leviwaldron at gmail.com
2007-Nov-22 19:00 UTC
[Rd] package gsl assumes incorrect gcc version during install (PR#10451)
Full_Name: Levi Waldron Version: 2.5.1 OS: Ubuntu Gutsy Submission from: (NULL) (206.248.157.88) I installed libgsl0-dev then tried to install the gsl cran package, unsuccessfully (see output below). As a workaround I created a symbolic link to /usr/bin/gcc-4.2, ie: sudo ln -s /usr/bin/gcc-4.1 /usr/bin/gcc-4.2 The correct behavior of the gsl package should be to use the executable '/usr/bin/gcc' which is already linked to the current gcc version.> install.packages("gsl",dependencies=T)Warning in install.packages("gsl", dependencies = T) : argument 'lib' is missing: using '/usr/local/lib/R/site-library' --- Please select a CRAN mirror for use in this session --- Loading Tcl/Tk interface ... done trying URL 'http://probability.ca/cran/src/contrib/gsl_1.8-8.tar.gz' Content type 'application/x-tar' length 59084 bytes opened URL =================================================downloaded 57Kb * Installing *source* package 'gsl' ... checking for gcc... gcc checking for C compiler default output... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ANSI C... none needed checking for gsl_sf_airy_Ai_e in -lgsl... yes checking how to run the C preprocessor... gcc -E checking for egrep... grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking gsl/gsl_version.h usability... yes checking gsl/gsl_version.h presence... yes checking for gsl/gsl_version.h... yes checking if GSL version >= 1.8... yes configure: creating ./config.status ** libs gcc-4.2 -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include -fpic -g -O2 -c airy.c -o airy.o /bin/bash: gcc-4.2: command not found make: *** [airy.o] Error 127 chmod: cannot access `/usr/local/lib/R/site-library/gsl/libs/*': No such file or directory ERROR: compilation failed for package 'gsl' ** Removing '/usr/local/lib/R/site-library/gsl' The downloaded packages are in /tmp/RtmpW60zFl/downloaded_packages Warning message: installation of package 'gsl' had non-zero exit status in: install.packages("gsl", dependencies = T)> version_ platform i486-pc-linux-gnu arch i486 os linux-gnu system i486, linux-gnu status major 2 minor 5.1 year 2007 month 06 day 27 svn rev 42083 language R version.string R version 2.5.1 (2007-06-27)>
Dirk Eddelbuettel
2007-Nov-23 18:28 UTC
[Rd] package gsl assumes incorrect gcc version during install (PR#10451)
On 22 November 2007 at 20:00, leviwaldron at gmail.com wrote:
| Full_Name: Levi Waldron
| Version: 2.5.1
| OS: Ubuntu Gutsy
| Submission from: (NULL) (206.248.157.88)
|
|
| I installed libgsl0-dev then tried to install the gsl cran package,
| unsuccessfully (see output below). As a workaround I created a symbolic link
to
| /usr/bin/gcc-4.2, ie:
|
| sudo ln -s /usr/bin/gcc-4.1 /usr/bin/gcc-4.2
I would strongly advise not to do that.
| The correct behavior of the gsl package should be to use the executable
| '/usr/bin/gcc' which is already linked to the current gcc version.
No. You misunderstand. It has nothing to do with the package.
When R is built, it 'stores' its compiler version etc in the file
Makeconf. The Debian (and hence Ubuntu) packages store that file for you as
/etc/R/Makeconf via a link; the file is as always in $RHOME/etc/Makeconf.
This file defines a variable CC for the compiler. All you need to do is to
set it back to 'gcc' from its value 'gcc-4.2'.
This really is a local admin issue (ie you need to fix it) and not a problem
with R, or gsl.
If you got R from Ubuntu, file a bug report _with Ubuntu_ as they seem to
have forgotten to switch from gcc-4.2 (which we use in Debian as default) to
gcc-4.1 (which is Ubuntu's default).
| > install.packages("gsl",dependencies=T)
| Warning in install.packages("gsl", dependencies = T) :
| argument 'lib' is missing: using
'/usr/local/lib/R/site-library'
| --- Please select a CRAN mirror for use in this session ---
| Loading Tcl/Tk interface ... done
| trying URL 'http://probability.ca/cran/src/contrib/gsl_1.8-8.tar.gz'
| Content type 'application/x-tar' length 59084 bytes
| opened URL
| =================================================| downloaded 57Kb
|
| * Installing *source* package 'gsl' ...
| checking for gcc... gcc
| checking for C compiler default output... a.out
| checking whether the C compiler works... yes
| checking whether we are cross compiling... no
| checking for suffix of executables...
| checking for suffix of object files... o
| checking whether we are using the GNU C compiler... yes
| checking whether gcc accepts -g... yes
| checking for gcc option to accept ANSI C... none needed
| checking for gsl_sf_airy_Ai_e in -lgsl... yes
| checking how to run the C preprocessor... gcc -E
| checking for egrep... grep -E
| checking for ANSI C header files... yes
| checking for sys/types.h... yes
| checking for sys/stat.h... yes
| checking for stdlib.h... yes
| checking for string.h... yes
| checking for memory.h... yes
| checking for strings.h... yes
| checking for inttypes.h... yes
| checking for stdint.h... yes
| checking for unistd.h... yes
| checking gsl/gsl_version.h usability... yes
| checking gsl/gsl_version.h presence... yes
| checking for gsl/gsl_version.h... yes
| checking if GSL version >= 1.8... yes
| configure: creating ./config.status
| ** libs
| gcc-4.2 -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include -fpic
-g
| -O2 -c airy.c -o airy.o
| /bin/bash: gcc-4.2: command not found
| make: *** [airy.o] Error 127
| chmod: cannot access `/usr/local/lib/R/site-library/gsl/libs/*': No such
file or
| directory
| ERROR: compilation failed for package 'gsl'
| ** Removing '/usr/local/lib/R/site-library/gsl'
|
| The downloaded packages are in
| /tmp/RtmpW60zFl/downloaded_packages
| Warning message:
| installation of package 'gsl' had non-zero exit status in:
| install.packages("gsl", dependencies = T)
|
| > version
| _
| platform i486-pc-linux-gnu
| arch i486
| os linux-gnu
| system i486, linux-gnu
| status
| major 2
| minor 5.1
| year 2007
| month 06
| day 27
| svn rev 42083
| language R
| version.string R version 2.5.1 (2007-06-27)
Also note that CRAN has prebuilt versions of the current R release, ie 2.6.0,
for Ubuntu Gutsy, see $CRAN/bin/linux/ubuntu
The CRAN version of R for Ubuntu is quite possibly of better quality than the
distro's version.
Dirk
| >
|
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