[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.Geistlinger at 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.Morgan at 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-bounces at r-project.org] on behalf of Ludwig Geistlinger [Ludwig.Geistlinger at bio.ifi.lmu.de] Sent: Wednesday, November 18, 2015 5:53 AM To: bioc-devel at 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 ?bersetzung von C/C++/Fortran ben?tigt.: ?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 ?berpr?ft ** 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 at 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 at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
-- Dipl.-Bioinf. Ludwig Geistlinger Lehr- und Forschungseinheit f?r Bioinformatik Institut f?r Informatik Ludwig-Maximilians-Universit?t M?nchen Amalienstrasse 17, 2. Stock, B?ro A201 80333 M?nchen Tel.: 089-2180-4067 eMail: Ludwig.Geistlinger at bio.ifi.lmu.de
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