----- Am 8. Nov 2016 um 18:14 schrieb George N. White III gnw...@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
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