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 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-8 LC_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 attached packages: >>> [1] BiocInstaller_1.21.1 >>> >>> loaded via a namespace (and not attached): >>> [1] tools_3.3.0 >>> >>> >>> Im installing the fortran through homebrew, actually, fortran is part >>> of >>> the gcc bottle there, thus I installed >>> brew install gcc >>> >>> and Im 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 >>>> <martin.mor...@roswellpark.org> >>>> 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. >>>> _______________________________________________ >>>> Bioc-devel@r-project.org mailing list >>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>> >>> >> >> >> -- >> Dipl.-Bioinf. Ludwig Geistlinger >> >> Lehr- und Forschungseinheit für Bioinformatik >> Institut für Informatik >> Ludwig-Maximilians-Universität München >> Amalienstrasse 17, 2. Stock, Büro A201 >> 80333 München >> >> Tel.: 089-2180-4067 >> eMail: ludwig.geistlin...@bio.ifi.lmu.de >> >> _______________________________________________ >> 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. >> > > > -- > Dipl.-Bioinf. Ludwig Geistlinger > > Lehr- und Forschungseinheit für Bioinformatik > Institut für Informatik > Ludwig-Maximilians-Universität München > Amalienstrasse 17, 2. Stock, Büro A201 > 80333 München > > Tel.: 089-2180-4067 > eMail: ludwig.geistlin...@bio.ifi.lmu.de > > > 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