Bioconductor Package Maintainer
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/RBGL |
| Branch: RELEASE_3_9 |
| Last Commit: ef24c17 |
| Last Changed Date: 2019-05-02 11:53:02 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:44:49 -0400 (Wed, 16 Oct 2019).
| Package 1315/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| RBGL 1.60.0 Bioconductor Package Maintainer
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | [ OK ] | |
| Package: RBGL |
| Version: 1.60.0 |
| Command: rm -rf RBGL.buildbin-libdir && mkdir RBGL.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh RBGL_1.60.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R RBGL.buildbin-libdir |
| StartedAt: 2019-10-16 09:13:28 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 09:16:18 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 170.3 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: RBGL_1.60.0.tgz |
| PackageFileSize: 2.648 MiB |
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###
### Running command:
###
### rm -rf RBGL.buildbin-libdir && mkdir RBGL.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh RBGL_1.60.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R RBGL.buildbin-libdir
###
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=RBGL.buildbin-libdir RBGL_1.60.0.tar.gz'
>>>>>>>
* installing *source* package ‘RBGL’ ...
** using staged installation
checking R package BH ... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c bbc.cpp -o bbc.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c cliques.cpp -o cliques.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c clusteringCoef.cpp -o clusteringCoef.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c dominatorTree.cpp -o dominatorTree.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c edmonds_optimum_branching.cpp -o edmonds_optimum_branching.o
In file included from edmonds_optimum_branching.cpp:3:
In file included from ./edmonds_optimum_branching.hpp:94:
./edmonds_optimum_branching_impl.hpp:520:71: warning: unused typedef 'EdgeIter' [-Wunused-local-typedef]
typedef typename graph_traits::edge_iterator EdgeIter;
^
./edmonds_optimum_branching_impl.hpp:521:71: warning: unused typedef 'weight_t' [-Wunused-local-typedef]
typedef typename property_traits::value_type weight_t;
^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c hcs.cpp -o hcs.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c incrConnComp.cpp -o incrConnComp.o
incrConnComp.cpp:74:32: warning: unused variable 'child_index' [-Wunused-variable]
BOOST_FOREACH(VertexIndex child_index, components[current_index]) {
^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c interfaces.cpp -o interfaces.o
interfaces.cpp:61:62: warning: unused typedef 'Color' [-Wunused-local-typedef]
typedef property_map::type Color;
^
interfaces.cpp:57:60: warning: unused typedef 'Edge' [-Wunused-local-typedef]
typedef graph_traits < Graph_dd >::edge_descriptor Edge;
^
interfaces.cpp:98:60: warning: unused typedef 'Edge' [-Wunused-local-typedef]
typedef graph_traits < Graph_dd >::edge_descriptor Edge;
^
interfaces.cpp:99:62: warning: unused typedef 'Vertex' [-Wunused-local-typedef]
typedef graph_traits < Graph_dd >::vertex_descriptor Vertex;
^
interfaces.cpp:143:62: warning: unused typedef 'Vertex' [-Wunused-local-typedef]
typedef graph_traits < Graph_dd >::vertex_descriptor Vertex;
^
interfaces.cpp:142:60: warning: unused typedef 'Edge' [-Wunused-local-typedef]
typedef graph_traits < Graph_dd >::edge_descriptor Edge;
^
interfaces.cpp:198:60: warning: unused typedef 'Edge' [-Wunused-local-typedef]
typedef graph_traits < Graph_ud >::edge_descriptor Edge;
^
interfaces.cpp:199:62: warning: unused typedef 'Vertex' [-Wunused-local-typedef]
typedef graph_traits < Graph_ud >::vertex_descriptor Vertex;
^
interfaces.cpp:225:60: warning: unused typedef 'Edge' [-Wunused-local-typedef]
typedef graph_traits < Graph_dd >::edge_descriptor Edge;
^
interfaces.cpp:226:62: warning: unused typedef 'Vertex' [-Wunused-local-typedef]
typedef graph_traits < Graph_dd >::vertex_descriptor Vertex;
^
interfaces.cpp:253:62: warning: unused typedef 'Vertex' [-Wunused-local-typedef]
typedef graph_traits < Graph_ud >::vertex_descriptor Vertex;
^
interfaces.cpp:252:60: warning: unused typedef 'Edge' [-Wunused-local-typedef]
typedef graph_traits < Graph_ud >::edge_descriptor Edge;
