[Bioc-devel] Troubles using R/Bioc-devel with Mac OS X El Capitan 10.11.1

Henrik Bengtsson henrik.bengtsson at gmail.com
Wed Nov 18 15:30:20 CET 2015


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 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 at r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>
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> >> Bioc-devel at 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.Geistlinger at bio.ifi.lmu.de
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
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