Pascal Schlosser
| Snapshot Date: 2024-03-26 09:00:03 -0400 (Tue, 26 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/netboost |
| git_branch: RELEASE_3_18 |
| git_last_commit: 5678175 |
| git_last_commit_date: 2023-10-24 11:14:09 -0400 (Tue, 24 Oct 2023) |
| Back to Mac ARM64 build report for BioC 3.18 |
|
This page was generated on 2024-03-28 11:32:25 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.1 Ventura | arm64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4376 |
| 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 1401/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| netboost 2.10.0 (landing page) Pascal Schlosser
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | OK | OK | WARNINGS | OK | | |||||||
|
To the developers/maintainers of the netboost package: - 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: netboost |
| Version: 2.10.0 |
| Command: rm -rf netboost.buildbin-libdir && mkdir netboost.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh netboost_2.10.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R netboost.buildbin-libdir |
| StartedAt: 2024-03-28 09:09:51 -0400 (Thu, 28 Mar 2024) |
| EndedAt: 2024-03-28 09:11:14 -0400 (Thu, 28 Mar 2024) |
| EllapsedTime: 83.7 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: netboost_2.10.0.tgz |
| PackageFileSize: 1.115 MiB |
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### Running command:
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### rm -rf netboost.buildbin-libdir && mkdir netboost.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh netboost_2.10.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R netboost.buildbin-libdir
###
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=netboost.buildbin-libdir netboost_2.10.0.tar.gz'
>>>>>>>
* installing *source* package ‘netboost’ ...
** using staged installation
CLEANUP cleanup
Clean build.
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... ./install-sh -c -d
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for gcc... clang -arch arm64
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether clang -arch arm64 accepts -g... yes
checking for clang -arch arm64 option to accept ISO C89... none needed
checking whether clang -arch arm64 understands -c and -o together... rm: conftest.dSYM: is a directory
yes
checking whether make supports the include directive... yes (GNU style)
checking dependency style of clang -arch arm64... none
checking how to run the C preprocessor... clang -arch arm64 -E
checking build system type... arm-apple-darwin22.6.0
checking host system type... arm-apple-darwin22.6.0
checking for x86 cpuid output... unknown
checking for x86-AVX xgetbv output... unknown
checking whether C compiler accepts -Wno-deprecated... yes
checking for strip... strip
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating src/mcupgma/clustering_util/Makefile
config.status: creating src/config.h
config.status: executing depfiles commands
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include `/Library/Frameworks/R.framework/Resources/bin/Rscript -e "Rcpp:::CxxFlags()"` -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include `/Library/Frameworks/R.framework/Resources/bin/Rscript -e "Rcpp:::CxxFlags()"` -fPIC -falign-functions=64 -Wall -g -O2 -c boosting.cpp -o boosting.o
boosting.cpp:79:15: warning: unused variable 'AVX_UNROLL' [-Wunused-const-variable]
constexpr int AVX_UNROLL = 4;
^
1 warning generated.
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include `/Library/Frameworks/R.framework/Resources/bin/Rscript -e "Rcpp:::CxxFlags()"` -fPIC -falign-functions=64 -Wall -g -O2 -c dist_tom.cpp -o dist_tom.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include `/Library/Frameworks/R.framework/Resources/bin/Rscript -e "Rcpp:::CxxFlags()"` -fPIC -falign-functions=64 -Wall -g -O2 -c tree_sort.cpp -o tree_sort.o
clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o netboost.so RcppExports.o boosting.o dist_tom.o tree_sort.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
strip -S netboost.so
installing via 'install.libs.R' to /Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/netboost.buildbin-libdir/00LOCK-netboost/00new/netboost
[1] "R_PACKAGE_SRC: /tmp/RtmpXMJ1XQ/R.INSTALL51524ac64a67/netboost"
[1] "R_PACKAGE_DIR: /Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/netboost.buildbin-libdir/00LOCK-netboost/00new/netboost"
[1] "R_ARCH: "
[1] "SHLIB_EXT: .so"
[1] "INSTALL PATH: /tmp/RtmpXMJ1XQ/R.INSTALL51524ac64a67/netboost/src/mcupgma/scripts/install_path.mk"
Clean build.
