Hi Li, Thank you for your quick answer. I think the problem is GCC 4.3 is more strict about headers, see [1] and [2]. I got RGBL to compile by including <climits> in boostIncl/boost/pending/relaxed_heap.hpp. [1] http://gcc.gnu.org/gcc-4.3/porting_to.html [2] http://mail-archive.com/pld-cvs-commit at lists.pld- linux.org/msg140605.html Thanks. Best regards, Rasmus Ory Nielsen Li Long skrev: > 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. >> >> My system is running Fedora 9 x86_64 with all upgrades. >> R-2.7.0-5.fc9.x86_64 >> gcc-4.3.0-8.x86_64 >> gcc-c++-4.3.0-8.x86_64 >> >> Thanks in advance. >> >> Best regards, >> Rasmus Ory Nielsen >> >> >> > biocLite(c("RBGL")) >> Running biocinstall version 2.2.9 with R version 2.7.0 >> Your version of R requires version 2.2 of BioConductor. >> Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = >> dependencies, : >> argument 'lib' is missing: using '/usr/lib64/R/library' >> trying URL >> 'http://bioconductor.org/packages/2.2/bioc/src/contrib/RBGL_1.16.0. tar.gz' >> Content type 'application/x-gzip' length 1327240 bytes (1.3 Mb) >> opened URL >> ================================================== >> downloaded 1.3 Mb >> >> * Installing *source* package 'RBGL' ... >> untarring boost include tree... >> ** libs >> g++ -m64 -I/usr/include/R -I/usr/local/include -IboostIncl -fpic -O2 >> -g >> -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector >> --param=ssp-buffer-size=4 -m64 -mtune=generic -c bbc.cpp -o bbc.o >> In file included from >> /usr/lib/gcc/x86_64-redhat- linux/4.3.0/../../../../include/c++/4.3.0/ext/hash_set:64, >> from boostIncl/boost/graph/adjacency_list.hpp:22, >> from RBGL.hpp:26, >> from bbc.cpp:1: >> /usr/lib/gcc/x86_64-redhat-linux/4.3.0/../../../../include/c++/4.3. 0/backward/backward_warning.h:32:2: >> warning: #warning This file includes at least one deprecated or antiquated >> header which may be removed without further notice at a future date. >> Please >> use a non-deprecated interface with equivalent functionality instead. For >> a >> listing of replacement headers and interfaces, consult the file >> backward_warning.h. To disable this warning use -Wno-deprecated. >> In file included from >> boostIncl/boost/graph/dijkstra_shortest_paths.hpp:19, >> from >> boostIncl/boost/graph/betweenness_centrality.hpp:14, >> from bbc.cpp:2: >> boostIncl/boost/pending/relaxed_heap.hpp: In member function 'size_t >> boost::relaxed_heap<indexedtype, compare,="" id="">::log_base_2(size_t)': >> boostIncl/boost/pending/relaxed_heap.hpp:101: error: 'CHAR_BIT' was not >> declared in this scope >> make: *** [bbc.o] Error 1 >> chmod: cannot access `/usr/lib64/R/library/RBGL/libs/*': No such file or >> directory >> ERROR: compilation failed for package 'RBGL' >> ** Removing '/usr/lib64/R/library/RBGL' >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >

Hi, Here's the patch. RBGL_1.16.0-fixheader.patch: diff -up RBGL/RBGL/src/boostIncl/boost/pending/relaxed_heap.hpp.fixheader RBGL/RBGL/src/boostIncl/boost/pending/relaxed_heap.hpp --- RBGL/RBGL/src/boostIncl/boost/pending/relaxed_heap.hpp.fixheader 2008-06-24 15:22:57.000000000 +0200 +++ RBGL/RBGL/src/boostIncl/boost/pending/relaxed_heap.hpp 2008-06-24 15:23:06.000000000 +0200 @@ -13,6 +13,7 @@ #include <boost property_map.hpp=""> #include <boost optional.hpp=""> #include <vector> +#include <climits> #ifdef BOOST_RELAXED_HEAP_DEBUG # include <iostream> Best regards, Rasmus Ory Nielsen Rasmus Ory Nielsen skrev: > Hi Li, > > OK, I see. > > In case other people experiences the same problem, I have attached a > short patch showing the fix I made. I don't know if it is "The Right > Way" to do it, but it works for me. > > Best regards, > Rasmus Ory Nielsen > > > Li Long skrev: >> It seems the issue is compiler related. >> >> Gcc 4.3.1 is released earlier this month, after 4.3.0 in Mar, which is >> pretty new. We don't have enough man-power to lock-step with each and >> every compiler release. >> >> Boost's new release complies with 4.2.1. Since the boost part is taken >> directly from release, it's not so hot idea (from my point of view) to >> manually tweek it