Rgraphviz compilation error
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When updating to Bioconductor 2.14 I get the following error from Rgraphviz. In file included from LL_funcs.c:1:0: common.h:16:17: fatal error: gvc.h: No such file or directory compilation terminated. make: *** [LL_funcs.o] Error 1 ERROR: compilation failed for package ???Rgraphviz??? The server runs Ubuntu 12.04 (LTS) and the necessary packages are available: ii graphviz 2.26.3-10ubuntu1.1 rich set of graph drawing tools ii graphviz-dev 2.26.3-10ubuntu1.1 transitional package for graphviz-dev rename ii libgraphviz-dev 2.26.3-10ubuntu1.1 graphviz libs and headers against which to build applications All the other packages were successfully updated. Thanks, Venkat -- output of sessionInfo(): > 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] BiocInstaller_1.14.1 loaded via a namespace (and not attached): [1] tools_3.1.0 -- Sent via the guest posting facility at bioconductor.org.
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@vladimir-zhurov-4990
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Venkat, What you described is an exactly same error that I got today during upgrade. My system is also Ubuntu 12.04 (LTS). Also in this particular mode of installation system graphviz version is irrelevant as by default Rgraphviz is bundled with the slimmed copy of graphviz 2.28. And default installation breaks with the gvc.h error. Installation using system graphviz of 2.26 or the most recent version (2.38) also did not work though with different errors. What worked for me in the end was to upgrade system graphviz from source to exactly 2.28, using just bug patch from Rgraphviz package (as I did not want to break system graphviz by slimming it). Then I was able to install Rgraphviz using system graphviz. The whole process is below. In shell: # download and unpack graphviz v.2.28 sources wget http://www.graphviz.org/pub/graphviz/stable/SOURCES/graphviz-2.28.0.ta r.gz tar xzf graphviz-2.28.0.tar.gz # download and unpack Rgraphviz source package wget http://www.bioconductor.org/packages/release/bioc/src/contrib/Rgraphvi z_2.8.0.tar.gz tar xzf Rgraphviz_2.8.0.tar.gz # patch, configure, build and install graphviz cd ./graphviz-2.28.0/ patch -p1 < ../Rgraphviz/inst/prepare/patches_2.28.0/graphviz-2.28.0-bugs.patch ./configure make sudo make install In R: source("http://bioconductor.org/biocLite.R") biocLite("Rgraphviz", configure.args="--with-graphviz") # uses system graphviz instead of bundled Hope this helps. Regards. Vladimir. On Tue, Apr 15, 2014 at 1:12 PM, Venkat Seshan [guest] < guest@bioconductor.org> wrote: > > When updating to Bioconductor 2.14 I get the following error from > Rgraphviz. > > In file included from LL_funcs.c:1:0: > common.h:16:17: fatal error: gvc.h: No such file or directory > compilation terminated. > make: *** [LL_funcs.o] Error 1 > ERROR: compilation failed for package ‘Rgraphviz’ > > The server runs Ubuntu 12.04 (LTS) and the necessary packages are > available: > > ii graphviz 2.26.3-10ubuntu1.1 > rich set of graph drawing tools > ii graphviz-dev 2.26.3-10ubuntu1.1 > transitional package for graphviz-dev rename > ii libgraphviz-dev 2.26.3-10ubuntu1.1 > graphviz libs and headers against which to build applications > > > All the other packages were successfully updated. > > Thanks, > Venkat > > > -- output of sessionInfo(): > > > 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] BiocInstaller_1.14.1 > > loaded via a namespace (and not attached): > [1] tools_3.1.0 > > > -- > 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 > -- Dr. Vladimir Zhurov Research Associate Department of Biology, BGS3051 and WSC339 University of Western Ontario Tel.: 519-661-2111 ext. 86794 and 86467 Fax: 519-661-3935 Skype: vzhurov.uwo http://www.spidermite.org [[alternative HTML version deleted]]
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What Vladimir suggests should not be necessary, and I am interesting in looking a bit at this. The error message Venkat posts is unfortunately completely uninformative. What happens during Rgraphviz installation is 1) The C(++) code of graphviz gets compiled 2) Rgraphviz gets compiled and linked to (1) The error message Venkat posts just tells us that (2) fails, which is usually because (1) fails, but we cannot see this. I really don't understand why Vladimir's suggestion of hand-compiling graphviz and then using --with-graphviz works, because that ought to be essentially what happens in a standard installation. I would like the following (1) The full output of the Rgraphviz installation (yes, I know it is long). (2) What is the specific version of the C compiler used. (3) What is the output of R CMD config CC and `R CMD config CC` --version Best, Kasper On Wed, Apr 16, 2014 at 5:39 AM, Vladimir Zhurov <vzhurov2@uwo.ca> wrote: > Venkat, > > What you described is an exactly same error that I got today during > upgrade. My system is also Ubuntu 12.04 (LTS). Also in this particular mode > of installation system graphviz version is irrelevant as by default > Rgraphviz is bundled with the slimmed copy of graphviz 2.28. And default > installation breaks with the gvc.h error. Installation using system > graphviz of 2.26 or the most recent version (2.38) also did not work though > with different errors. > > What worked for me in the end was to upgrade system graphviz from source to > exactly 2.28, using just bug patch from Rgraphviz package (as I did not > want to break system graphviz by slimming it). Then I was able to install > Rgraphviz using system graphviz. > > The whole process is below. > > In shell: > > # download and unpack graphviz v.2.28 sources > > wget > http://www.graphviz.org/pub/graphviz/stable/SOURCES/graphviz-2.28.0. tar.gz > tar xzf graphviz-2.28.0.tar.gz > > # download and unpack Rgraphviz source package > > wget > > http://www.bioconductor.org/packages/release/bioc/src/contrib/Rgraph viz_2.8.0.tar.gz > tar xzf Rgraphviz_2.8.0.tar.gz > > # patch, configure, build and install graphviz > > cd ./graphviz-2.28.0/ > patch -p1 < > ../Rgraphviz/inst/prepare/patches_2.28.0/graphviz-2.28.0-bugs.patch > ./configure > make > sudo make install > > > In R: > > source("http://bioconductor.org/biocLite.R") > biocLite("Rgraphviz", configure.args="--with-graphviz") # uses system > graphviz instead of bundled > > > Hope this helps. > > Regards. > > Vladimir. > > > > > > On Tue, Apr 15, 2014 at 1:12 PM, Venkat Seshan [guest] < > guest@bioconductor.org> wrote: > > > > > When updating to Bioconductor 2.14 I get the following error from > > Rgraphviz. > > > > In file included from LL_funcs.c:1:0: > > common.h:16:17: fatal error: gvc.h: No such file or directory > > compilation terminated. > > make: *** [LL_funcs.o] Error 1 > > ERROR: compilation failed for package ‘Rgraphviz’ > > > > The server runs Ubuntu 12.04 (LTS) and the necessary packages are > > available: > > > > ii graphviz 2.26.3-10ubuntu1.1 > > rich set of graph drawing tools > > ii graphviz-dev 2.26.3-10ubuntu1.1 > > transitional package for graphviz-dev rename > > ii libgraphviz-dev 2.26.3-10ubuntu1.1 > > graphviz libs and headers against which to build applications > > > > > > All the other packages were successfully