Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-11 15:43 -0400 (Tue, 11 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
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 1378/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
netboost 2.13.0 (landing page) Pascal Schlosser
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
To the developers/maintainers of the netboost package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/netboost.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: netboost |
Version: 2.13.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:netboost.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings netboost_2.13.0.tar.gz |
StartedAt: 2024-06-11 02:54:34 -0400 (Tue, 11 Jun 2024) |
EndedAt: 2024-06-11 02:58:03 -0400 (Tue, 11 Jun 2024) |
EllapsedTime: 208.4 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: netboost.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:netboost.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings netboost_2.13.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/netboost.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘netboost/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘netboost’ version ‘2.13.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘netboost’ can be installed ... WARNING Found the following significant warnings: boosting.cpp:418:18: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat] boosting.cpp:419:18: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat] boosting.cpp:646:29: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat] HierarchicalClustering_with_unknown_edges.cpp:85:68: warning: field 'isLeftGreater' is uninitialized when used here [-Wuninitialized] HierarchicalClustering_with_unknown_edges.cpp:86:68: warning: field 'isLeftGreater' is uninitialized when used here [-Wuninitialized] See ‘/Users/biocbuild/bbs-3.20-bioc/meat/netboost.Rcheck/00install.out’ for details. * used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ * used SDK: ‘MacOSX11.3.sdk’ * checking C++ specification ... NOTE Specified C++11: please drop specification unless essential * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE BugReports field is not a suitable URL but appears to contain an email address not specified by mailto: nor contained in < > use the Contact field instead * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking whether startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘BiocStyle’ All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... NOTE checkRd: (-1) cpp_filter_step.Rd:19: Lost braces 19 | Must be initialised before using @see{filter_base} | ^ * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in shell scripts ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements. * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking include directives in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed cut_trees 8.065 0.274 8.344 nb_mcupgma 7.317 0.253 7.574 tree_search 7.067 0.229 7.297 nb_dist 6.804 0.216 7.021 nb_summary 6.742 0.223 6.989 nb_clust 6.519 0.233 6.782 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 7 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/netboost.Rcheck/00check.log’ for details.
netboost.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL netboost ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘netboost’ ... ** using staged installation 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/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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:418:18: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat] (col+1) * nrow, ^~~~~~~~~~~~~~ boosting.cpp:419:18: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat] (col+1) * (nrow + 256/sizeof(double)) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ boosting.cpp:646:29: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat] bstep + 1, actual_sel + 1, actual_update); ^~~~~~~~~~~~~~ boosting.cpp:729:19: note: in instantiation of function template specialization 'Boosting::filter_column_gen<true, false, true>' requested here return boost->filter_column_gen<true,false,true>(col_y-1); ^ boosting.cpp:646:29: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat] bstep + 1, actual_sel + 1, actual_update); ^~~~~~~~~~~~~~ boosting.cpp:732:19: note: in instantiation of function template specialization 'Boosting::filter_column_gen<false, false, true>' requested here return boost->filter_column_gen<false,false,true>(col_y-1); ^ boosting.cpp:79:15: warning: unused variable 'AVX_UNROLL' [-Wunused-const-variable] constexpr int AVX_UNROLL = 4; ^ 5 warnings generated. clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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 /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-netboost/00new/netboost [1] "R_PACKAGE_SRC: /Users/biocbuild/bbs-3.20-bioc/meat/netboost" [1] "R_PACKAGE_DIR: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-netboost/00new/netboost" [1] "R_ARCH: " [1] "SHLIB_EXT: .so" [1] "INSTALL PATH: /Users/biocbuild/bbs-3.20-bioc/meat/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: /Users/biocbuild/bbs-3.20-bioc/meat/netboost/src/mcupgma" [1] "DEST: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-netboost/00new/netboost/mcupgma" [1] "INSTALL FROM: /Users/biocbuild/bbs-3.20-bioc/meat/netboost/src/mcupgma/clustering_round/bin TO: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-netboost/00new/netboost/mcupgma" [1] "INSTALL FROM: /Users/biocbuild/bbs-3.20-bioc/meat/netboost/src/mcupgma/clustering_util/bin TO: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-netboost/00new/netboost/mcupgma" [1] "INSTALL FROM: /Users/biocbuild/bbs-3.20-bioc/meat/netboost/src/mcupgma/scripts TO: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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)
netboost.Rcheck/netboost-Ex.timings
name | user | system | elapsed | |
cut_trees | 8.065 | 0.274 | 8.344 | |
dot-onAttach | 0 | 0 | 0 | |
mcupgma_exec | 0.030 | 0.027 | 0.075 | |
nb_clust | 6.519 | 0.233 | 6.782 | |
nb_dist | 6.804 | 0.216 | 7.021 | |
nb_filter | 4.567 | 0.195 | 4.763 | |
nb_mcupgma | 7.317 | 0.253 | 7.574 | |
nb_plot_dendro | 1.757 | 0.026 | 1.783 | |
nb_summary | 6.742 | 0.223 | 6.989 | |
nb_transfer | 1.776 | 0.020 | 1.797 | |
netboost | 1.798 | 0.024 | 1.823 | |
tree_search | 7.067 | 0.229 | 7.297 | |