Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:08 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 1669/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
RBGL 1.82.0 (landing page) Bioconductor Package Maintainer
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the RBGL package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RBGL.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: RBGL |
Version: 1.82.0 |
Command: rm -rf RBGL.buildbin-libdir && mkdir RBGL.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh RBGL_1.82.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R RBGL.buildbin-libdir |
StartedAt: 2024-12-21 16:09:47 -0500 (Sat, 21 Dec 2024) |
EndedAt: 2024-12-21 16:11:28 -0500 (Sat, 21 Dec 2024) |
EllapsedTime: 100.3 seconds |
RetCode: 0 |
Status: OK |
PackageFile: RBGL_1.82.0.tgz |
PackageFileSize: 3.375 MiB |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf RBGL.buildbin-libdir && mkdir RBGL.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh RBGL_1.82.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R RBGL.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=RBGL.buildbin-libdir RBGL_1.82.0.tar.gz' >>>>>>> * installing *source* package ‘RBGL’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bbc.cpp -o bbc.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c cliques.cpp -o cliques.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c clusteringCoef.cpp -o clusteringCoef.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c dominatorTree.cpp -o dominatorTree.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -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<TEdgeListGraph>::edge_iterator EdgeIter; ^ ./edmonds_optimum_branching_impl.hpp:521:71: warning: unused typedef 'weight_t' [-Wunused-local-typedef] typedef typename property_traits<TWeightMap>::value_type weight_t; ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c hcs.cpp -o hcs.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -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++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c interfaces.cpp -o interfaces.o interfaces.cpp:57:60: warning: unused typedef 'Edge' [-Wunused-local-typedef] typedef graph_traits < Graph_dd >::edge_descriptor Edge; ^ interfaces.cpp:61:62: warning: unused typedef 'Color' [-Wunused-local-typedef] typedef property_map<Graph_dd, vertex_color_t>::type Color; ^ 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:142:60: warning: unused typedef 'Edge' [-Wunused-local-typedef] typedef graph_traits < Graph_dd >::edge_descriptor Edge; ^ interfaces.cpp:143:62: warning: unused typedef 'Vertex' [-Wunused-local-typedef] typedef graph_traits < Graph_dd >::vertex_descriptor Vertex; ^ 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:226:62: warning: unused typedef 'Vertex' [-Wunused-local-typedef] typedef graph_traits < Graph_dd >::vertex_descriptor Vertex; ^ interfaces.cpp:225:60: warning: unused typedef 'Edge' [-Wunused-local-typedef] typedef graph_traits < Graph_dd >::edge_descriptor Edge; ^ interfaces.cpp:252:60: warning: unused typedef 'Edge' [-Wunused-local-typedef] typedef graph_traits < Graph_ud >::edge_descriptor Edge; ^ interfaces.cpp:253:62: warning: unused typedef 'Vertex' [-Wunused-local-typedef] typedef graph_traits < Graph_ud >::vertex_descriptor Vertex; ^ 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:360:60: warning: unused typedef 'Edge' [-Wunused-local-typedef] typedef graph_traits < Graph_ud >::edge_descriptor Edge; ^ interfaces.cpp:361:62: warning: unused typedef 'Vertex' [-Wunused-local-typedef] typedef graph_traits < Graph_ud >::vertex_descriptor Vertex; ^ 16 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -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++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c mincut.cpp -o mincut.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ordering.cpp -o ordering.o ordering.cpp:182:48: warning: unused variable 'id' [-Wunused-variable] property_map<Graph_dd, vertex_index_t>::type id = get(vertex_index, g); ^ ordering.cpp:133:53: warning: unused typedef 'Vertex' [-Wunused-local-typedef] typedef graph_traits<Graph_dd>::vertex_descriptor Vertex; ^ ordering.cpp:176:53: warning: unused typedef 'Vertex' [-Wunused-local-typedef] typedef graph_traits<Graph_dd>::vertex_descriptor Vertex; ^ ordering.cpp:232:47: warning: unused typedef 'Pair' [-Wunused-local-typedef] typedef std::pair<std::size_t, std::size_t> Pair; ^ 4 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c planar.cpp -o planar.o planar.cpp:225:30: warning: unused variable 'oi' [-Wunused-variable] Vertex_Vec_t::iterator oi, oi_end = ordering.end(); ^ planar.cpp:225:34: warning: unused variable 'oi_end' [-Wunused-variable] Vertex_Vec_t::iterator oi, oi_end = ordering.end(); ^ planar.cpp:429:32: warning: unused variable 'ki' [-Wunused-variable] Edge_Vec_t::iterator ki, ki_end = kuratowski_edges.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; ^ 5 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c registerSigHandlers.cpp -o registerSigHandlers.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -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++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -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++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c transitive_closure.cpp -o transitive_closure.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c wavefront.cpp -o wavefront.o clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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-3.20-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 PATHS TO DYNAMIC LIBRARIES FOR RBGL.buildbin-libdir/RBGL/libs/RBGL.so >>>>>>> >>>>>>> Paths before fix: RBGL.buildbin-libdir/RBGL/libs/RBGL.so: RBGL.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.2) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101) /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5) >>>>>>> Fix with install_name_tool: install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgcc_s.1.1.dylib" "RBGL.buildbin-libdir/RBGL/libs/RBGL.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "RBGL.buildbin-libdir/RBGL/libs/RBGL.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "RBGL.buildbin-libdir/RBGL/libs/RBGL.so" >>>>>>> Paths after fix: RBGL.buildbin-libdir/RBGL/libs/RBGL.so: RBGL.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.2) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101) /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)