updated. > > > > Thanks, > > Venkat > > > > > > -- output of sessionInfo(): > > > > > 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] BiocInstaller_1.14.1 > > > > loaded via a namespace (and not attached): > > [1] tools_3.1.0 > > > > > > -- > > 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 > > > > > > -- > Dr. Vladimir Zhurov > Research Associate > Department of Biology, BGS3051 and WSC339 > University of Western Ontario > Tel.: 519-661-2111 ext. 86794 and 86467 > Fax: 519-661-3935 > Skype: vzhurov.uwo > > http://www.spidermite.org > > [[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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Thanks Kasper & Vladimir. I got the same error with and without system graphviz packages. So the presence of system graphviz packages doesn't make a difference. Kasper - Attached is the log from the installation attempt (output of script). The other information you needed are below. Thanks, Venkat ebadmin at ebmaster:~$ gcc --version gcc (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3 Copyright (C) 2011 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. ebadmin at ebmaster:~$ R CMD config CC gcc -std=gnu99 ebadmin at ebmaster:~$ `R CMD config CC` --version gcc (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3 Copyright (C) 2011 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. On Wed, Apr 16, 2014 at 3:44 AM, Kasper Daniel Hansen <khansen at="" jhsph.edu="">wrote: > What Vladimir suggests should not be necessary, and I am interesting in > looking a bit at this. > > The error message Venkat posts is unfortunately completely uninformative. > What happens during Rgraphviz installation is > 1) The C(++) code of graphviz gets compiled > 2) Rgraphviz gets compiled and linked to (1) > > The error message Venkat posts just tells us that (2) fails, which is > usually because (1) fails, but we cannot see this. I really don't > understand why Vladimir's suggestion of hand-compiling graphviz and then > using --with-graphviz works, because that ought to be essentially what > happens in a standard installation. > > I would like the following > > (1) The full output of the Rgraphviz installation (yes, I know it is long). > (2) What is the specific version of the C compiler used. > (3) What is the output of > R CMD config CC > and > `R CMD config CC` --version > > Best, > Kasper > > > > On Wed, Apr 16, 2014 at 5:39 AM, Vladimir Zhurov <vzhurov2 at="" uwo.ca=""> wrote: > >> Venkat, >> >> What you described is an exactly same error that I got today during >> upgrade. My system is also Ubuntu 12.04 (LTS). Also in this particular >> mode >> of installation system graphviz version is irrelevant as by default >> Rgraphviz is bundled with the slimmed copy of graphviz 2.28. And default >> installation breaks with the gvc.h error. Installation using system >> graphviz of 2.26 or the most recent version (2.38) also did not work >> though >> with different errors. >> >> What worked for me in the end was to upgrade system graphviz from source >> to >> exactly 2.28, using just bug patch from Rgraphviz package (as I did not >> want to break system graphviz by slimming it). Then I was able to install >> Rgraphviz using system graphviz. >> >> The whole process is below. >> >> In shell: >> >> # download and unpack graphviz v.2.28 sources >> >> wget >> http://www.graphviz.org/pub/graphviz/stable/SOURCES/graphviz-2.28.0 .tar.gz >> tar xzf graphviz-2.28.0.tar.gz >> >> # download and unpack Rgraphviz source package >> >> wget >> >> http://www.bioconductor.org/packages/release/bioc/src/contrib/Rgrap hviz_2.8.0.tar.gz >> tar xzf Rgraphviz_2.8.0.tar.gz >> >> # patch, configure, build and install graphviz >> >> cd ./graphviz-2.28.0/ >> patch -p1 < >> ../Rgraphviz/inst/prepare/patches_2.28.0/graphviz-2.28.0-bugs.patch >> ./configure >> make >> sudo make install >> >> >> In R: >> >> source("http://bioconductor.org/biocLite.R") >> biocLite("Rgraphviz", configure.args="--with-graphviz") # uses system >> graphviz instead of bundled >> >> >> Hope this helps. >> >> Regards. >> >> Vladimir. >> >> >> >> >> >> On Tue, Apr 15, 2014 at 1:12 PM, Venkat Seshan [guest] < >> guest at bioconductor.org> wrote: >> >> > >> > When updating to Bioconductor 2.14 I get the following error from >> > Rgraphviz. >> > >> > In file included from LL_funcs.c:1:0: >> > common.h:16:17: fatal error: gvc.h: No such file or directory >> > compilation terminated. >> > make: *** [LL_funcs.o] Error 1 >> > ERROR: compilation failed for package ???Rgraphviz??? >> > >> > The server runs Ubuntu 12.04 (LTS) and the necessary packages are >> > available: >> > >> > ii graphviz 2.26.3-10ubuntu1.1 >> > rich set of graph drawing tools >> > ii graphviz-dev 2.26.3-10ubuntu1.1 >> > transitional package for graphviz-dev rename >> > ii libgraphviz-dev 2.26.3-10ubuntu1.1 >> > graphviz libs and headers against which to build applications >> > >> > >> > All the other packages were successfully updated. >> > >> > Thanks, >> > Venkat >> > >> > >> > -- output of sessionInfo(): >> > >> > > 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] BiocInstaller_1.14.1 >> > >> > loaded via a namespace (and not attached): >> > [1] tools_3.1.0 >> > >> > >> > -- >> > Sent via the guest posting facility at bioconductor.org. >> > >> > _______________________________________________ >> > Bioconductor mailing list >> > Bioconductor at r-project.org >> > https://stat.ethz.ch/mailman/listinfo/bioconductor >> > Search the archives: >> > http://news.gmane.org/gmane.science.biology.informatics.conductor >> > >> >> >> >> -- >> Dr. Vladimir Zhurov >> Research Associate >> Department of Biology, BGS3051 and WSC339 >> University of Western Ontario >> Tel.: 519-661-2111 ext. 86794 and 86467 >> Fax: 519-661-3935 >> Skype: vzhurov.uwo >> >> http://www.spidermite.org >> >> [[alternative HTML version deleted]] >> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > >
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Vladimir, Venkat, Chong I believe I have fixed the issue in Rgraphviz 2.9.1, which I just committed. Source tar balls should be available Tuesday in the development version of Bioconductor. If some of you could confirm that the issue is fixed, I will back port it to the recent release. Thanks for the report. It was a real bug, but manifested itself on Ubuntu due to compiler settings on Ubuntu-12.04 which are more aggressive than normal at flagging (potential) security errors. Best, Kasper On Apr 16, 2014, at 9:23 AM, Venkat Seshan <veseshan at="" gmail.com=""> wrote: > Thanks Kasper & Vladimir. I got the same error with and without system graphviz packages. So the presence of system graphviz packages doesn't make a difference. > > Kasper - Attached is the log from the installation attempt (output of script). The other information you needed are below. > > Thanks, > Venkat > > ebadmin at ebmaster:~$ gcc --version > gcc (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3 > Copyright (C) 2011 Free Software Foundation, Inc. > This is free software; see the source for copying conditions. There is NO > warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. > > ebadmin at ebmaster:~$ R CMD config CC > gcc -std=gnu99 > ebadmin at ebmaster:~$ `R CMD config CC` --version > gcc (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3 > Copyright (C) 2011 Free Software Foundation, Inc. > This is free software; see the source for copying conditions. There is NO > warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. > > > > > On Wed, Apr 16, 2014 at 3:44 AM, Kasper Daniel Hansen <khansen at="" jhsph.edu=""> wrote: > What Vladimir suggests should not be necessary, and I am interesting in looking a bit at this. > > The error message Venkat posts is unfortunately completely uninformative. What happens during Rgraphviz installation is > 1) The C(++) code of graphviz gets compiled > 2) Rgraphviz gets compiled and linked to (1) > > The error message Venkat posts just tells us that (2) fails, which is usually because (1) fails, but we cannot see this. I really don't understand why Vladimir's suggestion of hand-compiling graphviz and then using --with-graphviz works, because that ought to be essentially what happens in a standard installation. > > I would like the following > > (1) The full output of the Rgraphviz installation (yes, I know it is long). > (2) What is the specific version of the C compiler used. > (3) What is the output of > R CMD config CC > and > `R CMD config CC` --version > > Best, > Kasper > > > > On Wed, Apr 16, 2014 at 5:39 AM, Vladimir Zhurov <vzhurov2 at="" uwo.ca=""> wrote: > Venkat, > > What you described is an exactly same error that I got today during > upgrade. My system is also Ubuntu 12.04 (LTS). Also in this particular mode > of installation system graphviz version is irrelevant as by default > Rgraphviz is bundled with the slimmed copy of graphviz 2.28. And default > installation breaks with the gvc.h error. Installation using system > graphviz of 2.26 or the most recent version (2.38) also did not work though > with different errors. > > What worked for me in the end was to upgrade system graphviz from source to > exactly 2.28, using just bug patch from Rgraphviz package (as I did not > want to break system graphviz by slimming it). Then I was able to install > Rgraphviz using system graphviz. > > The whole process is below. > > In shell: > > # download and unpack graphviz v.2.28 sources > > wget > http://www.graphviz.org/pub/graphviz/stable/SOURCES/graphviz-2.28.0. tar.gz > tar xzf graphviz-2.28.0.tar.gz > > # download and unpack Rgraphviz source package > > wget > http://www.bioconductor.org/packages/release/bioc/src/contrib/Rgraph viz_2.8.0.tar.gz > tar xzf Rgraphviz_2.8.0.tar.gz > > # patch, configure, build and install graphviz > > cd ./graphviz-2.28.0/ > patch -p1 < > ../Rgraphviz/inst/prepare/patches_2.28.0/graphviz-2.28.0-bugs.patch > ./configure > make > sudo make install > > > In R: > > source("http://bioconductor.org/biocLite.R") > biocLite("Rgraphviz", configure.args="--with-graphviz") # uses system > graphviz instead of bundled > > > Hope this helps. > > Regards. > > Vladimir. > > > > > > On Tue, Apr 15, 2014 at 1:12 PM, Venkat Seshan [guest] < > guest at bioconductor.org> wrote: > > > > > When updating to Bioconductor 2.14 I get the following error from > > Rgraphviz. > > > > In file included from LL_funcs.c:1:0: > > common.h:16:17: fatal error: gvc.h: No such file or directory > > compilation terminated. > > make: *** [LL_funcs.o] Error 1 > > ERROR: compilation failed for package ???Rgraphviz??? > > > > The server runs Ubuntu 12.04 (LTS) and the necessary packages are > > available: > > > > ii graphviz 2.26.3-10ubuntu1.1 > > rich set of graph drawing tools > > ii graphviz-dev 2.26.3-10ubuntu1.1 > > transitional package for graphviz-dev rename > > ii libgraphviz-dev 2.26.3-10ubuntu1.1 > > graphviz libs and headers against which to build applications > > > > > > All the other packages were successfully updated. > > > > Thanks, > > Venkat > > > > > > -- output of sessionInfo(): > > > > > 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] BiocInstaller_1.14.1 > > > > loaded via a namespace (and not attached): > > [1] tools_3.1.0 > > > > > > -- > > Sent via the guest posting facility at bioconductor.org. > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > -- > Dr. Vladimir Zhurov > Research Associate > Department of Biology, BGS3051 and WSC339 > University of Western Ontario > Tel.: 519-661-2111 ext. 86794 and 86467 > Fax: 519-661-3935 > Skype: vzhurov.uwo > > http://www.spidermite.org > > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > > <rgraphviz.log>
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Kasper, Checked out revision 89654 - worked on my workstation. Regards. Vladimir. On Sun, Apr 27, 2014 at 10:28 PM, Kasper Hansen <khanse10@jhu.edu> wrote: > Vladimir, Venkat, Chong > > I believe I have fixed the issue in Rgraphviz 2.9.1, which I just > committed. Source tar balls should be available Tuesday in the development > version of Bioconductor. If some of you could confirm that the issue is > fixed, I will back port it to the recent release. > > Thanks for the report. It was a real bug, but manifested itself on Ubuntu > due to compiler settings on Ubuntu-12.04 which are more aggressive than > normal at flagging (potential) security errors. > > Best, > Kasper > > On Apr 16, 2014, at 9:23 AM, Venkat Seshan <veseshan@gmail.com> wrote: > > > Thanks Kasper & Vladimir. I got the same error with and without system > graphviz packages. So the presence of system graphviz packages doesn't make > a difference. > > > > Kasper - Attached is the log from the installation attempt (output of > script). The other information you needed are below. > > > > Thanks, > > Venkat > > > > ebadmin@ebmaster:~$ gcc --version > > gcc (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3 > > Copyright (C) 2011 Free Software Foundation, Inc. > > This is free software; see the source for copying conditions. There is > NO > > warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR > PURPOSE. > > > > ebadmin@ebmaster:~$ R CMD config CC > > gcc -std=gnu99 > > ebadmin@ebmaster:~$ `R CMD config CC` --version > > gcc (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3 > > Copyright (C) 2011 Free Software Foundation, Inc. > > This is free software; see the source for copying conditions. There is > NO > > warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR > PURPOSE. > > > > > > > > > > On Wed, Apr 16, 2014 at 3:44 AM, Kasper Daniel Hansen <khansen@jhsph.edu> > wrote: > > What Vladimir suggests should not be necessary, and I am interesting in > looking a bit at this. > > > > The error message Venkat posts is unfortunately completely > uninformative. What happens during Rgraphviz installation is > > 1) The C(++) code of graphviz gets compiled > > 2) Rgraphviz gets compiled and linked to (1) > > > > The error message Venkat posts just tells us that (2) fails, which is > usually because (1) fails, but we cannot see this. I really don't > understand why Vladimir's suggestion of hand-compiling graphviz and then > using --with-graphviz works, because that ought to be essentially what > happens in a standard installation. > > > > I would like the following > > > > (1) The full output of the Rgraphviz installation (yes, I know it is > long). > > (2) What is the specific version of the C compiler used. > > (3) What is the output of > > R CMD config CC > > and > > `R CMD config CC` --version > > > > Best, > > Kasper > > > > > > > > On Wed, Apr 16, 2014 at 5:39 AM, Vladimir Zhurov <vzhurov2@uwo.ca> > wrote: > > Venkat, > > > > What you described is an exactly same error that I got today during > > upgrade. My system is also Ubuntu 12.04 (LTS). Also in this particular > mode > > of installation system graphviz version is irrelevant as by default > > Rgraphviz is bundled with the slimmed copy of graphviz 2.28. And default > > installation breaks with the gvc.h error. Installation using system > > graphviz of 2.26 or the most recent version (2.38) also did not work > though > > with different errors. > > > > What worked for me in the end was to upgrade system graphviz from source > to > > exactly 2.28, using just bug patch from Rgraphviz package (as I did not > > want to break system graphviz by slimming it). Then I was able to install > > Rgraphviz using system graphviz. > > > > The whole process is below. > > > > In shell: > > > > # download and unpack graphviz v.2.28 sources > > > > wget > > > http://www.graphviz.org/pub/graphviz/stable/SOURCES/graphviz-2.28.0. tar.gz > > tar xzf graphviz-2.28.0.tar.gz > > > > # download and unpack Rgraphviz source package > > > > wget > > > http://www.bioconductor.org/packages/release/bioc/src/contrib/Rgraph viz_2.8.0.tar.gz > > tar xzf Rgraphviz_2.8.0.tar.gz > > > > # patch, configure, build and install graphviz > > > > cd ./graphviz-2.28.0/ > > patch -p1 < > > ../Rgraphviz/inst/prepare/patches_2.28.0/graphviz-2.28.0-bugs.patch > > ./configure > > make > > sudo make install > > > > > > In R: > > > > source("http://bioconductor.org/biocLite.R") > > biocLite("Rgraphviz", configure.args="--with-graphviz") # uses system > > graphviz instead of bundled > > > > > > Hope this helps. > > > > Regards. > > > > Vladimir. > > > > > > > > > > > > On Tue, Apr 15, 2014 at 1:12 PM, Venkat Seshan [guest] < > > guest@bioconductor.org> wrote: > > > > > > > > When updating to Bioconductor 2.14 I get the following error from > > > Rgraphviz. > > > > > > In file included from LL_funcs.c:1:0: > > > common.h:16:17: fatal error: gvc.h: No such file or directory > > > compilation terminated. > > > make: *** [LL_funcs.o] Error 1 > > > ERROR: compilation failed for package ‘Rgraphviz’ > > > > > > The server runs Ubuntu 12.04 (LTS) and the necessary packages are > > > available: > > > > > > ii graphviz 2.26.3-10ubuntu1.1 > > > rich set of graph drawing tools > > > ii graphviz-dev 2.26.3-10ubuntu1.1 > > > transitional package for graphviz-dev rename > > > ii libgraphviz-dev 2.26.3-10ubuntu1.1 > > > graphviz libs and headers against which to build applications > > > > > > > > > All the other packages were successfully updated. > > > > > > Thanks, > > > Venkat > > > > > > > > > -- output of sessionInfo(): > > > > > > > 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] BiocInstaller_1.14.1 > > > > > > loaded via a namespace (and not attached): > > > [1] tools_3.1.0 > > > > > > > > > -- > > > 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 > > > > > > > > > > > -- > > Dr. Vladimir Zhurov > > Research Associate > > Department of Biology, BGS3051 and WSC339 > > University of Western Ontario > > Tel.: 519-661-2111 ext. 86794 and 86467 > > Fax: 519-661-3935 > > Skype: vzhurov.uwo > > > > http://www.spidermite.org > > > > [[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 > > > > > > <rgraphviz.log> > > -- Dr. Vladimir Zhurov Research Associate Department of Biology, BGS3051 and WSC339 University of Western Ontario Tel.: 519-661-2111 ext. 86794 and 86467 Fax: 519-661-3935 Skype: vzhurov.uwo http://www.spidermite.org [[alternative HTML version deleted]]
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http://master.bioconductor.org/packages/devel/bioc/html/Rgraphviz.html still shows 2.9.0 Venkat On Tue, Apr 29, 2014 at 4:31 PM, Vladimir Zhurov <vzhurov2@uwo.ca> wrote: > Kasper, > > Checked out revision 89654 - worked on my workstation. > > Regards. > > Vladimir. > > > On Sun, Apr 27, 2014 at 10:28 PM, Kasper Hansen <khanse10@jhu.edu> wrote: > >> Vladimir, Venkat, Chong >> >> I believe I have fixed the issue in Rgraphviz 2.9.1, which I just >> committed. Source tar balls should be available Tuesday in the development >> version of Bioconductor. If some of you could confirm that the issue is >> fixed, I will back port it to the recent release. >> >> Thanks for the report. It was a real bug, but manifested itself on >> Ubuntu due to compiler settings on Ubuntu-12.04 which are more aggressive >> than normal at flagging (potential) security errors. >> >> Best, >> Kasper >> >> On Apr 16, 2014, at 9:23 AM, Venkat Seshan <veseshan@gmail.com> wrote: >> >> > Thanks Kasper & Vladimir. I got the same error with and without system >> graphviz packages. So the presence of system graphviz packages doesn't make >> a difference. >> > >> > Kasper - Attached is the log from the installation attempt (output of >> script). The other information you needed are below. >> > >> > Thanks, >> > Venkat >> > >> > ebadmin@ebmaster:~$ gcc --version >> > gcc (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3 >> > Copyright (C) 2011 Free Software Foundation, Inc. >> > This is free software; see the source for copying conditions. There is >> NO >> > warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR >> PURPOSE. >> > >> > ebadmin@ebmaster:~$ R CMD config CC >> > gcc -std=gnu99 >> > ebadmin@ebmaster:~$ `R CMD config CC` --version >> > gcc (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3 >> > Copyright (C) 2011 Free Software Foundation, Inc. >> > This is free software; see the source for copying conditions. There is >> NO >> > warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR >> PURPOSE. >> > >> > >> > >> > >> > On Wed, Apr 16, 2014 at 3:44 AM, Kasper Daniel Hansen < >> khansen@jhsph.edu> wrote: >> > What Vladimir suggests should not be necessary, and I am interesting in >> looking a bit at this. >> > >> > The error message Venkat posts is unfortunately completely >> uninformative. What happens during Rgraphviz installation is >> > 1) The C(++) code of graphviz gets compiled >> > 2) Rgraphviz gets compiled and linked to (1) >> > >> > The error message Venkat posts just tells us that (2) fails, which is >> usually because (1) fails, but we cannot see this. I really don't >> understand why Vladimir's suggestion of hand-compiling graphviz and then >> using --with-graphviz works, because that ought to be essentially what >> happens in a standard installation. >> > >> > I would like the following >> > >> > (1) The full output of the Rgraphviz installation (yes, I know it is >> long). >> > (2) What is the specific version of the C compiler used. >> > (3) What is the output of >> > R CMD config CC >> > and >> > `R CMD config CC` --version >> > >> > Best, >> > Kasper >> > >> > >> > >> > On Wed, Apr 16, 2014 at 5:39 AM, Vladimir Zhurov <vzhurov2@uwo.ca> >> wrote: >> > Venkat, >> > >> > What you described is an exactly same error that I got today during >> > upgrade. My system is also Ubuntu 12.04 (LTS). Also in this particular >> mode >> > of installation system graphviz version is irrelevant as by default >> > Rgraphviz is bundled with the slimmed copy of graphviz 2.28. And default >> > installation breaks with the gvc.h error. Installation using system >> > graphviz of 2.26 or the most recent version (2.38) also did not work >> though >> > with different errors. >> > >> > What worked for me in the end was to upgrade system graphviz from >> source to >> > exactly 2.28, using just bug patch from Rgraphviz package (as I did not >> > want to break system graphviz by slimming it). Then I was able to >> install >> > Rgraphviz using system graphviz. >> > >> > The whole process is below. >> > >> > In shell: >> > >> > # download and unpack graphviz v.2.28 sources >> > >> > wget >> > >> http://www.graphviz.org/pub/graphviz/stable/SOURCES/graphviz-2.28.0 .tar.gz >> > tar xzf graphviz-2.28.0.tar.gz >> > >> > # download and unpack Rgraphviz source package >> > >> > wget >> > >> http://www.bioconductor.org/packages/release/bioc/src/contrib/Rgrap hviz_2.8.0.tar.gz >> > tar xzf Rgraphviz_2.8.0.tar.gz >> > >> > # patch, configure, build and install graphviz >> > >> > cd ./graphviz-2.28.0/ >> > patch -p1 < >> > ../Rgraphviz/inst/prepare/patches_2.28.0/graphviz-2.28.0-bugs.patch >> > ./configure >> > make >> > sudo make install >> > >> > >> > In R: >> > >> > source("http://bioconductor.org/biocLite.R") >> > biocLite("Rgraphviz", configure.args="--with-graphviz") # uses system >> > graphviz instead of bundled >> > >> > >> > Hope this helps. >> > >> > Regards. >> > >> > Vladimir. >> > >> > >> > >> > >> > >> > On Tue, Apr 15, 2014 at 1:12 PM, Venkat Seshan [guest] < >> > guest@bioconductor.org> wrote: >> > >> > > >> > > When updating to Bioconductor 2.14 I get the following error from >> > > Rgraphviz. >> > > >> > > In file included from LL_funcs.c:1:0: >> > > common.h:16:17: fatal error: gvc.h: No such file or directory >> > > compilation terminated. >> > > make: *** [LL_funcs.o] Error 1 >> > > ERROR: compilation failed for package ‘Rgraphviz’ >> > > >> > > The server runs Ubuntu 12.04 (LTS) and the necessary packages are >> > > available: >> > > >> > > ii graphviz 2.26.3-10ubuntu1.1 >> > > rich set of graph drawing tools >> > > ii graphviz-dev 2.26.3-10ubuntu1.1 >> > > transitional package for graphviz-dev rename >> > > ii libgraphviz-dev 2.26.3-10ubuntu1.1 >> > > graphviz libs and headers against which to build applications >> > > >> > > >> > > All the other packages were successfully updated. >> > > >> > > Thanks, >> > > Venkat >> > > >> > > >> > > -- output of sessionInfo(): >> > > >> > > > 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] BiocInstaller_1.14.1 >> > > >> > > loaded via a namespace (and not attached): >> > > [1] tools_3.1.0 >> > > >> > > >> > > -- >> > > 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 >> > > >> > >> > >> > >> > -- >> > Dr. Vladimir Zhurov >> > Research Associate >> > Department of Biology, BGS3051 and WSC339 >> > University of Western Ontario >> > Tel.: 519-661-2111 ext. 86794 and 86467 >> > Fax: 519-661-3935 >> > Skype: vzhurov.uwo >> > >> > http://www.spidermite.org >> > >> > [[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 >> > >> > >> > <rgraphviz.log> >> >> > > > -- > Dr. Vladimir Zhurov > Research Associate > Department of Biology, BGS3051 and WSC339 > University of Western Ontario > Tel.: 519-661-2111 ext. 86794 and 86467 > Fax: 519-661-3935 > Skype: vzhurov.uwo > > http://www.spidermite.org > [[alternative HTML version deleted]]
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There may be a time lag between submission and building. The patch exists in the subversion repos; just checked. Best, Kasper On Wed, Apr 30, 2014 at 11:38 AM, Venkat Seshan <veseshan@gmail.com> wrote: > http://master.bioconductor.org/packages/devel/bioc/html/Rgraphviz.ht mlstill > shows 2.9.0 > > Venkat > > > On Tue, Apr 29, 2014 at 4:31 PM, Vladimir Zhurov <vzhurov2@uwo.ca> wrote: > > > Kasper, > > > > Checked out revision 89654 - worked on my workstation. > > > > Regards. > > > > Vladimir. > > > > > > On Sun, Apr 27, 2014 at 10:28 PM, Kasper Hansen <khanse10@jhu.edu> > wrote: > > > >> Vladimir, Venkat, Chong > >> > >> I believe I have fixed the issue in Rgraphviz 2.9.1, which I just > >> committed. Source tar balls should be available Tuesday in the > development > >> version of Bioconductor. If some of you could confirm that the issue is > >> fixed, I will back port it to the recent release. > >> > >> Thanks for the report. It was a real bug, but manifested itself on > >> Ubuntu due to compiler settings on Ubuntu-12.04 which are more > aggressive > >> than normal at flagging (potential) security errors. > >> > >> Best, > >> Kasper > >> > >> On Apr 16, 2014, at 9:23 AM, Venkat Seshan <veseshan@gmail.com> wrote: > >> > >> > Thanks Kasper & Vladimir. I got the same error with and without system > >> graphviz packages. So the presence of system graphviz packages doesn't > make > >> a difference. > >> > > >> > Kasper - Attached is the log from the installation attempt (output of > >> script). The other information you needed are below. > >> > > >> > Thanks, > >> > Venkat > >> > > >> > ebadmin@ebmaster:~$ gcc --version > >> > gcc (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3 > >> > Copyright (C) 2011 Free Software Foundation, Inc. > >> > This is free software; see the source for copying conditions. There > is > >> NO > >> > warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR > >> PURPOSE. > >> > > >> > ebadmin@ebmaster:~$ R CMD config CC > >> > gcc -std=gnu99 > >> > ebadmin@ebmaster:~$ `R CMD config CC` --version > >> > gcc (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3 > >> > Copyright (C) 2011 Free Software Foundation, Inc. > >> > This is free software; see the source for copying conditions. There > is > >> NO > >> > warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR > >> PURPOSE. > >> > > >> > > >> > > >> > > >> > On Wed, Apr 16, 2014 at 3:44 AM, Kasper Daniel Hansen < > >> khansen@jhsph.edu> wrote: > >> > What Vladimir suggests should not be necessary, and I am interesting > in > >> looking a bit at this. > >> > > >> > The error message Venkat posts is unfortunately completely > >> uninformative. What happens during Rgraphviz installation is > >> > 1) The C(++) code of graphviz gets compiled > >> > 2) Rgraphviz gets compiled and linked to (1) > >> > > >> > The error message Venkat posts just tells us that (2) fails, which is > >> usually because (1) fails, but we cannot see this. I really don't > >> understand why Vladimir's suggestion of hand-compiling graphviz and then > >> using --with-graphviz works, because that ought to be essentially what > >> happens in a standard installation. > >> > > >> > I would like the following > >> > > >> > (1) The full output of the Rgraphviz installation (yes, I know it is > >> long). > >> > (2) What is the specific version of the C compiler used. > >> > (3) What is the output of > >> > R CMD config CC > >> > and > >> > `R CMD config CC` --version > >> > > >> > Best, > >> > Kasper > >> > > >> > > >> > > >> > On Wed, Apr 16, 2014 at 5:39 AM, Vladimir Zhurov <vzhurov2@uwo.ca> > >> wrote: > >> > Venkat, > >> > > >> > What you described is an exactly same error that I got today during > >> > upgrade. My system is also Ubuntu 12.04 (LTS). Also in