Hi
I just upgraded my R from stabel/etch from 2.4.x to 2.6.2 via
sudo apt-get install r-base
which worked fine, installing all dependencies
From R, as root, I did
update.packages()
but a number of packages packages failed to install, either for missing
gfortran
or missing dependencies.
Warning messages:
1: In install.packages(update[instlib == l, "Package"], l, contriburl =
contriburl, :
installation of package 'maptools' had non-zero exit status
2: In install.packages(update[instlib == l, "Package"], l, contriburl =
contriburl, :
installation of package 'mvtnorm' had non-zero exit status
3: In install.packages(update[instlib == l, "Package"], l, contriburl =
contriburl, :
installation of package 'lmtest' had non-zero exit status
4: In install.packages(update[instlib == l, "Package"], l, contriburl =
contriburl, :
installation of package 'multcomp' had non-zero exit status
5: In install.packages(update[instlib == l, "Package"], l, contriburl =
contriburl, :
installation of package 'cluster' had non-zero exit status
6: In install.packages(update[instlib == l, "Package"], l, contriburl =
contriburl, :
installation of package 'KernSmooth' had non-zero exit status
7: In install.packages(update[instlib == l, "Package"], l, contriburl =
contriburl, :
installation of package 'mgcv' had non-zero exit status
...
OK, I installed r-base-dev to get gfortran and other dependencies, then
tried
update.packages() again. This time only rgl failed, complaining about
missing X11:
trying URL 'http://probability.ca/cran/src/contrib/rgl_0.77.tar.gz'
Content type 'application/x-tar' length 803692 bytes (784 Kb)
opened URL
==================================================
downloaded 784 Kb
* Installing *source* package 'rgl' ...
checking for gcc... gcc -std=gnu99
checking for C compiler default output file name... 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 -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ANSI C... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for gcc... (cached) gcc -std=gnu99
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc -std=gnu99 accepts -g... (cached) yes
checking for gcc -std=gnu99 option to accept ANSI C... (cached) none needed
checking for libpng-config... yes
configure: using libpng-config
configure: using libpng dynamic linkage
checking for X... no
configure: error: X11 not found but required, configure aborted.
ERROR: configuration failed for package 'rgl'
** Removing '/usr/lib/R/site-library/rgl'
** Restoring previous '/usr/lib/R/site-library/rgl'
The downloaded packages are in
/tmp/RtmpSFCuUT/downloaded_packages
Warning message:
In install.packages(update[instlib == l, "Package"], l, contriburl =
contriburl, :
installation of package 'rgl' had non-zero exit status
Finally, I tried to install r-cran-rgl, but with no joy:
euclid:~# apt-get install r-cran-rgl
Reading package lists... Done
Building dependency tree... Done
r-cran-rgl is already the newest version.
0 upgraded, 0 newly installed, 0 to remove and 267 not upgraded.
Can anyone suggest what is wrong and how to fix it?
thanks,
-Michael
Michael Friendly Email: friendly at yorku.ca
Professor, Psychology Dept.
York University Voice: 416 736-5115 x66249 Fax: 416 736-5814
4700 Keele Street http://www.math.yorku.ca/SCS/friendly.html
Toronto, ONT M3J 1P3 CANADA
Hi Michael,
* Michael Friendly <friendly at yorku.ca> [080409 22:00]:
Hi
I just upgraded my R from stabel/etch from 2.4.x to 2.6.2 via
sudo apt-get install r-base
which worked fine, installing all dependencies
I suppose you put some CRAN mirror into your /etc/apt/sources.list?
From R, as root, I did
update.packages()
but a number of packages packages failed to install, either for missing
gfortran
or missing dependencies.
Yes, you need to explicitly upgrade r-base-dev, too, if you want to
install packages from CRAN.
...
...
OK, I installed r-base-dev to get gfortran and other dependencies, then
tried
update.packages() again. This time only rgl failed, complaining about
missing X11:
trying URL 'http://probability.ca/cran/src/contrib/rgl_0.77.tar.gz'
Content type 'application/x-tar' length 803692 bytes (784 Kb)
opened URL
==================================================
downloaded 784 Kb
* Installing *source* package 'rgl' ...
checking for gcc... gcc -std=gnu99
checking for C compiler default output file name... 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 -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ANSI C... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for gcc... (cached) gcc -std=gnu99
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc -std=gnu99 accepts -g... (cached) yes
checking for gcc -std=gnu99 option to accept ANSI C... (cached) none needed
checking for libpng-config... yes
configure: using libpng-config
configure: using libpng dynamic linkage
checking for X... no
configure: error: X11 not found but required, configure aborted.