^
interfaces.cpp:295:60: warning: unused typedef 'Edge' [-Wunused-local-typedef]
typedef graph_traits < Graph_ud >::edge_descriptor Edge;
^
interfaces.cpp:320:62: warning: unused typedef 'Vertex' [-Wunused-local-typedef]
typedef graph_traits < Graph_ud >::vertex_descriptor Vertex;
^
interfaces.cpp:361:62: warning: unused typedef 'Vertex' [-Wunused-local-typedef]
typedef graph_traits < Graph_ud >::vertex_descriptor Vertex;
^
interfaces.cpp:360:60: warning: unused typedef 'Edge' [-Wunused-local-typedef]
typedef graph_traits < Graph_ud >::edge_descriptor Edge;
^
16 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c minST.cpp -o minST.o
minST.cpp:14:62: warning: unused typedef 'Vertex' [-Wunused-local-typedef]
typedef graph_traits < Graph_dd >::vertex_descriptor Vertex;
^
minST.cpp:48:62: warning: unused typedef 'Vertex' [-Wunused-local-typedef]
typedef graph_traits < Graph_ud >::vertex_descriptor Vertex;
^
minST.cpp:81:60: warning: unused typedef 'Edge' [-Wunused-local-typedef]
typedef graph_traits < Graph_ud >::edge_descriptor Edge;
^
3 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c mincut.cpp -o mincut.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c ordering.cpp -o ordering.o
ordering.cpp:182:48: warning: unused variable 'id' [-Wunused-variable]
property_map::type id = get(vertex_index, g);
^
ordering.cpp:133:53: warning: unused typedef 'Vertex' [-Wunused-local-typedef]
typedef graph_traits::vertex_descriptor Vertex;
^
ordering.cpp:176:53: warning: unused typedef 'Vertex' [-Wunused-local-typedef]
typedef graph_traits::vertex_descriptor Vertex;
^
ordering.cpp:232:47: warning: unused typedef 'Pair' [-Wunused-local-typedef]
typedef std::pair Pair;
^
4 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c planar.cpp -o planar.o
planar.cpp:225:34: warning: unused variable 'oi_end' [-Wunused-variable]
Vertex_Vec_t::iterator oi, oi_end = ordering.end();
^
planar.cpp:429:36: warning: unused variable 'ki_end' [-Wunused-variable]
Edge_Vec_t::iterator ki, ki_end = kuratowski_edges.end();
^
planar.cpp:461:6: warning: unused variable 'i' [-Wunused-variable]
int i, j = 0;
^
3 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c registerSigHandlers.cpp -o registerSigHandlers.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c shortestPath.cpp -o shortestPath.o
shortestPath.cpp:17:60: warning: unused typedef 'Edge' [-Wunused-local-typedef]
typedef graph_traits < Graph_dd >::edge_descriptor Edge;
^
shortestPath.cpp:136:60: warning: unused typedef 'Edge' [-Wunused-local-typedef]
typedef graph_traits < Graph_dd >::edge_descriptor Edge;
^
shortestPath.cpp:180:39: warning: unused typedef 'Edge' [-Wunused-local-typedef]
typedef std::pair < int, int >Edge;
^
shortestPath.cpp:177:81: warning: unused typedef 'Graph' [-Wunused-local-typedef]
property< edge_weight_t, double, property< edge_weight2_t, double > > > Graph;
^
4 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c sna.cpp -o sna.o
sna.cpp:161:9: warning: unused variable 'res_cap' [-Wunused-variable]
res_cap = get(edge_residual_capacity, flow_g);
^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c transitive_closure.cpp -o transitive_closure.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c wavefront.cpp -o wavefront.o
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o RBGL.so bbc.o cliques.o clusteringCoef.o dominatorTree.o edmonds_optimum_branching.o hcs.o incrConnComp.o interfaces.o minST.o mincut.o ordering.o planar.o registerSigHandlers.o shortestPath.o sna.o transitive_closure.o wavefront.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.9-bioc/meat/RBGL.buildbin-libdir/00LOCK-RBGL/00new/RBGL/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RBGL)
>>>>>>>
>>>>>>> FIXING LINKS FOR RBGL.buildbin-libdir/RBGL/libs//RBGL.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgcc_s.1.dylib" "RBGL.buildbin-libdir/RBGL/libs//RBGL.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgfortran.3.dylib" "RBGL.buildbin-libdir/RBGL/libs//RBGL.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.5.2.dylib" "RBGL.buildbin-libdir/RBGL/libs//RBGL.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.dylib" "RBGL.buildbin-libdir/RBGL/libs//RBGL.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libquadmath.0.dylib" "RBGL.buildbin-libdir/RBGL/libs//RBGL.so"