[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
Re: [Bioc-devel] Troubles using R/Bioc-devel with Mac OS X El Capitan 10.11.1
ages:
> [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-de
Re: [Bioc-devel] Troubles using R/Bioc-devel with Mac OS X El Capitan 10.11.1
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_MONE
Re: [Bioc-devel] Troubles using R/Bioc-devel with Mac OS X El Capitan 10.11.1
> 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-8LC_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’
> >>
> >> ver
Re: [Bioc-devel] Troubles using R/Bioc-devel with Mac OS X El Capitan 10.11.1
SS=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
