATE__ \ --enable-R-framework=no \ --enable-memory-profiling \ --enable-R-shlib I never had any problems anymore with missing fortran compilers on OS X Hope that helps, cheers, jo > On 18 Nov 2015, at 12:12, Morgan, Martin > wrote: > > Probably the definitive answer will be the R-SIG-Mac mailing list > > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > perhaps specifically this thread > > https://stat.ethz.ch/pipermail/r-sig-mac/2015-October/011641.html > > which points to the R-admin manual and especially > > https://cran.r-project.org/doc/manuals/r-release/R-admin.html#OS-X > > From the discussion (especially the posts by Brian Ripley) it seems like it > should be possible to use gfortran-5.2 via editing the R_HOME/etc/Makeconf or > ~/.R/Makevars. > > Martin > > > > From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Ludwig > Geistlinger [ludwig.geistlin...@bio.ifi.lmu.de] > Sent: Wednesday, November 18, 2015 5:53 AM > To: bioc-devel@r-project.org > Subject: [Bioc-devel] Troubles using R/Bioc-devel with Mac OS X El Capitan > 10.11.1 > > Hi, > > I am experiencing troubles installing "Hmisc", especially its dependency > "acepack", via > >> biocLite("acepack") > > in R-devel installed from the "R-devel-mavericks-signed.pkg" downloaded > from https://r.research.att.com/. > > The error reads: > > > BioC_mirror: https://bioconductor.org > Using Bioconductor 3.3 (BiocInstaller 1.21.1), R Under development (unstable) > (2015-11-16 r69640). > Installing package(s) ‘acepack’ > Paket, das nur als Quelltext vorliegt und eventuell Übersetzung von > C/C++/Fortran benötigt.: ‘acepack’ > Do you want to attempt to install these from sources? > y/n: y > installing the source package ‘acepack’ > > versuche URL 'https://cran.rstudio.com/src/contrib/acepack_1.3-3.3.tar.gz' > Content type 'application/x-gzip' length 33590 bytes (32 KB) > == > downloaded 32 KB > > * installing *source* package ‘acepack’ ... > ** Paket ‘acepack’ erfolgreich entpackt und MD5 Summen überprüft > ** libs > gfortran-4.8 -fPIC -g -O2 -c ace.f -o ace.o > make: gfortran-4.8: No such file or directory > make: *** [ace.o] Error 1 > ERROR: compilation failed for package ‘acepack’ > * removing > ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/acepack’ > > > which indicates that "gfortran-4.8" is missing. > I have however installed the recommended "gfortran-5.2" for El Capitan > from here: > > https://gcc.gnu.org/wiki/GFortranBinaries#MacOS > > Yesterday, I tried quite some time to install 4.8-versions of gfortran > available from the website above, however they are not compatible with El > Capitan (Error reads: kern.osversion not recognized: »15.0.0) and searched > through several newsgroups reporting on that issue, I was however not able > to fix that. > > Did anyone of the community here experienced similar issues and have some > suggestions for me!? > > Thank you very much! > > Best, > Ludwig > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > This email message may contain legally privileged and/or confidential > information. If you are not the intended recipient(s), or the employee or > agent responsible for the delivery of this message to the intended > recipient(s), you are hereby notified that any disclosure, copying, > distribution, or use of this email message is prohibited. If you have > received this message in error, please notify the sender immediately by > e-mail and delete this email message from your computer. Thank you. > _
Re: [Bioc-devel] Troubles using R/Bioc-devel with Mac OS X El Capitan 10.11.1
