Can't install Rgraphviz
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enricoferrero ▴ 660
@enricoferrero-6037
Last seen 2.4 years ago
Switzerland
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]]
Rgraphviz Rgraphviz • 1.7k views
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@kasper-daniel-hansen-2979
Last seen 10 months ago
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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 > [[alternative HTML version deleted]]
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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 [[alternative HTML version deleted]]
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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 [[alternative HTML version deleted]]
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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 > [[alternative HTML version deleted]]
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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 [[alternative HTML version deleted]]
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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 > [[alternative HTML version deleted]]
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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]]
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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 > [[alternative HTML version deleted]]
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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 >> > > [[alternative HTML version deleted]]
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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 [[alternative HTML version deleted]]
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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 > [[alternative HTML version deleted]]
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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]]
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