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-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 > > > > > > 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 <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 > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel