Back to Mac ARM64 build report for BioC 3.19 |
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This page was generated on 2024-05-07 11:32:30 -0400 (Tue, 07 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4461 |
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 185/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BiocNeighbors 1.22.0 (landing page) Aaron Lun
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | ||||||||
To the developers/maintainers of the BiocNeighbors 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: BiocNeighbors |
Version: 1.22.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BiocNeighbors.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BiocNeighbors_1.22.0.tar.gz |
StartedAt: 2024-05-06 19:56:47 -0400 (Mon, 06 May 2024) |
EndedAt: 2024-05-06 19:58:26 -0400 (Mon, 06 May 2024) |
EllapsedTime: 99.0 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: BiocNeighbors.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BiocNeighbors.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BiocNeighbors_1.22.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/BiocNeighbors.Rcheck’ * using R version 4.4.0 (2024-04-24) * 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 13.6.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘BiocNeighbors/DESCRIPTION’ ... OK * this is package ‘BiocNeighbors’ version ‘1.22.0’ * 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 ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘BiocNeighbors’ can be installed ... OK * used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ * 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 ... OK * 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 dependencies in R code ... OK * 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 ... WARNING checkRd: (5) BiocNeighborIndex.Rd:24: \item in \describe must have non-empty label checkRd: (5) BiocNeighborIndex.Rd:25: \item in \describe must have non-empty label checkRd: (5) BiocNeighborIndex.Rd:26: \item in \describe must have non-empty label checkRd: (5) BiocNeighborIndex.Rd:27: \item in \describe must have non-empty label checkRd: (5) BiocNeighborParam.Rd:18: \item in \describe must have non-empty label checkRd: (5) BiocNeighborParam.Rd:19: \item in \describe must have non-empty label checkRd: (5) BiocNeighborParam.Rd:20: \item in \describe must have non-empty label checkRd: (5) BiocNeighborParam.Rd:21: \item in \describe must have non-empty label * 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 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 ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... WARNING Note: information on .o files is not available File ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BiocNeighbors/libs/BiocNeighbors.so’: Found ‘_sprintf’, possibly from ‘sprintf’ (C) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf. The detected symbols are linked into the code but might come from libraries and not actually be called. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * 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: 2 WARNINGs, 1 NOTE See ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/BiocNeighbors.Rcheck/00check.log’ for details.
BiocNeighbors.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BiocNeighbors ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘BiocNeighbors’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using C++11 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppHNSW/include' -I/opt/R/arm64/include -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../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppHNSW/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c annoy.cpp -o annoy.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppHNSW/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c build_annoy.cpp -o build_annoy.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppHNSW/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c build_hnsw.cpp -o build_hnsw.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppHNSW/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c build_vptree.cpp -o build_vptree.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppHNSW/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c distances.cpp -o distances.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppHNSW/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c exhaustive.cpp -o exhaustive.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppHNSW/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c find_annoy.cpp -o find_annoy.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppHNSW/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c find_exhaustive.cpp -o find_exhaustive.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppHNSW/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c find_hnsw.cpp -o find_hnsw.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppHNSW/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c find_kmknn.cpp -o find_kmknn.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppHNSW/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c find_mutual_nns.cpp -o find_mutual_nns.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppHNSW/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c find_vptree.cpp -o find_vptree.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppHNSW/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c hnsw.cpp -o hnsw.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppHNSW/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c kmknn.cpp -o kmknn.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppHNSW/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c query_annoy.cpp -o query_annoy.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppHNSW/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c query_exhaustive.cpp -o query_exhaustive.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppHNSW/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c query_hnsw.cpp -o query_hnsw.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppHNSW/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c query_kmknn.cpp -o query_kmknn.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppHNSW/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c query_vptree.cpp -o query_vptree.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppHNSW/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c utils.cpp -o utils.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppHNSW/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c vptree.cpp -o vptree.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 BiocNeighbors.so RcppExports.o annoy.o build_annoy.o build_hnsw.o build_vptree.o distances.o exhaustive.o find_annoy.o find_exhaustive.o find_hnsw.o find_kmknn.o find_mutual_nns.o find_vptree.o hnsw.o kmknn.o query_annoy.o query_exhaustive.o query_hnsw.o query_kmknn.o query_vptree.o utils.o vptree.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-BiocNeighbors/00new/BiocNeighbors/libs ** R ** 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 (BiocNeighbors)
BiocNeighbors.Rcheck/tests/testthat.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(BiocNeighbors) > test_check("BiocNeighbors") [ FAIL 0 | WARN 494 | SKIP 2 | PASS 3289 ] ══ Skipped tests (2) ═══════════════════════════════════════════════════════════ • out of sync with RcppAnnoy, skipping tests (2): 'test-find-annoy.R:5:1', 'test-query-annoy.R:5:1' [ FAIL 0 | WARN 494 | SKIP 2 | PASS 3289 ] > > proc.time() user system elapsed 36.268 3.472 62.039
BiocNeighbors.Rcheck/BiocNeighbors-Ex.timings
name | user | system | elapsed | |
AnnoyIndex | 0.140 | 0.003 | 0.143 | |
AnnoyParam | 0.004 | 0.000 | 0.004 | |
BiocNeighbors-raw-index | 0.619 | 0.003 | 0.623 | |
BiocNeighbors-ties | 0.003 | 0.000 | 0.004 | |
ExhaustiveIndex | 0.006 | 0.001 | 0.006 | |
ExhaustiveParam | 0.000 | 0.000 | 0.001 | |
HnswIndex | 0.349 | 0.003 | 0.352 | |
HnswParam | 0.002 | 0.000 | 0.002 | |
KmknnIndex | 0.155 | 0.011 | 0.166 | |
KmknnParam | 0.001 | 0.000 | 0.002 | |
VptreeIndex | 0.010 | 0.001 | 0.010 | |
VptreeParam | 0.000 | 0.000 | 0.001 | |
buildAnnoy | 0.128 | 0.002 | 0.129 | |
buildExhaustive | 0.003 | 0.000 | 0.003 | |
buildHnsw | 0.344 | 0.003 | 0.347 | |
buildIndex | 0.242 | 0.003 | 0.245 | |
buildKmknn | 0.197 | 0.001 | 0.199 | |
buildVptree | 0.007 | 0.000 | 0.007 | |
findKNN-functions | 1.587 | 0.020 | 1.607 | |
findKNN-methods | 2.014 | 0.006 | 2.020 | |
findMutualNN | 0.012 | 0.000 | 0.011 | |
findNeighbors-functions | 2.045 | 0.082 | 2.128 | |
findNeighbors-methods | 1.882 | 0.003 | 1.886 | |
queryKNN-functions | 0.788 | 0.019 | 0.807 | |
queryKNN-methods | 0.664 | 0.006 | 0.670 | |
queryNeighbors-functions | 0.199 | 0.001 | 0.200 | |
queryNeighbors-methods | 0.417 | 0.000 | 0.417 | |