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package with fortran failing to install
9 messages · Kasper Daniel Hansen, Simon Urbanek, Devin Johnson +1 more
You need to install Xcode. Kasper
On Mon, Mar 29, 2010 at 4:45 PM, Devin Johnson <Devin.Johnson at noaa.gov> wrote:
Hi,
I have a problem compiling/installing a package that has fortran source code in it. I've compiled earlier versions of this package many times in the past as I've worked on it, but, now it's failing to install. I've recently go through an upgrade to snow leopard and installation/migration of my home directory for networking purposes at work (use AdmitMac with a domain account). I'm not sure which one of these might be causing the issue. Everything was fine before this. Here's the error:
$ R CMD INSTALL crawl
* installing to library ?/Users/johnsond/Library/R/?
* installing *source* package ?crawl? ...
** libs
** arch - i386
sh: make: command not found
ERROR: compilation failed for package ?crawl?
* removing ?/Users/johnsond/Library/R//crawl?
* restoring previous ?/Users/johnsond/Library/R//crawl?
Here's the gfortran version:
$ gfortran --version
GNU Fortran (GCC) 4.2.3
Copyright (C) 2007 Free Software Foundation, Inc.
GNU Fortran comes with NO WARRANTY, to the extent permitted by law.
You may redistribute copies of GNU Fortran
under the terms of the GNU General Public License.
For more information about these matters, see the file named COPYING
$ which gfortran
/usr/local/bin/gfortran
The package ("crawl") is currently on CRAN and when I download the source, I get the same message. I've tried reinstalling R 2.10.1, gfortran 2.4.3, and poking around where I could, but I'm at a loss for what to check next. Any help would be greatly appreciated.
----------------------------------------------------------
Devin S. Johnson, Ph.D.
Statistician
NOAA National Marine Mammal Laboratory
7600 Sand Point Way NE
Seattle, WA 98115
Phone: (206) 526-6867
Fax: (206) 526-6115
Email: devin.johnson at noaa.gov
----------------------------------------------------------
? ? ? ?[[alternative HTML version deleted]]
_______________________________________________ R-SIG-Mac mailing list R-SIG-Mac at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
On Mar 29, 2010, at 16:45 , Devin Johnson wrote:
Hi, I have a problem compiling/installing a package that has fortran source code in it. I've compiled earlier versions of this package many times in the past as I've worked on it, but, now it's failing to install. I've recently go through an upgrade to snow leopard and installation/migration of my home directory for networking purposes at work (use AdmitMac with a domain account). I'm not sure which one of these might be causing the issue. Everything was fine before this. Here's the error: $ R CMD INSTALL crawl * installing to library ?/Users/johnsond/Library/R/? * installing *source* package ?crawl? ... ** libs ** arch - i386 sh: make: command not found
Please see the FAQ - you don't even have Xcode installed. Cheers, Simon
ERROR: compilation failed for package ?crawl?
* removing ?/Users/johnsond/Library/R//crawl?
* restoring previous ?/Users/johnsond/Library/R//crawl?
Here's the gfortran version:
$ gfortran --version
GNU Fortran (GCC) 4.2.3
Copyright (C) 2007 Free Software Foundation, Inc.
GNU Fortran comes with NO WARRANTY, to the extent permitted by law.
You may redistribute copies of GNU Fortran
under the terms of the GNU General Public License.
For more information about these matters, see the file named COPYING
$ which gfortran
/usr/local/bin/gfortran
The package ("crawl") is currently on CRAN and when I download the
source, I get the same message. I've tried reinstalling R 2.10.1,
gfortran 2.4.3, and poking around where I could, but I'm at a loss
for what to check next. Any help would be greatly appreciated.
----------------------------------------------------------
Devin S. Johnson, Ph.D.
Statistician
NOAA National Marine Mammal Laboratory
7600 Sand Point Way NE
Seattle, WA 98115
Phone: (206) 526-6867
Fax: (206) 526-6115
Email: devin.johnson at noaa.gov
----------------------------------------------------------
[[alternative HTML version deleted]]
_______________________________________________ R-SIG-Mac mailing list R-SIG-Mac at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Thanks for the quick replies, I had Xcode on before the upgrade to SL. I didn't think to reinstall. --Devin
On Mar 29, 2010, at 2:18 PM, Simon Urbanek wrote:
On Mar 29, 2010, at 16:45 , Devin Johnson wrote:
Hi, I have a problem compiling/installing a package that has fortran source code in it. I've compiled earlier versions of this package many times in the past as I've worked on it, but, now it's failing to install. I've recently go through an upgrade to snow leopard and installation/migration of my home directory for networking purposes at work (use AdmitMac with a domain account). I'm not sure which one of these might be causing the issue. Everything was fine before this. Here's the error: $ R CMD INSTALL crawl * installing to library ?/Users/johnsond/Library/R/? * installing *source* package ?crawl? ... ** libs ** arch - i386 sh: make: command not found
Please see the FAQ - you don't even have Xcode installed. Cheers, Simon
ERROR: compilation failed for package ?crawl?
* removing ?/Users/johnsond/Library/R//crawl?
* restoring previous ?/Users/johnsond/Library/R//crawl?
Here's the gfortran version:
$ gfortran --version
GNU Fortran (GCC) 4.2.3
Copyright (C) 2007 Free Software Foundation, Inc.
GNU Fortran comes with NO WARRANTY, to the extent permitted by law.
You may redistribute copies of GNU Fortran
under the terms of the GNU General Public License.
For more information about these matters, see the file named COPYING
$ which gfortran
/usr/local/bin/gfortran
The package ("crawl") is currently on CRAN and when I download the source, I get the same message. I've tried reinstalling R 2.10.1, gfortran 2.4.3, and poking around where I could, but I'm at a loss for what to check next. Any help would be greatly appreciated.
----------------------------------------------------------
Devin S. Johnson, Ph.D.
Statistician
NOAA National Marine Mammal Laboratory
7600 Sand Point Way NE
Seattle, WA 98115
Phone: (206) 526-6867
Fax: (206) 526-6115
Email: devin.johnson at noaa.gov
----------------------------------------------------------
[[alternative HTML version deleted]]
_______________________________________________ R-SIG-Mac mailing list R-SIG-Mac at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
---------------------------------------------------------- Devin S. Johnson, Ph.D. Statistician NOAA National Marine Mammal Laboratory 7600 Sand Point Way NE Seattle, WA 98115 Phone: (206) 526-6867 Fax: (206) 526-6115 Email: devin.johnson at noaa.gov
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On Mar 29, 2010, at 18:08 , Devin Johnson wrote:
After installing Xcode again (3.2.1) I get the new error when building from the source posted on CRAN $ R CMD INSTALL crawl_1.1-0.tar.gz * installing to library ?/Users/johnsond/Library/R/? * installing *source* package ?crawl? ... ** libs ** arch - i386 gfortran-4.2 -arch i386 -fno-common -mtune=core2 -g -O2 -c crwDriftN2ll.f90 -o crwDriftN2ll.o crwDriftN2ll.f90:0: error: bad value (core2) for -mtune= switch make: *** [crwDriftN2ll.o] Error 1 ERROR: compilation failed for package ?crawl? * removing ?/Users/johnsond/Library/R//crawl? * restoring previous ?/Users/johnsond/Library/R//crawl? Is there something else that disappeared with my upgrade to SL? Or is this now a gfortran problem?
The problem is still the same - you failing to read the docs! If you bothered to read the e-mails you'd know that you have to install Xcode 3.2 (or 3.2.1) and the corresponding Fortran from http://r.research.att.com/tools/ Cheers, Simon
On Mar 29, 2010, at 2:18 PM, Simon Urbanek wrote:
On Mar 29, 2010, at 16:45 , Devin Johnson wrote:
Hi, I have a problem compiling/installing a package that has fortran source code in it. I've compiled earlier versions of this package many times in the past as I've worked on it, but, now it's failing to install. I've recently go through an upgrade to snow leopard and installation/migration of my home directory for networking purposes at work (use AdmitMac with a domain account). I'm not sure which one of these might be causing the issue. Everything was fine before this. Here's the error: $ R CMD INSTALL crawl * installing to library ?/Users/johnsond/Library/R/? * installing *source* package ?crawl? ... ** libs ** arch - i386 sh: make: command not found
Please see the FAQ - you don't even have Xcode installed. Cheers, Simon
ERROR: compilation failed for package ?crawl?
* removing ?/Users/johnsond/Library/R//crawl?
* restoring previous ?/Users/johnsond/Library/R//crawl?
Here's the gfortran version:
$ gfortran --version
GNU Fortran (GCC) 4.2.3
Copyright (C) 2007 Free Software Foundation, Inc.
GNU Fortran comes with NO WARRANTY, to the extent permitted by law.
You may redistribute copies of GNU Fortran
under the terms of the GNU General Public License.
For more information about these matters, see the file named COPYING
$ which gfortran
/usr/local/bin/gfortran
The package ("crawl") is currently on CRAN and when I download the
source, I get the same message. I've tried reinstalling R 2.10.1,
gfortran 2.4.3, and poking around where I could, but I'm at a loss
for what to check next. Any help would be greatly appreciated.
----------------------------------------------------------
Devin S. Johnson, Ph.D.
