User: Li.Long@isb-sib.ch

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Posts by Li.Long@isb-sib.ch

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Answer: A: RBGL fails to compile / install
... the issue is mostly related to gcc. Like you said, your gcc is 3.3, pretty old. There were fixes put in to address gcc-related issues. The reason that the problem (only) shows up in RBGL is because RBGL uses boost-library, which depends on templates in C++ heavily. Li > Hello all, > > ...
written 9.7 years ago by Li.Long@isb-sib.ch510
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Comment: C: problem on install package RBGL
... yes. For R 2.10.0/BioConductor 2.5 release, RBGL is 1.22.0 Li > is RBGL 1.20.0 old? > > Li Long ??????: >> you are using an old version of RBGL. The latest release has taken care >> of this issue. >> >> Li >> >> >>> hi, >>> I met ...
written 9.9 years ago by Li.Long@isb-sib.ch510
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Answer: A: problem on install package RBGL
... you are using an old version of RBGL. The latest release has taken care of this issue. Li > > > hi, > ? I met a problem when install RBGL package. > here is > the error information: > * Installing > *source* package ‘RBGL’ ... > untarring boost include > tree... > ...
written 9.9 years ago by Li.Long@isb-sib.ch510
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Answer: A: R graphs: all paths lengths between two nodes in a directed graph
... you can take a look at BioC/RBGL package, which contains quite a number of often-used graph algorithms. Li > I would need help in obtaining all path lengths between two nodes in a > directed graph. > > Suppose I have the following directed graph (below) called "mygraph": > >> ...
written 10.4 years ago by Li.Long@isb-sib.ch510
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Answer: A: RBGL installation issues
... RBGL uses C++ templates extensively, previously we encountered various issues using different C++ compilers, even different versions of g++ compilers. Somehow the error msg in the mail is scrambled, I cannot tell what it complains about, but it looks like something related to C++. Probably you co ...
written 11.0 years ago by Li.Long@isb-sib.ch510
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Answer: A: Problems building RBGL package
... Since CHAR_BIT is set in /usr/include/limits.h (or similar include path from the system), you should also check to make sure your gcc looks into those dirs as well. Li > Hi, > > I am not able to build the RBGL package (needed for the GOstats package). > See > build output below. & ...
written 11.2 years ago by Li.Long@isb-sib.ch510
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Answer: A: Problems building RBGL package
... I suggest double-check the options you used: > -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector > --param=ssp-buffer-size=4 -m64 -mtune=generic by default, we don't set any of these for RBGL. I suspect they alter the options when expanding templates, and lead to > err ...
written 11.2 years ago by Li.Long@isb-sib.ch510
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Comment: C: Rgraphviz, R 2.7.0 and Windows XP
... > > In the short - and likely even medium term that may be the only > solution. There do not seem to be easy ways to build a DLL that is > compliant (which is why the very old one was retained for such a long > time) and it requires a substantial effort with every new version of & ...
written 11.3 years ago by Li.Long@isb-sib.ch510
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Answer: A: Rgraphviz, R 2.7.0 and Windows XP
... Hi, There are some major changes in Rgraphviz on Windows from BioC 2.6 to 2.7, mainly to support various versions of graphviz. Before BioC 2.6, Rgraphviz on Windows uses VERY OLD graphviz (more than 2 year old) only. Since BioC 2.7, Rgraphviz on Windows is parallel to that on Linux, i.e., you ca ...
written 11.3 years ago by Li.Long@isb-sib.ch510
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Answer: A: a bug in hypergraph?
... Hi, Tony, I suspect "nodes" as parameter name is in conflict w/ function "nodes"... I tried and tested some new codes... and checked in methods- Hypergraph.R Let me know what you think. Li > According to the man pages for Hypergraph-class, the following example of > a > very trivial h ...
written 11.5 years ago by Li.Long@isb-sib.ch510

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