==== compiling clustering_util sources using external Makefile (clustering_util/Makefile) recursively
make -C clustering_util -f Makefile mcupgma_install
mkdir -p bin
mkdir -p obj.arm64_Darwin
c++ -Wall -Wno-deprecated -O3 -DNDEBUG -c -o obj.arm64_Darwin/HashingMergerMain.cmdline.o HashingMergerMain.cmdline.c
c++ -Wall -Wno-deprecated -O3 -DNDEBUG -Wall -Wno-deprecated -O3 -DNDEBUG -c -o obj.arm64_Darwin/ClusteringUtil.o ClusteringUtil.cpp
c++ -Wall -Wno-deprecated -O3 -DNDEBUG -Wall -Wno-deprecated -O3 -DNDEBUG -c -o obj.arm64_Darwin/Tree.o Tree.cpp
c++ -Wall -Wno-deprecated -O3 -DNDEBUG -o bin/edges2valid_clusters HashingMergerMain.cpp obj.arm64_Darwin/HashingMergerMain.cmdline.o obj.arm64_Darwin/ClusteringUtil.o obj.arm64_Darwin/Tree.o
c++ -Wall -Wno-deprecated -O3 -DNDEBUG -c -o obj.arm64_Darwin/EdgeCollatorMain.cmdline.o EdgeCollatorMain.cmdline.c
c++ -Wall -Wno-deprecated -O3 -DNDEBUG -o bin/edge_collator EdgeCollatorMain.cpp obj.arm64_Darwin/EdgeCollatorMain.cmdline.o obj.arm64_Darwin/ClusteringUtil.o obj.arm64_Darwin/Tree.o
==== compiling sources using external Makefile (clustering_round/Makefile) recursively
make -C clustering_round -f Makefile
mkdir -p dep.arm64_Darwin
test -d dep.arm64_Darwin && c++ -MM -MT 'dep.arm64_Darwin/test_heap.d obj.arm64_Darwin/test_heap.o obj.arm64_Darwin.debug/test_heap.o' -O3 -ftemplate-depth-64 -I./ test_heap.cpp > dep.arm64_Darwin/test_heap.d
test -d dep.arm64_Darwin && c++ -MM -MT 'dep.arm64_Darwin/HierarchicalClustering_with_unknown_edges.d obj.arm64_Darwin/HierarchicalClustering_with_unknown_edges.o obj.arm64_Darwin.debug/HierarchicalClustering_with_unknown_edges.o' -O3 -ftemplate-depth-64 -I./ HierarchicalClustering_with_unknown_edges.cpp > dep.arm64_Darwin/HierarchicalClustering_with_unknown_edges.d
test -d dep.arm64_Darwin && c++ -MM -MT 'dep.arm64_Darwin/HierarchicalClustering_main.d obj.arm64_Darwin/HierarchicalClustering_main.o obj.arm64_Darwin.debug/HierarchicalClustering_main.o' -O3 -ftemplate-depth-64 -I./ HierarchicalClustering_main.cpp > dep.arm64_Darwin/HierarchicalClustering_main.d
mkdir -p obj.arm64_Darwin
mkdir -p bin
c++ -O3 -ftemplate-depth-64 -I./ -c HierarchicalClustering_main.cpp -o obj.arm64_Darwin/HierarchicalClustering_main.o
HierarchicalClustering_main.cpp:79:17: warning: using directive refers to implicitly-defined namespace 'std'
using namespace std;
^
1 warning generated.
cc -O3 -I./ -c HierarchicalClustering_main.cmdline.c -o obj.arm64_Darwin/HierarchicalClustering_main.cmdline.o
c++ -O3 -ftemplate-depth-64 -I./ -c HierarchicalClustering_with_unknown_edges.cpp -o obj.arm64_Darwin/HierarchicalClustering_with_unknown_edges.o
HierarchicalClustering_with_unknown_edges.cpp:26:17: warning: using directive refers to implicitly-defined namespace 'std'
using namespace std;
^
HierarchicalClustering_with_unknown_edges.cpp:85:68: warning: field 'isLeftGreater' is uninitialized when used here [-Wuninitialized]
ubEdgeHeap(edges.begin(), edges.size(), CompareEdgesByUpperBound(isLeftGreater)),
^
HierarchicalClustering_with_unknown_edges.cpp:86:68: warning: field 'isLeftGreater' is uninitialized when used here [-Wuninitialized]
lbEdgeHeap(edges.begin(), edges.size(), CompareEdgesByLowerBound(isLeftGreater)),
^
3 warnings generated.
c++ obj.arm64_Darwin/HierarchicalClustering_main.o obj.arm64_Darwin/HierarchicalClustering_main.cmdline.o obj.arm64_Darwin/HierarchicalClustering_with_unknown_edges.o -o bin/hierarchical_clustering -O3
c++ -O3 -ftemplate-depth-64 -I./ -c test_heap.cpp -o obj.arm64_Darwin/test_heap.o
test_heap.cpp:20:17: warning: using directive refers to implicitly-defined namespace 'std'
using namespace std;
^
1 warning generated.
cc -O3 -I./ -c test_heap.cmdline.c -o obj.arm64_Darwin/test_heap.cmdline.o
c++ obj.arm64_Darwin/test_heap.o obj.arm64_Darwin/test_heap.cmdline.o -o bin/test_heap -O3
[1] "SRC: /tmp/RtmpXMJ1XQ/R.INSTALL51524ac64a67/netboost/src/mcupgma"
[1] "DEST: /Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/netboost.buildbin-libdir/00LOCK-netboost/00new/netboost/mcupgma"
[1] "INSTALL FROM: /tmp/RtmpXMJ1XQ/R.INSTALL51524ac64a67/netboost/src/mcupgma/clustering_round/bin TO: /Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/netboost.buildbin-libdir/00LOCK-netboost/00new/netboost/mcupgma"
[1] "INSTALL FROM: /tmp/RtmpXMJ1XQ/R.INSTALL51524ac64a67/netboost/src/mcupgma/clustering_util/bin TO: /Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/netboost.buildbin-libdir/00LOCK-netboost/00new/netboost/mcupgma"
[1] "INSTALL FROM: /tmp/RtmpXMJ1XQ/R.INSTALL51524ac64a67/netboost/src/mcupgma/scripts TO: /Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/netboost.buildbin-libdir/00LOCK-netboost/00new/netboost/mcupgma"
[1] "netboost.so"
** R
** data
*** moving datasets to lazyload DB
** 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 (netboost)
>>>>>>>
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR netboost.buildbin-libdir/netboost/libs/netboost.so
>>>>>>>
>>>>>>> Paths before fix:
netboost.buildbin-libdir/netboost/libs/netboost.so:
netboost.so (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.3)
/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/4.3-arm64/Resources/lib/libgcc_s.1.1.dylib" "netboost.buildbin-libdir/netboost/libs/netboost.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgfortran.5.dylib" "netboost.buildbin-libdir/netboost/libs/netboost.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libquadmath.0.dylib" "netboost.buildbin-libdir/netboost/libs/netboost.so"
>>>>>>> Paths after fix:
netboost.buildbin-libdir/netboost/libs/netboost.so:
netboost.so (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.3)
/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)