Probably the definitive answer will be the R-SIG-Mac mailing list https://stat.ethz.ch/mailman/listinfo/r-sig-mac perhaps specifically this thread https://stat.ethz.ch/pipermail/r-sig-mac/2015-October/011641.html which points to the R-admin manual and especially https://cran.r-project.org/doc/manuals/r-release/R-admin.html#OS-X >From the discussion (especially the posts by Brian Ripley) it seems like it >should be possible to use gfortran-5.2 via editing the R_HOME/etc/Makeconf or >~/.R/Makevars. Martin From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Ludwig Geistlinger [ludwig.geistlin...@bio.ifi.lmu.de] Sent: Wednesday, November 18, 2015 5:53 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] Troubles using R/Bioc-devel with Mac OS X El Capitan 10.11.1 Hi, I am experiencing troubles installing "Hmisc", especially its dependency "acepack", via > biocLite("acepack") in R-devel installed from the "R-devel-mavericks-signed.pkg" downloaded from https://r.research.att.com/. The error reads: BioC_mirror: https://bioconductor.org Using Bioconductor 3.3 (BiocInstaller 1.21.1), R Under development (unstable) (2015-11-16 r69640). Installing package(s) ‘acepack’ Paket, das nur als Quelltext vorliegt und eventuell Übersetzung von C/C++/Fortran benötigt.: ‘acepack’ Do you want to attempt to install these from sources? y/n: y installing the source package ‘acepack’ versuche URL 'https://cran.rstudio.com/src/contrib/acepack_1.3-3.3.tar.gz' Content type 'application/x-gzip' length 33590 bytes (32 KB) == downloaded 32 KB * installing *source* package ‘acepack’ ... ** Paket ‘acepack’ erfolgreich entpackt und MD5 Summen überprüft ** libs gfortran-4.8 -fPIC -g -O2 -c ace.f -o ace.o make: gfortran-4.8: No such file or directory make: *** [ace.o] Error 1 ERROR: compilation failed for package ‘acepack’ * removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/acepack’ which indicates that "gfortran-4.8" is missing. I have however installed the recommended "gfortran-5.2" for El Capitan from here: https://gcc.gnu.org/wiki/GFortranBinaries#MacOS Yesterday, I tried quite some time to install 4.8-versions of gfortran available from the website above, however they are not compatible with El Capitan (Error reads: kern.osversion not recognized: »15.0.0) and searched through several newsgroups reporting on that issue, I was however not able to fix that. Did anyone of the community here experienced similar issues and have some suggestions for me!? Thank you very much! Best, Ludwig ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Troubles using R/Bioc-devel with Mac OS X El Capitan 10.11.1
Hi, I am experiencing troubles installing "Hmisc", especially its dependency "acepack", via > biocLite("acepack") in R-devel installed from the "R-devel-mavericks-signed.pkg" downloaded from https://r.research.att.com/. The error reads: BioC_mirror: https://bioconductor.org Using Bioconductor 3.3 (BiocInstaller 1.21.1), R Under development (unstable) (2015-11-16 r69640). Installing package(s) acepack Paket, das nur als Quelltext vorliegt und eventuell Übersetzung von C/C++/Fortran benötigt.: acepack Do you want to attempt to install these from sources? y/n: y installing the source package acepack versuche URL 'https://cran.rstudio.com/src/contrib/acepack_1.3-3.3.tar.gz' Content type 'application/x-gzip' length 33590 bytes (32 KB) == downloaded 32 KB * installing *source* package acepack ... ** Paket acepack erfolgreich entpackt und MD5 Summen überprüft ** libs gfortran-4.8 -fPIC -g -O2 -c ace.f -o ace.o make: gfortran-4.8: No such file or directory make: *** [ace.o] Error 1 ERROR: compilation failed for package acepack * removing /Library/Frameworks/R.framework/Versions/3.3/Resources/library/acepack which indicates that "gfortran-4.8" is missing. I have however installed the recommended "gfortran-5.2" for El Capitan from here: https://gcc.gnu.org/wiki/GFortranBinaries#MacOS Yesterday, I tried quite some time to install 4.8-versions of gfortran available from the website above, however they are not compatible with El Capitan (Error reads: kern.osversion not recognized: »15.0.0) and searched through several newsgroups reporting on that issue, I was however not able to fix that. Did anyone of the community here experienced similar issues and have some suggestions for me!? Thank you very much! Best, Ludwig ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel