________________________________________
From: Ludwig Geistlinger [Ludwig.Geistlinger at bio.ifi.lmu.de]
Sent: Wednesday, November 18, 2015 10:14 AM
To: Morgan, Martin
Subject: RE: [Bioc-devel] Troubles using R/Bioc-devel with Mac OS X El
Capitan 10.11.1
Dear Martin,
it should be possible to use gfortran-5.2 via editing the
R_HOME/etc/Makeconf or ~/.R/Makevars.
I will of course try that - it's not about taking your suggestion lightly,
just trying out what is working for me.
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.
Is this refering to linux issue, I reported? And what is the meaning of
your suggestions here? Should I wait for Michael Lawrence commits to take
place?
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?
Thx,
Ludwig
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-bounces at r-project.org] on behalf of Ludwig
Geistlinger [Ludwig.Geistlinger at bio.ifi.lmu.de]
Sent: Wednesday, November 18, 2015 8:46 AM
To: bioc-devel at 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_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
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--
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
_______________________________________________
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.
--
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
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.