Statistician
NOAA National Marine Mammal Laboratory
7600 Sand Point Way NE
Seattle, WA 98115
Phone: (206) 526-6867
Fax: (206) 526-6115
Email: devin.johnson at noaa.gov
----------------------------------------------------------
[[alternative HTML version deleted]]
_______________________________________________ R-SIG-Mac mailing list R-SIG-Mac at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
---------------------------------------------------------- Devin S. Johnson, Ph.D. Statistician NOAA National Marine Mammal Laboratory 7600 Sand Point Way NE Seattle, WA 98115 Phone: (206) 526-6867 Fax: (206) 526-6115 Email: devin.johnson at noaa.gov ----------------------------------------------------------
As you can see from the previous email I have installed Xcode 3.2.1 and from the first email, I've installed gfortran 4.2.3 from http://r.research.att.com/tools/. Is this not the corresponding gfortran? -Devin
On Mar 29, 2010, at 3:18 PM, Simon Urbanek wrote:
On Mar 29, 2010, at 18:08 , Devin Johnson wrote:
After installing Xcode again (3.2.1) I get the new error when building from the source posted on CRAN $ R CMD INSTALL crawl_1.1-0.tar.gz * installing to library ?/Users/johnsond/Library/R/? * installing *source* package ?crawl? ... ** libs ** arch - i386 gfortran-4.2 -arch i386 -fno-common -mtune=core2 -g -O2 -c crwDriftN2ll.f90 -o crwDriftN2ll.o crwDriftN2ll.f90:0: error: bad value (core2) for -mtune= switch make: *** [crwDriftN2ll.o] Error 1 ERROR: compilation failed for package ?crawl? * removing ?/Users/johnsond/Library/R//crawl? * restoring previous ?/Users/johnsond/Library/R//crawl? Is there something else that disappeared with my upgrade to SL? Or is this now a gfortran problem?
The problem is still the same - you failing to read the docs! If you bothered to read the e-mails you'd know that you have to install Xcode 3.2 (or 3.2.1) and the corresponding Fortran from http://r.research.att.com/tools/ Cheers, Simon
On Mar 29, 2010, at 2:18 PM, Simon Urbanek wrote:
On Mar 29, 2010, at 16:45 , Devin Johnson wrote:
Hi, I have a problem compiling/installing a package that has fortran source code in it. I've compiled earlier versions of this package many times in the past as I've worked on it, but, now it's failing to install. I've recently go through an upgrade to snow leopard and installation/migration of my home directory for networking purposes at work (use AdmitMac with a domain account). I'm not sure which one of these might be causing the issue. Everything was fine before this. Here's the error: $ R CMD INSTALL crawl * installing to library ?/Users/johnsond/Library/R/? * installing *source* package ?crawl? ... ** libs ** arch - i386 sh: make: command not found
Please see the FAQ - you don't even have Xcode installed. Cheers, Simon
ERROR: compilation failed for package ?crawl?
* removing ?/Users/johnsond/Library/R//crawl?
* restoring previous ?/Users/johnsond/Library/R//crawl?
Here's the gfortran version:
$ gfortran --version
GNU Fortran (GCC) 4.2.3
Copyright (C) 2007 Free Software Foundation, Inc.
GNU Fortran comes with NO WARRANTY, to the extent permitted by law.
You may redistribute copies of GNU Fortran
under the terms of the GNU General Public License.
For more information about these matters, see the file named COPYING
$ which gfortran
/usr/local/bin/gfortran
The package ("crawl") is currently on CRAN and when I download the source, I get the same message. I've tried reinstalling R 2.10.1, gfortran 2.4.3, and poking around where I could, but I'm at a loss for what to check next. Any help would be greatly appreciated.
----------------------------------------------------------
Devin S. Johnson, Ph.D.
Statistician
NOAA National Marine Mammal Laboratory
7600 Sand Point Way NE
Seattle, WA 98115
Phone: (206) 526-6867
Fax: (206) 526-6115
Email: devin.johnson at noaa.gov
----------------------------------------------------------
[[alternative HTML version deleted]]
_______________________________________________ R-SIG-Mac mailing list R-SIG-Mac at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
---------------------------------------------------------- Devin S. Johnson, Ph.D. Statistician NOAA National Marine Mammal Laboratory 7600 Sand Point Way NE Seattle, WA 98115 Phone: (206) 526-6867 Fax: (206) 526-6115 Email: devin.johnson at noaa.gov ----------------------------------------------------------
---------------------------------------------------------- Devin S. Johnson, Ph.D. Statistician NOAA National Marine Mammal Laboratory 7600 Sand Point Way NE Seattle, WA 98115 Phone: (206) 526-6867 Fax: (206) 526-6115 Email: devin.johnson at noaa.gov
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