Ruuid requires specific MAKEFLAGS setting on Fedora Core 2

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Jan T. Kim ▴ 70

@jan-t-kim-1050

Last seen 9.6 years ago

Dear all, in the process of upgrading from R 2.0.1 to 2.1.0, I just installed Bioconductor (again), and again, the installation of Ruuid (triggered by getBioC("graph") required manual intervention because the glib headers are not found by default: MAKEFLAGS='CFLAGS=-I/usr/include/glib-2.0\ -I/usr/lib/glib-2.0/include' R CMD INSTALL Ruuid This is on a Fedora Core 2 system. Is it just me or the system being weird and requiring this MAKEFLAGS setting? I seem to recall seeing messages reporting difficulties installing Ruuid / Rgraphviz and thinking that these may be related to this issue... so, perhaps, the MAKEFLAGS hack above might be useful to others, and perhaps, (other) others can tell me what's weird with my system? Best regards, Jan -- +- Jan T. Kim -------------------------------------------------------+ | *NEW* email: jtk@cmp.uea.ac.uk | | *NEW* WWW: http://www.cmp.uea.ac.uk/people/jtk | *-----=< hierarchical systems are for files, not for humans >=-----*

Ruuid Rgraphviz PROcess Ruuid Rgraphviz PROcess • 922 views

ADD COMMENT • link updated 18.9 years ago by Uri David Akavia ▴ 80 • written 18.9 years ago by Jan T. Kim ▴ 70

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Uri David Akavia ▴ 80

@uri-david-akavia-1277

Last seen 9.6 years ago

Jan T. Kim wrote: > Dear all, > > in the process of upgrading from R 2.0.1 to 2.1.0, I just installed > Bioconductor (again), and again, the installation of Ruuid (triggered > by getBioC("graph") required manual intervention because the glib headers > are not found by default: > > MAKEFLAGS='CFLAGS=-I/usr/include/glib-2.0\ -I/usr/lib/glib-2.0/include' R CMD INSTALL Ruuid > > Could getBioC be upgraded to use pkg-config? This is a very small script/program which gives locations of header files, and libraries, in a format suitable for compilation. IIRC, the syntax is something like pkg-config --include glib-2.0.

ADD COMMENT • link 18.9 years ago Uri David Akavia ▴ 80

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Basically the simple answer is yes, and we should have something working in the next few days; it looks for glib-config (which, while deprecated in some systems is not in the ones I use and that makes testing pkg-config a pain). Best wishes Robert Uri David Akavia wrote: > Jan T. Kim wrote: > >> Dear all, >> >> in the process of upgrading from R 2.0.1 to 2.1.0, I just installed >> Bioconductor (again), and again, the installation of Ruuid (triggered >> by getBioC("graph") required manual intervention because the glib headers >> are not found by default: >> >> MAKEFLAGS='CFLAGS=-I/usr/include/glib-2.0\ >> -I/usr/lib/glib-2.0/include' R CMD INSTALL Ruuid >> >> > Could getBioC be upgraded to use pkg-config? This is a very small > script/program which gives locations of header files, and libraries, in > a format suitable for compilation. > IIRC, the syntax is something like pkg-config --include glib-2.0. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >

ADD REPLY • link 18.9 years ago rgentleman ★ 5.5k

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