ERROR: configuration failed for package 'rgl'
** Removing '/usr/lib/R/site-library/rgl'
** Restoring previous '/usr/lib/R/site-library/rgl'
Ok, I just did this on one of my etch boxes with CRAN R (and X
installed):
cecking for X... libraries , headers
checking GL/gl.h usability... yes
checking GL/gl.h presence... yes
checking for GL/gl.h... yes
checking GL/glu.h usability... yes
checking GL/glu.h presence... yes
checking for GL/glu.h... yes
checking for glEnd in -lGL... yes
checking for gluProject in -lGLU... yes
configure: creating ./config.status
config.status: creating src/Makevars
So it works over here... On another box, without OpenGL, it fails, as
one would expect. On a third box, where I have no X installed, it fails,
too, with exactly the error message you quoted above.
Could you give us the output of
apt-cache policy xserver-xorg-core
or just tell us if you have Xorg installed?
Best regards,
Johannes
Finally, I tried to install r-cran-rgl, but with no joy:
euclid:~# apt-get install r-cran-rgl
Reading package lists... Done
Building dependency tree... Done
r-cran-rgl is already the newest version.
0 upgraded, 0 newly installed, 0 to remove and 267 not upgraded.
Can anyone suggest what is wrong and how to fix it?
thanks,
-Michael
--
Michael Friendly Email: friendly at yorku.ca
Professor, Psychology Dept.
York University Voice: 416 736-5115 x66249 Fax: 416 736-5814
4700 Keele Street http://www.math.yorku.ca/SCS/friendly.html
Toronto, ONT M3J 1P3 CANADA
From R, as root, I did
update.packages()
but a number of packages packages failed to install, either for missing
gfortran
or missing dependencies.
Yes, you need to explicitly upgrade r-base-dev, too, if you want to
install packages from CRAN.
...
...
OK, I installed r-base-dev to get gfortran and other dependencies, then
tried
update.packages() again. This time only rgl failed, complaining about
missing X11:
trying URL 'http://probability.ca/cran/src/contrib/rgl_0.77.tar.gz'
Content type 'application/x-tar' length 803692 bytes (784 Kb)
opened URL
==================================================
downloaded 784 Kb
* Installing *source* package 'rgl' ...
checking for gcc... gcc -std=gnu99
checking for C compiler default output file name... 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 -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ANSI C... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for gcc... (cached) gcc -std=gnu99
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc -std=gnu99 accepts -g... (cached) yes
checking for gcc -std=gnu99 option to accept ANSI C... (cached) none needed
checking for libpng-config... yes
configure: using libpng-config
configure: using libpng dynamic linkage
checking for X... no
configure: error: X11 not found but required, configure aborted.
ERROR: configuration failed for package 'rgl'
** Removing '/usr/lib/R/site-library/rgl'
** Restoring previous '/usr/lib/R/site-library/rgl'
Could you give us the output of
apt-cache policy xserver-xorg-core
or just tell us if you have Xorg installed?
Finally, I tried to install r-cran-rgl, but with no joy:
euclid:~# apt-get install r-cran-rgl
Reading package lists... Done
Building dependency tree... Done
r-cran-rgl is already the newest version.
0 upgraded, 0 newly installed, 0 to remove and 267 not upgraded.
Can anyone suggest what is wrong and how to fix it?
Michael Friendly Email: friendly at yorku.ca
Professor, Psychology Dept.
York University Voice: 416 736-5115 x66249 Fax: 416 736-5814
4700 Keele Street http://www.math.yorku.ca/SCS/friendly.html
Toronto, ONT M3J 1P3 CANADA
Michael,
I haven't had time to follow this closely but it seems that you that
reckon that because
a) you have (or had) r-cran-rgl installed
you should be able to
b) build either r-cran-rgl, or rgl
which is not true. We differentiate between Depends (to run) and
Build-Depends (to compile and link).
What you may need is a simple
sudo apt-get build-dep r-cran-rgl
which should give you everything needed to build rgl (even if you do not turn
it into a local .deb)
I may have misunderstood, in which case I apologize for adding further
confusion.
Hth. Dirk
--
Three out of two people have difficulties with fractions.
... We differentiate between Depends (to run) and
Build-Depends (to compile and link).
yes, probably just xserver-xorg-dev is missing, but your suggestion is
much better:
What you may need is a simple
sudo apt-get build-dep r-cran-rgl
which should give you everything needed to build rgl (even if you do not turn
it into a local .deb)
Right, if newer rgl versions have not added dependencies not present in
r-cran-rgl from etch.
I may have misunderstood, in which case I apologize for adding further
confusion.
On the contrary, I think you are right on!
Johannes
What you may need is a simple
sudo apt-get build-dep r-cran-rgl
which should give you everything needed to build rgl (even if you do not turn
it into a local .deb)
Worked like a charm. Thanks for your help.
-Michael
Michael Friendly Email: friendly at yorku.ca
Professor, Psychology Dept.
York University Voice: 416 736-5115 x66249 Fax: 416 736-5814
4700 Keele Street http://www.math.yorku.ca/SCS/friendly.html
Toronto, ONT M3J 1P3 CANADA