Question: Problems building RBGL package
0
gravatar for Rasmus Ory Nielsen
11.1 years ago by
Rasmus Ory Nielsen50 wrote:
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/b ackward/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'
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ADD COMMENTlink modified 11.1 years ago • written 11.1 years ago by Rasmus Ory Nielsen50
Answer: Problems building RBGL package
0
gravatar for Li.Long@isb-sib.ch
11.1 years ago by
Li.Long@isb-sib.ch510 wrote:
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 > error: 'CHAR_BIT' was not declared in this scope which is from boost. 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.t ar.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 >
ADD COMMENTlink written 11.1 years ago by Li.Long@isb-sib.ch510
Answer: Problems building RBGL package
0
gravatar for Li.Long@isb-sib.ch
11.1 years ago by
Li.Long@isb-sib.ch510 wrote:
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.t ar.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 >
ADD COMMENTlink written 11.1 years ago by Li.Long@isb-sib.ch510
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 >> >
ADD REPLYlink written 11.1 years ago by Rasmus Ory Nielsen50
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_1.16.0 .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 >>> >> > > _______________________________________________ > 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
ADD REPLYlink written 11.1 years ago by Rasmus Ory Nielsen50
Answer: Problems building RBGL package
0
gravatar for Rasmus Ory Nielsen
11.1 years ago by
Rasmus Ory Nielsen50 wrote:
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_1.16 .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 >>>>> >>> _______________________________________________ >>> 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 >> >
ADD COMMENTlink written 11.1 years ago by Rasmus Ory Nielsen50
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
ADD REPLYlink written 11.1 years ago by Rasmus Ory Nielsen50
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