Aaron Lun
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/BiocNeighbors |
| Branch: RELEASE_3_12 |
| Last Commit: 889bc91 |
| Last Changed Date: 2020-12-06 19:54:29 -0400 (Sun, 06 Dec 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:26:59 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the BiocNeighbors package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 163/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BiocNeighbors 1.8.2 (landing page) Aaron Lun
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: BiocNeighbors |
| Version: 1.8.2 |
| Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:BiocNeighbors.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings BiocNeighbors_1.8.2.tar.gz |
| StartedAt: 2021-05-05 23:26:24 -0400 (Wed, 05 May 2021) |
| EndedAt: 2021-05-05 23:30:59 -0400 (Wed, 05 May 2021) |
| EllapsedTime: 274.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BiocNeighbors.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:BiocNeighbors.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings BiocNeighbors_1.8.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/BiocNeighbors.Rcheck’
* using R version 4.0.5 (2021-03-31)
* 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 ‘1.8.2’
* 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 13.4Mb
sub-directories of 1Mb or more:
libs 12.9Mb
* 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 7.720 0.000 7.729
rangeFind-methods 6.584 0.324 6.917
findKNN 6.580 0.020 6.608
find-methods 5.188 0.012 5.216
* 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-3.12-bioc/meat/BiocNeighbors.Rcheck/00check.log’
for details.
BiocNeighbors.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL BiocNeighbors ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’ * installing *source* package ‘BiocNeighbors’ ... ** using staged installation ** libs g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-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-3.12-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_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-3.12-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.12-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 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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")
══ Skipped tests ═══════════════════════════════════════════════════════════════
• not attempting to compare to latest RcppAnnoy (2)
[ FAIL 0 | WARN 6 | SKIP 2 | PASS 3216 ]
>
> proc.time()
user system elapsed
95.620 4.676 165.296
BiocNeighbors.Rcheck/BiocNeighbors-Ex.timings
| name | user | system | elapsed | |
| AnnoyIndex | 0.608 | 0.020 | 0.628 | |
| AnnoyParam | 0.012 | 0.000 | 0.012 | |
| BiocNeighbors-raw-index | 2.072 | 0.004 | 2.079 | |
| BiocNeighbors-ties | 0.008 | 0.000 | 0.010 | |
| ExhaustiveIndex | 0.016 | 0.000 | 0.016 | |
| ExhaustiveParam | 0.004 | 0.000 | 0.003 | |
| HnswIndex | 0.900 | 0.000 | 0.901 | |
| HnswParam | 0.004 | 0.000 | 0.006 | |
| KmknnIndex | 0.516 | 0.000 | 0.514 | |
| KmknnParam | 0.000 | 0.000 | 0.002 | |
| VptreeIndex | 0.028 | 0.000 | 0.030 | |
| VptreeParam | 0.004 | 0.000 | 0.002 | |
| buildAnnoy | 0.504 | 0.008 | 0.513 | |
| buildExhaustive | 0.016 | 0.000 | 0.013 | |
| buildHnsw | 1.028 | 0.000 | 1.029 | |
| buildIndex | 0.608 | 0.000 | 0.608 | |
| buildKmknn | 0.192 | 0.004 | 0.196 | |
| buildVptree | 0.020 | 0.000 | 0.017 | |
| find-methods | 5.188 | 0.012 | 5.216 | |
| findKNN | 6.580 | 0.020 | 6.608 | |
| findNeighbors | 7.720 | 0.000 | 7.729 | |
| query-methods | 2.572 | 0.008 | 2.584 | |
| queryKNN | 1.964 | 0.016 | 1.979 | |
| queryNeighbors | 1.256 | 0.004 | 1.264 | |
| rangeFind-methods | 6.584 | 0.324 | 6.917 | |
| rangeQuery-methods | 0.684 | 0.008 | 0.695 | |