Hi Kasper,

It still fails, but with a different error: there's definitely some
progress!

RHEL 5.10, Linux 2.6.18-371.3.1.el5, gcc 4.1.2, R 3.0.2, Bioconductor 2.13:
http://pastebin.com/75HX4sMm
RHEL 6.5, Linux 2.6.32-358.18.1.el6.x86_64, gcc 4.4.7, R 3.0.2,
Bioconductor 2.13: http://pastebin.com/RiH1N5RP

No worries about the timing: I'm not in a particular hurry as I have a
local R installation on Cygwin.
Ideally though, I'd be able to run the same code and load the same packages
on the Linux servers for bigger projects.
I'm not sure if I'll have access to the RHEL6.5 machine in the future, so
it'd be best to have it working on RHEL5.10, if possible.

Thank you very much.
All the best,


On 24 February 2014 15:29, Kasper Daniel Hansen <
kasperdanielhansen@gmail.com> wrote:

> New version posted, same url.  If this doesn't make the error be a bit
> different, I am going to have to wait thinking about this until next week.
>
> Kasper
>
>
> On Mon, Feb 24, 2014 at 5:56 AM, Enrico Ferrero <enricoferrero86@gmail.com
> > wrote:
>
>> Hi Kasper,
>>
>> Many thanks for taking the time to look into this.
>> I tried installing the new package on both systems, not good news I'm
>> afraid.
>>
>> RHEL 5.10, Linux 2.6.18-371.3.1.el5, gcc 4.1.2, R 3.0.2, Bioconductor
>> 2.13: http://pastebin.com/c3hyFD70
>> RHEL 6.5, Linux 2.6.32-358.18.1.el6.x86_64, gcc 4.4.7, R 3.0.2,
>> Bioconductor 2.13: http://pastebin.com/f7UueebY
>>
>> Thank you.
>> Best,
>>
>>
>> On 23 February 2014 16:31, Kasper Daniel Hansen <
>> kasperdanielhansen@gmail.com> wrote:
>>
>>> Thanks
>>>
>>> Unfortunately, I don't have time to really investigate this until the
>>> week starting the 3rd of March.
>>>
>>> I do have time to hypothesize a bit.  And that may be good enough. At
>>>  http://www.biostat.jhsph.edu/~khansen/Rgraphviz_2.7.1.tar.gz
>>> is a new tarball.  It may very well fail, but I hope it gets further
>>> along.  Could you try to install it on both of your systems and show me the
>>> output as well using the very nice pastebin website.
>>>
>>> Thanks,
>>> Kasper
>>>
>>>
>>> On Sat, Feb 22, 2014 at 10:22 AM, Enrico Ferrero <
>>> enricoferrero86@gmail.com> wrote:
>>>
>>>> Hi Kasper,
>>>>
>>>> I just wanted to report that I tried installing Rgraphviz on a newer
>>>> machine (RHEL 6.5) with gcc 4.4.7 and the installation fails exactly in the
>>>> same way.
>>>>
>>>> $ gcc --version
>>>> gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4)
>>>>
>>>> $ uname -r
>>>> 2.6.32-358.18.1.el6.x86_64
>>>>
>>>> $ cat /etc/redhat-version
>>>> Red Hat Enterprise Linux Server release 6.5 (Santiago)
>>>>
>>>>  Full log here: http://pastebin.com/FxA3CA8K
>>>>
>>>> Hope that helps, thank you.
>>>> Best,
>>>>
>>>>
>>>> On 21 February 2014 15:47, Enrico Ferrero <enricoferrero86@gmail.com>wrote:
>>>>
>>>>> Hi Kasper,
>>>>>
>>>>> Here's the full output: http://pastebin.com/RXaDucn1
>>>>>
>>>>> The system is RHEL5 x86_64 with gcc 4.1.2:
>>>>>
>>>>> $ gcc --version
>>>>> gcc (GCC) 4.1.2 20080704 (Red Hat 4.1.2-54)
>>>>>
>>>>> $ uname -r
>>>>> 2.6.18-371.3.1.el5
>>>>>
>>>>> $ cat /etc/redhat-version
>>>>> Red Hat Enterprise Linux Server release 5.10 (Tikanga)
>>>>>
>>>>> Thank you!
>>>>>
>>>>>
>>>>> On 21 February 2014 15:32, Kasper Daniel Hansen <
>>>>> kasperdanielhansen@gmail.com> wrote:
>>>>>
>>>>>> Please post the _entire_ installation output from Rgraphviz using
>>>>>> option #1.  What happens is clearly that graphviz fails to install.
>>>>>>
>>>>>> Which version of gcc are you using?
>>>>>>
>>>>>> Kasper
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Fri, Feb 21, 2014 at 10:23 AM, Enrico Ferrero <
>>>>>> enricoferrero86@gmail.com> wrote:
>>>>>>
>>>>>>> Hi Everyone,
>>>>>>>
>>>>>>> I  tried installing Rgraphviz on  a RHEL5 64bit server and failed
>>>>>>> miserably.
>>>>>>>
>>>>>>> I tried 2 different approaches, using either the Graphviz bundled
>>>>>>> with
>>>>>>> Rgraphviz (v2.28) or the latest version built from source and
>>>>>>> installed on
>>>>>>> the system (v2.36).
>>>>>>>
>>>>>>> Approach #1, using the bundled Graphviz (v2.28), from R:
>>>>>>> biocLite("Rgraphviz")
>>>>>>> It fails here: http://pastebin.com/96cpdXVM
>>>>>>>
>>>>>>> Approach #2, using the system Graphviz (v2.36), from the shell:
>>>>>>> R CMD INSTALL
>>>>>>> --configure-args='--with-graphviz=/path/to/system/graphviz'
>>>>>>> Rgraphviz_2.6.0.tar.gz
>>>>>>> It fails here: http://pastebin.com/VxZ0QEqc
>>>>>>>
>>>>>>> In approach #1, Rgraphviz can't find some graphviz header files,
>>>>>>> which
>>>>>>> prompted me to try approach #2.
>>>>>>> In both cases the problem appears to be in the src/common.h file,
>>>>>>> but I
>>>>>>> have no clue on how I can fix this.
>>>>>>>
>>>>>>> *Any* help or hint in the right direction would be very much
>>>>>>> appreciated.
>>>>>>> Thank you!
>>>>>>>
>>>>>>> Best,
>>>>>>>
>>>>>>> --
>>>>>>> Enrico Ferrero
>>>>>>> Department of Genetics
>>>>>>> Cambridge Systems Biology Centre
>>>>>>> University of Cambridge
>>>>>>>
>>>>>>>         [[alternative HTML version deleted]]
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Bioconductor mailing list
>>>>>>> Bioconductor@r-project.org
>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>>>> Search the archives:
>>>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Enrico Ferrero
>>>>> Department of Genetics
>>>>> Cambridge Systems Biology Centre
>>>>> University of Cambridge
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Enrico Ferrero
>>>> Department of Genetics
>>>> Cambridge Systems Biology Centre
>>>> University of Cambridge
>>>>
>>>
>>>
>>
>>
>> --
>> Enrico Ferrero
>> Department of Genetics
>> Cambridge Systems Biology Centre
>> University of Cambridge
>>
>
>


-- 
Enrico Ferrero
Department of Genetics
Cambridge Systems Biology Centre
University of Cambridge

	[[alternative HTML version deleted]]