individually. Probably we'll wait for the part that's >> compiler-related. I might do something to put in the newer functions >> from >> Graph sometime in the summer. >> >> Even if we have new codes, it wouldn't be in release until Oct. >> >> Li >> >> >> >>> Hi Li, >>> >>> Any hope for an updated version of the RBGL package? >>> >>> Best regards, >>> Rasmus Ory Nielsen >>> >>> >>> Rasmus Ory Nielsen skrev: >>>> Hi Li, >>>> >>>> Thank you for your quick answer. >>>> >>>> I think the problem is GCC 4.3 is more strict about headers, see [1] >>>> and >>>> [2]. >>>> I got RGBL to compile by including <climits> in >>>> boostIncl/boost/pending/relaxed_heap.hpp. >>>> >>>> [1] http://gcc.gnu.org/gcc-4.3/porting_to.html >>>> [2] >>>> http://mail-archive.com/pld-cvs-commit at lists.pld- linux.org/msg140605.html >>>> >>>> >>>> Thanks. >>>> >>>> Best regards, >>>> Rasmus Ory Nielsen >>>> >>>> >>>> Li Long skrev: >>>>> 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. >>>>>> >>>>>> My system is running Fedora 9 x86_64 with all upgrades. >>>>>> R-2.7.0-5.fc9.x86_64 >>>>>> gcc-4.3.0-8.x86_64 >>>>>> gcc-c++-4.3.0-8.x86_64 >>>>>> >>>>>> Thanks in advance. >>>>>> >>>>>> Best regards, >>>>>> Rasmus Ory Nielsen >>>>>> >>>>>> >>>>>> > biocLite(c("RBGL")) >>>>>> Running biocinstall version 2.2.9 with R version 2.7.0 >>>>>> Your version of R requires version 2.2 of BioConductor. >>>>>> Warning in install.packages(pkgs = pkgs, repos = repos, >>>>>> dependencies = >>>>>> dependencies, : >>>>>> argument 'lib' is missing: using '/usr/lib64/R/library' >>>>>> trying URL >>>>>> 'http://bioconductor.org/packages/2.2/bioc/src/contrib/RBGL_1.1 6.0.tar.gz' >>>>>> >>>>>> >>>>>> Content type 'application/x-gzip' length 1327240 bytes (1.3 Mb) >>>>>> opened URL >>>>>> ================================================== >>>>>> downloaded 1.3 Mb >>>>>> >>>>>> * Installing *source* package 'RBGL' ... >>>>>> untarring boost include tree... >>>>>> ** libs >>>>>> g++ -m64 -I/usr/include/R -I/usr/local/include -IboostIncl -fpic >>>>>> -O2 >>>>>> -g >>>>>> -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack- protector >>>>>> --param=ssp-buffer-size=4 -m64 -mtune=generic -c bbc.cpp -o bbc.o >>>>>> In file included from >>>>>> /usr/lib/gcc/x86_64-redhat- linux/4.3.0/../../../../include/c++/4.3.0/ext/hash_set:64, >>>>>> >>>>>> >>>>>> from boostIncl/boost/graph/adjacency_list.hpp:22, >>>>>> from RBGL.hpp:26, >>>>>> from bbc.cpp:1: >>>>>> /usr/lib/gcc/x86_64-redhat-linux/4.3.0/../../../../include/c++/ 4.3.0/backward/backward_warning.h:32:2: >>>>>> >>>>>> >>>>>> warning: #warning This file includes at least one deprecated or >>>>>> antiquated >>>>>> header which may be removed without further notice at a future date. >>>>>> Please >>>>>> use a non-deprecated interface with equivalent functionality instead. >>>>>> For >>>>>> a >>>>>> listing of replacement headers and interfaces, consult the file >>>>>> backward_warning.h. To disable this warning use -Wno- deprecated. >>>>>> In file included from >>>>>> boostIncl/boost/graph/dijkstra_shortest_paths.hpp:19, >>>>>> from >>>>>> boostIncl/boost/graph/betweenness_centrality.hpp:14, >>>>>> from bbc.cpp:2: >>>>>> boostIncl/boost/pending/relaxed_heap.hpp: In member function 'size_t >>>>>> boost::relaxed_heap<indexedtype, compare,="" id="">::log_base_2(size_t)': >>>>>> boostIncl/boost/pending/relaxed_heap.hpp:101: error: 'CHAR_BIT' was >>>>>> not >>>>>> declared in this scope >>>>>> make: *** [bbc.o] Error 1 >>>>>> chmod: cannot access `/usr/lib64/R/library/RBGL/libs/*': No such file >>>>>> or >>>>>> directory >>>>>> ERROR: compilation failed for package 'RBGL' >>>>>> ** Removing '/usr/lib64/R/library/RBGL' >>>>>> >>>>>> _______________________________________________ >>>>>> Bioconductor mailing list >>>>>> Bioconductor at stat.math.ethz.ch >>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>> Search the archives: >>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at stat.math.ethz.ch >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> > > > -------------------------------------------------------------------- ---- > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor