[Bioc-devel] Troubles using R/Bioc-devel with Mac OS X El Capitan 10.11.1
Rainer Johannes
Johannes.Rainer at eurac.edu
Wed Nov 18 15:15:05 CET 2015
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 <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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>>
>>
>
>
> --
> 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
>
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