R SIG Debian - Nov 2016 - proplems installing R 2.5 on Ubuntu 14.04

----- Am 8. Nov 2016 um 15:26 schrieb Johannes Ranke johannes.ranke at jrwb.de:
> Hi
> 
> try
> 
> apt-get build-dep r-base
> 
> this installs the headers required for building current R, which probably
also
> covers older versions - at least it will give you X11 headers.
> 
> Good luck,
> 
> Johannes
> 
> 
Hi Johannes,

i tried that and it didn't work.

Bernd
 

Helmholtz Zentrum Muenchen
Deutsches Forschungszentrum fuer Gesundheit und Umwelt (GmbH)
Ingolstaedter Landstr. 1
85764 Neuherberg
www.helmholtz-muenchen.de
Aufsichtsratsvorsitzende: MinDir'in Baerbel Brumme-Bothe
Geschaeftsfuehrer: Prof. Dr. Guenther Wess, Dr. Alfons Enhsen
Registergericht: Amtsgericht Muenchen HRB 6466
USt-IdNr: DE 129521671

On Tue, Nov 8, 2016 at 10:45 AM, Lentes, Bernd <
bernd.lentes at helmholtz-muenchen.de> wrote:
>
>
> ----- Am 8. Nov 2016 um 15:26 schrieb Johannes Ranke
> johannes.ranke at jrwb.de:
>
> > Hi
> >
> > try
> >
> > apt-get build-dep r-base
> >
> > this installs the headers required for building current R, which
> probably also
> > covers older versions - at least it will give you X11 headers.
> >
> > Good luck,
> >
> > Johannes
> >
> >
> Hi Johannes,
>
> i tried that and it didn't work.
>
> Bernd
>
If you expect people to help you need to be much more explicit about what
you mean by "it didn't work".    As you have discovered, building
an old
version of R on a current system may not be a simple task.  Over my career
I have resorted to porting old software to current platforms a few times in
order to understand puzzling results from some past calculation.  I have
learned to hang on to old manuals so I at least have documentation for
function arguments and compiler flags on the original system.

You might consider alternatives:

1. running an older OS and R in a VM

2. porting your old R package to a current version of R

3. finding a current R package with the functionality of the old package

4. building an old version of R without X11 graphics, as in:
http://stackoverflow.com/questions/26263934/compile-r-with-cairo-support-without-x11

5. building the current version of R to ensure that you have a working
build environment, then porting the old version of R to that environment.
Since I
have access to a system with the development packages needed for a current
R, I just tried "./configure" for R-2.5.1 and get:

configure: error: --with-x=yes (default) and X11 headers/libs are not
available

Looking in config.log, I see:

configure:44433: gcc -std=gnu99 -o conftest -g -O2  -I/usr/local/include
 -L/usr
/local/lib64 conftest.c -lXt -ldl -lm  >&5
/tmp/cc8fJIay.o: In function `main':
/home/gwhite/Documents/Testing/R-2.5.1/conftest.c:205: undefined reference
to `XrmInitialize'
collect2: error: ld returned 1 exit status
configure:44439: $? = 1
configure: failed program was:
| /* confdefs.h.  */
| #define PACKAGE_NAME "R"
| #define PACKAGE_TARNAME "R"
| #define PACKAGE_VERSION "2.5.1"
| #define PACKAGE_STRING "R 2.5.1"
[...]
 #define SUPPORT_MBCS 1
| /* end confdefs.h.  */
| #include <X11/Xlib.h>
| #ifdef F77_DUMMY_MAIN
|
| #  ifdef __cplusplus
|      extern "C"
| #  endif
|    int F77_DUMMY_MAIN() { return 1; }
|
| #endif
| int
| main ()
| {
| XrmInitialize ()
|   ;
|   return 0;
| }
configure:44503: result: no
configure:46230: error: --with-x=yes (default) and X11 headers/libs are not
available
>From past experience, this led me to try:
./configure LIBS=X11

which worked, as did "make" and "make check".


