Hi Kasper, Yes it builds correctly on both systems. That's great to hear, thanks very much. Best, On 26 February 2014 16:43, Kasper Daniel Hansen < kasperdanielhansen@gmail.com> wrote: > You tested both compilers, right? > > I'll incorporate these fixes into the official devel version later today I > hope. > > Kasper > > > On Wed, Feb 26, 2014 at 4:14 AM, Enrico Ferrero <enricoferrero86@gmail.com> > wrote: > >> Hi Kasper, >> >> Amazing, it worked! >> Thank you very much, this is going to have a considerable impact on my >> future research. >> Log here: http://hastebin.com/loqututenu.hs >> >> Best, >> >> >> On 25 February 2014 15:20, Kasper Daniel Hansen < >> kasperdanielhansen@gmail.com> wrote: >> >>> New version same place. This might work fully; please test on both >>> systems. >>> >>> Kasper >>> >>> >>> On Mon, Feb 24, 2014 at 1:48 PM, Kasper Daniel Hansen < >>> kasperdanielhansen@gmail.com> wrote: >>> >>>> Thanks, this is very encouraging. I believe I am able to fix this, by >>>> applying the same strategy across the entire graphviz codebase. Unless of >>>> course something else turns up. >>>> >>>> I will get to this within a week. >>>> >>>> Kasper >>>> >>>> >>>> On Mon, Feb 24, 2014 at 11:58 AM, Enrico Ferrero < >>>> enricoferrero86@gmail.com> wrote: >>>> >>>>> 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 >>>>> >>>> >>>> >>> >> >> >> -- >> 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]]