Aaron Lun
| Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/BiocNeighbors |
| git_branch: RELEASE_3_17 |
| git_last_commit: 4b19ef2 |
| git_last_commit_date: 2023-04-25 11:02:50 -0400 (Tue, 25 Apr 2023) |
| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:36:51 -0400 (Mon, 16 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
| 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 181/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BiocNeighbors 1.18.0 (landing page) Aaron Lun
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the BiocNeighbors package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BiocNeighbors.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: BiocNeighbors |
| Version: 1.18.0 |
| 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_1.18.0.tar.gz |
| StartedAt: 2023-10-15 23:02:21 -0400 (Sun, 15 Oct 2023) |
| EndedAt: 2023-10-15 23:13:32 -0400 (Sun, 15 Oct 2023) |
| EllapsedTime: 670.9 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_1.18.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/BiocNeighbors.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiocNeighbors/DESCRIPTION’ ... OK
* this is package ‘BiocNeighbors’ version ‘1.18.0’
* 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 14.0.0 (clang-1400.0.29.202)’
* 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 R 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/4.3-x86_64/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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
findNeighbors-functions 8.416 0.694 12.150
findKNN-methods 8.393 0.127 11.361
findNeighbors-methods 7.306 0.050 9.339
findKNN-functions 6.142 0.155 8.847
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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-3.17-bioc/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/4.3-x86_64/Resources/library’ * installing *source* package ‘BiocNeighbors’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using C++11 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppHNSW/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppHNSW/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c annoy.cpp -o annoy.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppHNSW/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c build_annoy.cpp -o build_annoy.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppHNSW/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c build_hnsw.cpp -o build_hnsw.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppHNSW/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c build_vptree.cpp -o build_vptree.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppHNSW/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c distances.cpp -o distances.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppHNSW/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c exhaustive.cpp -o exhaustive.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppHNSW/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c find_annoy.cpp -o find_annoy.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppHNSW/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c find_exhaustive.cpp -o find_exhaustive.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppHNSW/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c find_hnsw.cpp -o find_hnsw.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppHNSW/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c find_kmknn.cpp -o find_kmknn.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppHNSW/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c find_mutual_nns.cpp -o find_mutual_nns.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppHNSW/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c find_vptree.cpp -o find_vptree.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppHNSW/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c hnsw.cpp -o hnsw.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppHNSW/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c kmknn.cpp -o kmknn.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppHNSW/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c query_annoy.cpp -o query_annoy.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppHNSW/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c query_exhaustive.cpp -o query_exhaustive.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppHNSW/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c query_hnsw.cpp -o query_hnsw.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppHNSW/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c query_kmknn.cpp -o query_kmknn.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppHNSW/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c query_vptree.cpp -o query_vptree.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppHNSW/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c utils.cpp -o utils.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppHNSW/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c vptree.cpp -o vptree.o clang++ -arch x86_64 -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/opt/R/x86_64/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/4.3-x86_64/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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (64-bit)
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
180.890 14.325 427.941
BiocNeighbors.Rcheck/BiocNeighbors-Ex.timings
| name | user | system | elapsed | |
| AnnoyIndex | 0.590 | 0.053 | 0.913 | |
| AnnoyParam | 0.027 | 0.002 | 0.040 | |
| BiocNeighbors-raw-index | 2.526 | 0.025 | 3.555 | |
| BiocNeighbors-ties | 0.026 | 0.001 | 0.037 | |
| ExhaustiveIndex | 0.029 | 0.003 | 0.041 | |
| ExhaustiveParam | 0.004 | 0.000 | 0.004 | |
| HnswIndex | 1.255 | 0.027 | 1.718 | |
| HnswParam | 0.018 | 0.001 | 0.022 | |
| KmknnIndex | 0.320 | 0.114 | 0.660 | |
| KmknnParam | 0.007 | 0.001 | 0.016 | |
| VptreeIndex | 0.054 | 0.006 | 0.088 | |
| VptreeParam | 0.005 | 0.000 | 0.007 | |
| buildAnnoy | 0.522 | 0.041 | 0.812 | |
| buildExhaustive | 0.015 | 0.001 | 0.026 | |
| buildHnsw | 1.246 | 0.022 | 1.843 | |
| buildIndex | 0.792 | 0.043 | 1.232 | |
| buildKmknn | 0.283 | 0.005 | 0.423 | |
| buildVptree | 0.025 | 0.001 | 0.032 | |
| findKNN-functions | 6.142 | 0.155 | 8.847 | |
| findKNN-methods | 8.393 | 0.127 | 11.361 | |
| findMutualNN | 0.070 | 0.001 | 0.093 | |
| findNeighbors-functions | 8.416 | 0.694 | 12.150 | |
| findNeighbors-methods | 7.306 | 0.050 | 9.339 | |
| queryKNN-functions | 2.960 | 0.168 | 3.967 | |
| queryKNN-methods | 2.448 | 0.148 | 3.642 | |
| queryNeighbors-functions | 0.678 | 0.032 | 1.070 | |
| queryNeighbors-methods | 1.392 | 0.055 | 1.960 | |