Hi, I am currently trying to install the bioconductor package 'flowStats' which depends upon the bioconductor package 'Rgraphviz'. As I understand from the Rgraphviz github there may be some issues with getting it installed on 12.04 which should be fixed by using the bundled Graphviz. However I keep on getting the same issues even when using install_github from the devtools package, stating gvc.h: No such file or directory. Which is very weird, as gvc.h can be found (find / -iname gvc.h) in the usr/local/include/graphviz directory. On the other hand, when using the local graphviz installation by R CMD INSTALL --configure-args='--with-graphviz=/usr/local' Rgraphviz_*.tar.gz I get the following output, that I cannot seem to understand: configure: Using external Graphviz. configure: Using Graphviz dir '/usr/local' configure: Found Graphviz version '2.38.0'. configure: Graphviz major version is '2' and minor version is '38'. checking for stdbool.h that conforms to C99... no checking for _Bool... no checking for whether compiler has bool... no configure: Using the following compilation and linking flags for Rgraphviz configure: PKG_CFLAGS=-I/usr/local/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=38 configure: PKG_LIBS=-L/usr/local/lib/graphviz -L/usr/local/lib -lgvc configure: GVIZ_DEFS= configure: Compiling using Graphviz version: '2.38.0'. configure: Using bundled Graphviz: 'FALSE'. configure: creating ./config.status config.status: creating R/graphviz_build_version.R config.status: creating src/Makevars ** libs gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/local/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=38 -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c LL_funcs.c -o LL_funcs.o In file included from LL_funcs.c:1:0: common.h:22:1: error: unknown type name Agdict_t (...) LL_funcs.c:531:13: error: too few arguments to function agedge /usr/local/include/graphviz/cgraph.h:286:18: note: declared here make: *** [LL_funcs.o] Error 1 ERROR: compilation failed for package Rgraphviz * removing ??/home/fpkerckh/R/x86_64-pc-linux-gnu- library/3.1/Rgraphviz?? Does anybody have some pointers here? I have been trying a lot of things, including compiling from source and using github package versions and so on so I would be very happy if somebody can help me out. -- output of sessionInfo(): R version 3.1.0 (2014-04-10) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] devtools_1.5 BiocInstaller_1.14.2 loaded via a namespace (and not attached): [1] digest_0.6.4 evaluate_0.5.3 httr_0.3 memoise_0.2.1 parallel_3.1.0 [6] RCurl_1.95-4.1 stringr_0.6.2 tools_3.1.0 whisker_0.3-2 -- Sent via the guest posting facility at bioconductor.org.

You are trying two things 1) Install very latest Rgraphviz from github 2) Install Rgraphviz using an external Graphviz, which is what you show the output of. 2) is likely to fail given how new a Graphviz you're using. I would like to see full output of 1). Best, Kasper On Mon, Apr 28, 2014 at 2:09 PM, Frederiek - Maarten Kerckhof [guest] < guest@bioconductor.org> wrote: > > Hi, > > I am currently trying to install the bioconductor package 'flowStats' > which depends upon the bioconductor package 'Rgraphviz'. As I understand > from the Rgraphviz github there may be some issues with getting it > installed on 12.04 which should be fixed by using the bundled Graphviz. > However I keep on getting the same issues even when using install_github > from the devtools package, stating gvc.h: No such file or directory. Which > is very weird, as gvc.h can be found (find / -iname gvc.h) in the > usr/local/include/graphviz directory. On the other hand, when using the > local graphviz installation by R CMD INSTALL > --configure-args='--with-graphviz=/usr/local' Rgraphviz_*.tar.gz I get the > following output, that I cannot seem to understand: > > configure: Using external Graphviz. > configure: Using Graphviz dir '/usr/local' > configure: Found Graphviz version '2.38.0'. > configure: Graphviz major version is '2' and minor version is '38'. > checking for stdbool.h that conforms to C99... no > checking for _Bool... no > checking for whether compiler has bool... no > configure: Using the following compilation and linking flags for Rgraphviz > configure: PKG_CFLAGS=-I/usr/local/include/graphviz -DGRAPHVIZ_MAJOR=2 > -DGRAPHVIZ_MINOR=38 > configure: PKG_LIBS=-L/usr/local/lib/graphviz -L/usr/local/lib -lgvc > configure: GVIZ_DEFS= > configure: Compiling using Graphviz version: '2.38.0'. > configure: Using bundled Graphviz: 'FALSE'. > configure: creating ./config.status > config.status: creating R/graphviz_build_version.R > config.status: creating src/Makevars > ** libs > gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG > -I/usr/local/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=38 -fpic > -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat > -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c > LL_funcs.c -o LL_funcs.o > In file included from LL_funcs.c:1:0: > common.h:22:1: error: unknown type name Agdict_t > (...) > LL_funcs.c:531:13: error: too few arguments to function agedge > /usr/local/include/graphviz/cgraph.h:286:18: note: declared here > make: *** [LL_funcs.o] Error 1 > ERROR: compilation failed for package Rgraphviz > * removing â/home/fpkerckh/R/x86_64-pc-linux-gnu- library/3.1/Rgraphvizâ > > Does anybody have some pointers here? I have been trying a lot of things, > including compiling from source and using github package versions and so on > so I would be very happy if somebody can help me out. > > > -- output of sessionInfo(): > > R version 3.1.0 (2014-04-10) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] devtools_1.5 BiocInstaller_1.14.2 > > loaded via a namespace (and not attached): > [1] digest_0.6.4 evaluate_0.5.3 httr_0.3 memoise_0.2.1 > parallel_3.1.0 > [6] RCurl_1.95-4.1 stringr_0.6.2 tools_3.1.0 whisker_0.3-2 > > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > 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]]

Dear Kasper, Also on our system the installation with install_github now works. We are glad this issue is resolved now. Don't worry about forgetting to push to github... that can happen to anybody. Kind regards, Ir. Frederiek ? Maarten Kerckhof Laboratory of Microbial Ecology and Technology (LabMET) Faculty of Bioscience Engineering - Ghent University Coupure Links 653, B-9000 Ghent, Belgium Phone +32 (0)9 264 59 80 - Fax ??+32 (0)9 264 62 48 Frederiekmaarten.kerckhof at ugent.be - http://www.LabMET.UGent.be Email disclaimer -----Original Message----- From: Kasper Hansen [mailto:khanse10@jhu.edu] Sent: dinsdag 29 april 2014 17:13 To: Frederiek - Maarten Kerckhof Cc: Kasper Daniel Hansen; Frederiek - Maarten Kerckhof [guest]; bioconductor at r-project.org; Benjamin Buysschaert Subject: Re: [BioC] RGraphiz installation keeps on failing ubuntu 12.04 LTS server This was embarrassing. I never pushed my commits to github. I have done so now, and have verified that the patch has been incorporated by using install_github as below. For me it works, with my ubunutu-like compiler settings, but I would love to get confirmation. Please try it and report back. Best, Kasper On Apr 29, 2014, at 3:06 AM, Frederiek - Maarten Kerckhof <frederiekmaarten.kerckhof at="" ugent.be=""> wrote: > install_github("kasperdanielhansen/Rgraphviz")