-- 
George N. White III <aa056 at chebucto.ns.ca>
Head of St. Margarets Bay, Nova Scotia

	[[alternative HTML version deleted]]

----- Am 8. Nov 2016 um 18:14 schrieb George N. White III gnwiii at gmail.com:


> If you expect people to help you need to be much more explicit about what
you
> mean by "it didn't work". As you have discovered, building an
old version of R
> on a current system may not be a simple task. Over my career I have
resorted to
> porting old software to current platforms a few times in order to
understand
> puzzling results from some past calculation. I have learned to hang on to
old
> manuals so I at least have documentation for function arguments and
compiler
> flags on the original system.
> You might consider alternatives:
> 1. running an older OS and R in a VM
I have a software which requires Ubuntu 14.04 and R 2.5. If VM or physical host
does not matter.
> 2. porting your old R package to a current version of R
see above
> 3. finding a current R package with the functionality of the old package
The doc of the software says:
"Most of the GenePattern modules available in the Broad Institute
repository (Modules & Pipelines>Install from repository) work with R 2.5.
                                                                                
^^^^^^^^^^^^^^^
However, some GenePattern modules require different versions of R; for example,
ComBat v2 requires R 2.7. Unfortunately,
R is not backward compatible. If you simply install and run the latest version
of R,    <=====modules may fail or (worse) may produce invalid results even
though they do not fail."  <=====                                       
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

A current package does not help.
> 4. building an old version of R without X11 graphics, as in:
>
http://stackoverflow.com/questions/26263934/compile-r-with-cairo-support-without-x11
I will check that.
> 5. building the current version of R to ensure that you have a working
build
> environment, then porting the old version of R to that environment. Since I
> have access to a system with the development packages needed for a current
R, I
> just tried " ./configure " for R-2.5.1 and get:
> configure: error: --with-x=yes (default) and X11 headers/libs are not
available
> Looking in config.log , I see:
> configure:44433: gcc -std=gnu99 -o conftest -g -O2 -I/usr/local/include
-L/usr
> /local/lib64 conftest.c -lXt -ldl -lm >&5
> /tmp/cc8fJIay.o: In function `main':
> /home/gwhite/Documents/Testing/R-2.5.1/conftest.c:205: undefined reference
to
> `XrmInitialize'
> collect2: error: ld returned 1 exit status
> configure:44439: $? = 1
> configure: failed program was:
> | /* confdefs.h. */
> | #define PACKAGE_NAME "R"
> | #define PACKAGE_TARNAME "R"
> | #define PACKAGE_VERSION "2.5.1"
> | #define PACKAGE_STRING "R 2.5.1"
> [...]
> #define SUPPORT_MBCS 1
> | /* end confdefs.h. */
> | #include <X11/Xlib.h>
> | #ifdef F77_DUMMY_MAIN
> | # ifdef __cplusplus
> | extern "C"
> | # endif
> | int F77_DUMMY_MAIN() { return 1; }
> | #endif
> | int
> | main ()
> | {
> | XrmInitialize ()
> | ;
> | return 0;
> | }
> configure:44503: result: no
> configure:46230: error: --with-x=yes (default) and X11 headers/libs are not
> available
> From past experience, this led me to try:
> ./configure LIBS=X11
> which worked, as did " make " and " make check ".
I will check taht. Thanks.

Bernd
 

Helmholtz Zentrum Muenchen
Deutsches Forschungszentrum fuer Gesundheit und Umwelt (GmbH)
Ingolstaedter Landstr. 1
85764 Neuherberg
www.helmholtz-muenchen.de
Aufsichtsratsvorsitzende: MinDir'in Baerbel Brumme-Bothe
Geschaeftsfuehrer: Prof. Dr. Guenther Wess, Dr. Alfons Enhsen
Registergericht: Amtsgericht Muenchen HRB 6466
USt-IdNr: DE 129521671