Back to Multiple platform build/check report for BioC 3.15 |
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This page was generated on 2022-10-19 13:20:01 -0400 (Wed, 19 Oct 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4386 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" | 4138 |
merida1 | macOS 10.14.6 Mojave | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4205 |
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 |
To the developers/maintainers of the BiocNeighbors package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 163/2140 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BiocNeighbors 1.14.0 (landing page) Aaron Lun
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
Package: BiocNeighbors |
Version: 1.14.0 |
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:BiocNeighbors.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings BiocNeighbors_1.14.0.tar.gz |
StartedAt: 2022-10-18 18:44:49 -0400 (Tue, 18 Oct 2022) |
EndedAt: 2022-10-18 18:49:17 -0400 (Tue, 18 Oct 2022) |
EllapsedTime: 268.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: BiocNeighbors.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:BiocNeighbors.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings BiocNeighbors_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/BiocNeighbors.Rcheck’ * using R version 4.2.1 (2022-06-23) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘BiocNeighbors/DESCRIPTION’ ... OK * this is package ‘BiocNeighbors’ version ‘1.14.0’ * 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 * checking installed package size ... NOTE installed size is 9.9Mb sub-directories of 1Mb or more: libs 9.4Mb * 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 ... OK * 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 ... 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 findNeighbors-functions 6.376 0.515 6.892 findKNN-methods 5.399 0.040 5.440 findNeighbors-methods 5.179 0.017 5.195 * 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 NOTEs See ‘/home/biocbuild/bbs-3.15-bioc/meat/BiocNeighbors.Rcheck/00check.log’ for details.
BiocNeighbors.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL BiocNeighbors ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’ * installing *source* package ‘BiocNeighbors’ ... ** using staged installation ** libs g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/RcppHNSW/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/RcppHNSW/include' -I/usr/local/include -fpic -g -O2 -Wall -c annoy.cpp -o annoy.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/RcppHNSW/include' -I/usr/local/include -fpic -g -O2 -Wall -c build_annoy.cpp -o build_annoy.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/RcppHNSW/include' -I/usr/local/include -fpic -g -O2 -Wall -c build_hnsw.cpp -o build_hnsw.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/RcppHNSW/include' -I/usr/local/include -fpic -g -O2 -Wall -c build_vptree.cpp -o build_vptree.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/RcppHNSW/include' -I/usr/local/include -fpic -g -O2 -Wall -c distances.cpp -o distances.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/RcppHNSW/include' -I/usr/local/include -fpic -g -O2 -Wall -c exhaustive.cpp -o exhaustive.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/RcppHNSW/include' -I/usr/local/include -fpic -g -O2 -Wall -c find_annoy.cpp -o find_annoy.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/RcppHNSW/include' -I/usr/local/include -fpic -g -O2 -Wall -c find_exhaustive.cpp -o find_exhaustive.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/RcppHNSW/include' -I/usr/local/include -fpic -g -O2 -Wall -c find_hnsw.cpp -o find_hnsw.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/RcppHNSW/include' -I/usr/local/include -fpic -g -O2 -Wall -c find_kmknn.cpp -o find_kmknn.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/RcppHNSW/include' -I/usr/local/include -fpic -g -O2 -Wall -c find_mutual_nns.cpp -o find_mutual_nns.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/RcppHNSW/include' -I/usr/local/include -fpic -g -O2 -Wall -c find_vptree.cpp -o find_vptree.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/RcppHNSW/include' -I/usr/local/include -fpic -g -O2 -Wall -c hnsw.cpp -o hnsw.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/RcppHNSW/include' -I/usr/local/include -fpic -g -O2 -Wall -c kmknn.cpp -o kmknn.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/RcppHNSW/include' -I/usr/local/include -fpic -g -O2 -Wall -c query_annoy.cpp -o query_annoy.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/RcppHNSW/include' -I/usr/local/include -fpic -g -O2 -Wall -c query_exhaustive.cpp -o query_exhaustive.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/RcppHNSW/include' -I/usr/local/include -fpic -g -O2 -Wall -c query_hnsw.cpp -o query_hnsw.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/RcppHNSW/include' -I/usr/local/include -fpic -g -O2 -Wall -c query_kmknn.cpp -o query_kmknn.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/RcppHNSW/include' -I/usr/local/include -fpic -g -O2 -Wall -c query_vptree.cpp -o query_vptree.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/RcppHNSW/include' -I/usr/local/include -fpic -g -O2 -Wall -c utils.cpp -o utils.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/RcppHNSW/include' -I/usr/local/include -fpic -g -O2 -Wall -c vptree.cpp -o vptree.o g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.15-bioc/R/lib -L/usr/local/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 -L/home/biocbuild/bbs-3.15-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.15-bioc/R/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 4.2.1 (2022-06-23) -- "Funny-Looking Kid" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (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 488 | SKIP 0 | PASS 3516 ] [ FAIL 0 | WARN 488 | SKIP 0 | PASS 3516 ] > > proc.time() user system elapsed 116.104 8.335 177.667
BiocNeighbors.Rcheck/BiocNeighbors-Ex.timings
name | user | system | elapsed | |
AnnoyIndex | 0.405 | 0.003 | 0.410 | |
AnnoyParam | 0.013 | 0.001 | 0.013 | |
BiocNeighbors-raw-index | 1.49 | 0.00 | 1.49 | |
BiocNeighbors-ties | 0.012 | 0.000 | 0.012 | |
ExhaustiveIndex | 0.011 | 0.003 | 0.015 | |
ExhaustiveParam | 0.000 | 0.001 | 0.002 | |
HnswIndex | 0.807 | 0.001 | 0.808 | |
HnswParam | 0.009 | 0.001 | 0.008 | |
KmknnIndex | 0.213 | 0.051 | 0.265 | |
KmknnParam | 0.003 | 0.000 | 0.004 | |
VptreeIndex | 0.029 | 0.001 | 0.029 | |
VptreeParam | 0.003 | 0.000 | 0.002 | |
buildAnnoy | 0.372 | 0.004 | 0.377 | |
buildExhaustive | 0.007 | 0.003 | 0.009 | |
buildHnsw | 0.814 | 0.000 | 0.815 | |
buildIndex | 0.551 | 0.008 | 0.559 | |
buildKmknn | 0.199 | 0.000 | 0.199 | |
buildVptree | 0.016 | 0.000 | 0.017 | |
findKNN-functions | 4.134 | 0.044 | 4.178 | |
findKNN-methods | 5.399 | 0.040 | 5.440 | |
findMutualNN | 0.04 | 0.00 | 0.04 | |
findNeighbors-functions | 6.376 | 0.515 | 6.892 | |
findNeighbors-methods | 5.179 | 0.017 | 5.195 | |
queryKNN-functions | 1.885 | 0.028 | 1.913 | |
queryKNN-methods | 1.566 | 0.028 | 1.594 | |
queryNeighbors-functions | 0.386 | 0.019 | 0.405 | |
queryNeighbors-methods | 0.889 | 0.009 | 0.897 | |