this particular > >> mode > >> > of installation system graphviz version is irrelevant as by default > >> > Rgraphviz is bundled with the slimmed copy of graphviz 2.28. And > default > >> > installation breaks with the gvc.h error. Installation using system > >> > graphviz of 2.26 or the most recent version (2.38) also did not work > >> though > >> > with different errors. > >> > > >> > What worked for me in the end was to upgrade system graphviz from > >> source to > >> > exactly 2.28, using just bug patch from Rgraphviz package (as I did > not > >> > want to break system graphviz by slimming it). Then I was able to > >> install > >> > Rgraphviz using system graphviz. > >> > > >> > The whole process is below. > >> > > >> > In shell: > >> > > >> > # download and unpack graphviz v.2.28 sources > >> > > >> > wget > >> > > >> > http://www.graphviz.org/pub/graphviz/stable/SOURCES/graphviz-2.28.0. tar.gz > >> > tar xzf graphviz-2.28.0.tar.gz > >> > > >> > # download and unpack Rgraphviz source package > >> > > >> > wget > >> > > >> > http://www.bioconductor.org/packages/release/bioc/src/contrib/Rgraph viz_2.8.0.tar.gz > >> > tar xzf Rgraphviz_2.8.0.tar.gz > >> > > >> > # patch, configure, build and install graphviz > >> > > >> > cd ./graphviz-2.28.0/ > >> > patch -p1 < > >> > ../Rgraphviz/inst/prepare/patches_2.28.0/graphviz-2.28.0-bugs.patch > >> > ./configure > >> > make > >> > sudo make install > >> > > >> > > >> > In R: > >> > > >> > source("http://bioconductor.org/biocLite.R") > >> > biocLite("Rgraphviz", configure.args="--with-graphviz") # uses system > >> > graphviz instead of bundled > >> > > >> > > >> > Hope this helps. > >> > > >> > Regards. > >> > > >> > Vladimir. > >> > > >> > > >> > > >> > > >> > > >> > On Tue, Apr 15, 2014 at 1:12 PM, Venkat Seshan [guest] < > >> > guest@bioconductor.org> wrote: > >> > > >> > > > >> > > When updating to Bioconductor 2.14 I get the following error from > >> > > Rgraphviz. > >> > > > >> > > In file included from LL_funcs.c:1:0: > >> > > common.h:16:17: fatal error: gvc.h: No such file or directory > >> > > compilation terminated. > >> > > make: *** [LL_funcs.o] Error 1 > >> > > ERROR: compilation failed for package ‘Rgraphviz’ > >> > > > >> > > The server runs Ubuntu 12.04 (LTS) and the necessary packages are > >> > > available: > >> > > > >> > > ii graphviz 2.26.3-10ubuntu1.1 > >> > > rich set of graph drawing tools > >> > > ii graphviz-dev 2.26.3-10ubuntu1.1 > >> > > transitional package for graphviz-dev rename > >> > > ii libgraphviz-dev 2.26.3-10ubuntu1.1 > >> > > graphviz libs and headers against which to build applications > >> > > > >> > > > >> > > All the other packages were successfully updated. > >> > > > >> > > Thanks, > >> > > Venkat > >> > > > >> > > > >> > > -- output of sessionInfo(): > >> > > > >> > > > 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] BiocInstaller_1.14.1 > >> > > > >> > > loaded via a namespace (and not attached): > >> > > [1] tools_3.1.0 > >> > > > >> > > > >> > > -- > >> > > 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 > >> > > > >> > > >> > > >> > > >> > -- > >> > Dr. Vladimir Zhurov > >> > Research Associate > >> > Department of Biology, BGS3051 and WSC339 > >> > University of Western Ontario > >> > Tel.: 519-661-2111 ext. 86794 and 86467 > >> > Fax: 519-661-3935 > >> > Skype: vzhurov.uwo > >> > > >> > http://www.spidermite.org > >> > > >> > [[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 > >> > > >> > > >> > <rgraphviz.log> > >> > >> > > > > > > -- > > Dr. Vladimir Zhurov > > Research Associate > > Department of Biology, BGS3051 and WSC339 > > University of Western Ontario > > Tel.: 519-661-2111 ext. 86794 and 86467 > > Fax: 519-661-3935 > > Skype: vzhurov.uwo > > > > http://www.spidermite.org > > > > [[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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----- Original Message ----- > From: "Kasper Daniel Hansen" <khansen at="" jhsph.edu=""> > To: "Venkat Seshan" <veseshan at="" gmail.com=""> > Cc: "Chong Tang" <tangc3 at="" unr.edu="">, "Bioconductor mailing list" <bioconductor at="" r-project.org="">, "Kasper Hansen" > <khanse10 at="" jhu.edu=""> > Sent: Wednesday, April 30, 2014 10:23:52 AM > Subject: Re: [BioC] Rgraphviz compilation error > > There may be a time lag between submission and building. The patch > exists > in the subversion repos; just checked. > 2.9.1 is available via biocLite(); the web page should be updated soon. Dan > Best, > Kasper > > > On Wed, Apr 30, 2014 at 11:38 AM, Venkat Seshan <veseshan at="" gmail.com=""> > wrote: > > > http://master.bioconductor.org/packages/devel/bioc/html/Rgraphviz. htmlstill > > shows 2.9.0 > > > > Venkat > > > > > > On Tue, Apr 29, 2014 at 4:31 PM, Vladimir Zhurov <vzhurov2 at="" uwo.ca=""> > > wrote: > > > > > Kasper, > > > > > > Checked out revision 89654 - worked on my workstation. > > > > > > Regards. > > > > > > Vladimir. > > > > > > > > > On Sun, Apr 27, 2014 at 10:28 PM, Kasper Hansen > > > <khanse10 at="" jhu.edu=""> > > wrote: > > > > > >> Vladimir, Venkat, Chong > > >> > > >> I believe I have fixed the issue in Rgraphviz 2.9.1, which I > > >> just > > >> committed. Source tar balls should be available Tuesday in the > > development > > >> version of Bioconductor. If some of you could confirm that the > > >> issue is > > >> fixed, I will back port it to the recent release. > > >> > > >> Thanks for the report. It was a real bug, but manifested itself > > >> on > > >> Ubuntu due to compiler settings on Ubuntu-12.04 which are more > > aggressive > > >> than normal at flagging (potential) security errors. > > >> > > >> Best, > > >> Kasper > > >> > > >> On Apr 16, 2014, at 9:23 AM, Venkat Seshan <veseshan at="" gmail.com=""> > > >> wrote: > > >> > > >> > Thanks Kasper & Vladimir. I got the same error with and > > >> > without system > > >> graphviz packages. So the presence of system graphviz packages > > >> doesn't > > make > > >> a difference. > > >> > > > >> > Kasper - Attached is the log from the installation attempt > > >> > (output of > > >> script). The other information you needed are below. > > >> > > > >> > Thanks, > > >> > Venkat > > >> > > > >> > ebadmin at ebmaster:~$ gcc --version > > >> > gcc (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3 > > >> > Copyright (C) 2011 Free Software Foundation, Inc. > > >> > This is free software; see the source for copying conditions. > > >> > There > > is > > >> NO > > >> > warranty; not even for MERCHANTABILITY or FITNESS FOR A > > >> > PARTICULAR > > >> PURPOSE. > > >> > > > >> > ebadmin at ebmaster:~$ R CMD config CC > > >> > gcc -std=gnu99 > > >> > ebadmin at ebmaster:~$ `R CMD config CC` --version > > >> > gcc (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3 > > >> > Copyright (C) 2011 Free Software Foundation, Inc. > > >> > This is free software; see the source for copying conditions. > > >> > There > > is > > >> NO > > >> > warranty; not even for MERCHANTABILITY or FITNESS FOR A > > >> > PARTICULAR > > >> PURPOSE. > > >> > > > >> > > > >> > > > >> > > > >> > On Wed, Apr 16, 2014 at 3:44 AM, Kasper Daniel Hansen < > > >> khansen at jhsph.edu> wrote: > > >> > What Vladimir suggests should not be necessary, and I am > > >> > interesting > > in > > >> looking a bit at this. > > >> > > > >> > The error message Venkat posts is unfortunately completely > > >> uninformative. What happens during Rgraphviz installation is > > >> > 1) The C(++) code of graphviz gets compiled > > >> > 2) Rgraphviz gets compiled and linked to (1) > > >> > > > >> > The error message Venkat posts just tells us that (2) fails, > > >> > which is > > >> usually because (1) fails, but we cannot see this. I really > > >> don't > > >> understand why Vladimir's suggestion of hand-compiling graphviz > > >> and then > > >> using --with-graphviz works, because that ought to be > > >> essentially what > > >> happens in a standard installation. > > >> > > > >> > I would like the following > > >> > > > >> > (1) The full output of the Rgraphviz installation (yes, I know > > >> > it is > > >> long). > > >> > (2) What is the specific version of the C compiler used. > > >> > (3) What is the output of > > >> > R CMD config CC > > >> > and > > >> > `R CMD config CC` --version > > >> > > > >> > Best, > > >> > Kasper > > >> > > > >> > > > >> > > > >> > On Wed, Apr 16, 2014 at 5:39 AM, Vladimir Zhurov > > >> > <vzhurov2 at="" uwo.ca=""> > > >> wrote: > > >> > Venkat, > > >> > > > >> > What you described is an exactly same error that I got today > > >> > during > > >> > upgrade. My system is also Ubuntu 12.04 (LTS). Also in this > > >> > particular > > >> mode > > >> > of installation system graphviz version is irrelevant as by > > >> > default > > >> > Rgraphviz is bundled with the slimmed copy of graphviz 2.28. > > >> > And > > default > > >> > installation breaks with the gvc.h error. Installation using > > >> > system > > >> > graphviz of 2.26 or the most recent version (2.38) also did > > >> > not work > > >> though > > >> > with different errors. > > >> > > > >> > What worked for me in the end was to upgrade system graphviz > > >> > from > > >> source to > > >> > exactly 2.28, using just bug patch from Rgraphviz package (as > > >> > I did > > not > > >> > want to break system graphviz by slimming it). Then I was able > > >> > to > > >> install > > >> > Rgraphviz using system graphviz. > > >> > > > >> > The whole process is below. > > >> > > > >> > In shell: > > >> > > > >> > # download and unpack graphviz v.2.28 sources > > >> > > > >> > wget > > >> > > > >> > > http://www.graphviz.org/pub/graphviz/stable/SOURCES/graphviz-2.28. 0.tar.gz > > >> > tar xzf graphviz-2.28.0.tar.gz > > >> > > > >> > # download and unpack Rgraphviz source package > > >> > > > >> > wget > > >> > > > >> > > http://www.bioconductor.org/packages/release/bioc/src/contrib/Rgra phviz_2.8.0.tar.gz > > >> > tar xzf Rgraphviz_2.8.0.tar.gz > > >> > > > >> > # patch, configure, build and install graphviz > > >> > > > >> > cd ./graphviz-2.28.0/ > > >> > patch -p1 < > > >> > ../Rgraphviz/inst/prepare/patches_2.28.0/graphviz-2.28.0-bugs.patch > > >> > ./configure > > >> > make > > >> > sudo make install > > >> > > > >> > > > >> > In R: > > >> > > > >> > source("http://bioconductor.org/biocLite.R") > > >> > biocLite("Rgraphviz", configure.args="--with-graphviz") # uses > > >> > system > > >> > graphviz instead of bundled > > >> > > > >> > > > >> > Hope this helps. > > >> > > > >> > Regards. > > >> > > > >> > Vladimir. > > >> > > > >> > > > >> > > > >> > > > >> > > > >> > On Tue, Apr 15, 2014 at 1:12 PM, Venkat Seshan [guest] < > > >> > guest at bioconductor.org> wrote: > > >> > > > >> > > > > >> > > When updating to Bioconductor 2.14 I get the following error > > >> > > from > > >> > > Rgraphviz. > > >> > > > > >> > > In file included from LL_funcs.c:1:0: > > >> > > common.h:16:17: fatal error: gvc.h: No such file or > > >> > > directory > > >> > > compilation terminated. > > >> > > make: *** [LL_funcs.o] Error 1 > > >> > > ERROR: compilation failed for package ???Rgraphviz??? > > >> > > > > >> > > The server runs Ubuntu 12.04 (LTS) and the necessary > > >> > > packages are > > >> > > available: > > >> > > > > >> > > ii graphviz 2.26.3-10ubuntu1.1 > > >> > > rich set of graph drawing tools > > >> > > ii graphviz-dev 2.26.3-10ubuntu1.1 > > >> > > transitional package for graphviz-dev rename > > >> > > ii libgraphviz-dev 2.26.3-10ubuntu1.1 > > >> > > graphviz libs and headers against which to build > > >> > > applications > > >> > > > > >> > > > > >> > > All the other packages were successfully updated. > > >> > > > > >> > > Thanks, > > >> > > Venkat > > >> > > > > >> > > > > >> > > -- output of sessionInfo(): > > >> > > > > >> > > > 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] BiocInstaller_1.14.1 > > >> > > > > >> > > loaded via a namespace (and not attached): > > >> > > [1] tools_3.1.0 > > >> > > > > >> > > > > >> > > -- > > >> > > Sent via the guest posting facility at bioconductor.org. > > >> > > > > >> > > _______________________________________________ > > >> > > Bioconductor mailing list > > >> > > Bioconductor at r-project.org > > >> > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > >> > > Search the archives: > > >> > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > >> > > > > >> > > > >> > > > >> > > > >> > -- > > >> > Dr. Vladimir Zhurov > > >> > Research Associate > > >> > Department of Biology, BGS3051 and WSC339 > > >> > University of Western Ontario > > >> > Tel.: 519-661-2111 ext. 86794 and 86467 > > >> > Fax: 519-661-3935 > > >> > Skype: vzhurov.uwo > > >> > > > >> > http://www.spidermite.org > > >> > > > >> > [[alternative HTML version deleted]] > > >> > > > >> > > > >> > _______________________________________________ > > >> > Bioconductor mailing list > > >> > Bioconductor at r-project.org > > >> > https://stat.ethz.ch/mailman/listinfo/bioconductor > > >> > Search the archives: > > >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > >> > > > >> > > > >> > <rgraphviz.log> > > >> > > >> > > > > > > > > > -- > > > Dr. Vladimir Zhurov > > > Research Associate > > > Department of Biology, BGS3051 and WSC339 > > > University of Western Ontario > > > Tel.: 519-661-2111 ext. 86794 and 86467 > > > Fax: 519-661-3935 > > > Skype: vzhurov.uwo > > > > > > http://www.spidermite.org > > > > > > > [[alternative HTML version deleted]] > > > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at 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]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor
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Kasper: I too can confirm that 2.9.1 compiles on my server. Thanks, Venkat On Wed, Apr 30, 2014 at 1:23 PM, Kasper Daniel Hansen <khansen@jhsph.edu>wrote: > There may be a time lag between submission and building. The patch exists > in the subversion repos; just checked. > > Best, > Kasper > > > On Wed, Apr 30, 2014 at 11:38 AM, Venkat Seshan <veseshan@gmail.com>wrote: > >> >> http://master.bioconductor.org/packages/devel/bioc/html/Rgraphviz.h tmlstill >> >> shows 2.9.0 >> >> Venkat >> >> >> On Tue, Apr 29, 2014 at 4:31 PM, Vladimir Zhurov <vzhurov2@uwo.ca> wrote: >> >> > Kasper, >> > >> > Checked out revision 89654 - worked on my workstation. >> > >> > Regards. >> > >> > Vladimir. >> > >> > >> > On Sun, Apr 27, 2014 at 10:28 PM, Kasper Hansen <khanse10@jhu.edu> >> wrote: >> > >> >> Vladimir, Venkat, Chong >> >> >> >> I believe I have fixed the issue in Rgraphviz 2.9.1, which I just >> >> committed. Source tar balls should be available Tuesday in the >> development >> >> version of Bioconductor. If some of you could confirm that the issue >> is >> >> fixed, I will back port it to the recent release. >> >> >> >> Thanks for the report. It was a real bug, but manifested itself on >> >> Ubuntu due to compiler settings on Ubuntu-12.04 which are more >> aggressive >> >> than normal at flagging (potential) security errors. >> >> >> >> Best, >> >> Kasper >> >> >> >> On Apr 16, 2014, at 9:23 AM, Venkat Seshan <veseshan@gmail.com> wrote: >> >> >> >> > Thanks Kasper & Vladimir. I got the same error with and without >> system >> >> graphviz packages. So the presence of system graphviz packages doesn't >> make >> >> a difference. >> >> > >> >> > Kasper - Attached is the log from the installation attempt (output of >> >> script). The other information you needed are below. >> >> > >> >> > Thanks, >> >> > Venkat >> >> > >> >> > ebadmin@ebmaster:~$ gcc --version >> >> > gcc (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3 >> >> > Copyright (C) 2011 Free Software Foundation, Inc. >> >> > This is free software; see the source for copying conditions. There >> is >> >> NO >> >> > warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR >> >> PURPOSE. >> >> > >> >> > ebadmin@ebmaster:~$ R CMD config CC >> >> > gcc -std=gnu99 >> >> > ebadmin@ebmaster:~$ `R CMD config CC` --version >> >> > gcc (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3 >> >> > Copyright (C) 2011 Free Software Foundation, Inc. >> >> > This is free software; see the source for copying conditions. There >> is >> >> NO >> >> > warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR >> >> PURPOSE. >> >> > >> >> > >> >> > >> >> > >> >> > On Wed, Apr 16, 2014 at 3:44 AM, Kasper Daniel Hansen < >> >> khansen@jhsph.edu> wrote: >> >> > What Vladimir suggests should not be necessary, and I am interesting >> in >> >> looking a bit at this. >> >> > >> >> > The error message Venkat posts is unfortunately completely >> >> uninformative. What happens during Rgraphviz installation is >> >> > 1) The C(++) code of graphviz gets compiled >> >> > 2) Rgraphviz gets compiled and linked to (1) >> >> > >> >> > The error message Venkat posts just tells us that (2) fails, which is >> >> usually because (1) fails, but we cannot see this. I really don't >> >> understand why Vladimir's suggestion of hand-compiling graphviz and >> then >> >> using --with-graphviz works, because that ought to be essentially what >> >> happens in a standard installation. >> >> > >> >> > I would like the following >> >> > >> >> > (1) The full output of the Rgraphviz installation (yes, I know it is >> >> long). >> >> > (2) What is the specific version of the C compiler used. >> >> > (3) What is the output of >> >> > R CMD config CC >> >> > and >> >> > `R CMD config CC` --version >> >> > >> >> > Best, >> >> > Kasper >> >> > >> >> > >> >> > >> >> > On Wed, Apr 16, 2014 at 5:39 AM, Vladimir Zhurov <vzhurov2@uwo.ca> >> >> wrote: >> >> > Venkat, >> >> > >> >> > What you described is an exactly same error that I got today during >> >> > upgrade. My system is also Ubuntu 12.04 (LTS). Also in this >> particular >> >> mode >> >> > of installation system graphviz version is irrelevant as by default >> >> > Rgraphviz is bundled with the slimmed copy of graphviz 2.28. And >> default >> >> > installation breaks with the gvc.h error. Installation using system >> >> > graphviz of 2.26 or the most recent version (2.38) also did not work >> >> though >> >> > with different errors. >> >> > >> >> > What worked for me in the end was to upgrade system graphviz from >> >> source to >> >> > exactly 2.28, using just bug patch from Rgraphviz package (as I did >> not >> >> > want to break system graphviz by slimming it). Then I was able to >> >> install >> >> > Rgraphviz using system graphviz. >> >> > >> >> > The whole process is below. >> >> > >> >> > In shell: >> >> > >> >> > # download and unpack graphviz v.2.28 sources >> >> > >> >> > wget >> >> > >> >> >> http://www.graphviz.org/pub/graphviz/stable/SOURCES/graphviz-2.28.0 .tar.gz >> >> > tar xzf graphviz-2.28.0.tar.gz >> >> > >> >> > # download and unpack Rgraphviz source package >> >> > >> >> > wget >> >> > >> >> >> http://www.bioconductor.org/packages/release/bioc/src/contrib/Rgrap hviz_2.8.0.tar.gz >> >> > tar xzf Rgraphviz_2.8.0.tar.gz >> >> > >> >> > # patch, configure, build and install graphviz >> >> > >> >> > cd ./graphviz-2.28.0/ >> >> > patch -p1 < >> >> > ../Rgraphviz/inst/prepare/patches_2.28.0/graphviz-2.28.0-bugs.patch >> >> > ./configure >> >> > make >> >> > sudo make install >> >> > >> >> > >> >> > In R: >> >> > >> >> > source("http://bioconductor.org/biocLite.R") >> >> > biocLite("Rgraphviz", configure.args="--with-graphviz") # uses system >> >> > graphviz instead of bundled >> >> > >> >> > >> >> > Hope this helps. >> >> > >> >> > Regards. >> >> > >> >> > Vladimir. >> >> > >> >> > >> >> > >> >> > >> >> > >> >> > On Tue, Apr 15, 2014 at 1:12 PM, Venkat Seshan [guest] < >> >> > guest@bioconductor.org> wrote: >> >> > >> >> > > >> >> > > When updating to Bioconductor 2.14 I get the following error from >> >> > > Rgraphviz. >> >> > > >> >> > > In file included from LL_funcs.c:1:0: >> >> > > common.h:16:17: fatal error: gvc.h: No such file or directory >> >> > > compilation terminated. >> >> > > make: *** [LL_funcs.o] Error 1 >> >> > > ERROR: compilation failed for package ‘Rgraphviz’ >> >> > > >> >> > > The server runs Ubuntu 12.04 (LTS) and the necessary packages are >> >> > > available: >> >> > > >> >> > > ii graphviz 2.26.3-10ubuntu1.1 >> >> > > rich set of graph drawing tools >> >> > > ii graphviz-dev 2.26.3-10ubuntu1.1 >> >> > > transitional package for graphviz-dev rename >> >> > > ii libgraphviz-dev 2.26.3-10ubuntu1.1 >> >> > > graphviz libs and headers against which to build applications >> >> > > >> >> > > >> >> > > All the other packages were successfully updated. >> >> > > >> >> > > Thanks, >> >> > > Venkat >> >> > > >> >> > > >> >> > > -- output of sessionInfo(): >> >> > > >> >> > > > 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] BiocInstaller_1.14.1 >> >> > > >> >> > > loaded via a namespace (and not attached): >> >> > > [1] tools_3.1.0 >> >> > > >> >> > > >> >> > > -- >> >> > > 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 >> >> > > >> >> > >> >> > >> >> > >> >> > -- >> >> > Dr. Vladimir Zhurov >> >> > Research Associate >> >> > Department of Biology, BGS3051 and WSC339 >> >> > University of Western Ontario >> >> > Tel.: 519-661-2111 ext. 86794 and 86467 >> >> > Fax: 519-661-3935 >> >> > Skype: vzhurov.uwo >> >> > >> >> > http://www.spidermite.org >> >> > >> >> > [[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 >> >> > >> >> > >> >> > <rgraphviz.log> >> >> >> >> >> > >> > >> > -- >> > Dr. Vladimir Zhurov >> > Research Associate >> > Department of Biology, BGS3051 and WSC339 >> > University of Western Ontario >> > Tel.: 519-661-2111 ext. 86794 and 86467 >> > Fax: 519-661-3935 >> > Skype: vzhurov.uwo >> > >> > http://www.spidermite.org >> > >> >> [[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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