Aaron Lun
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/BiocNeighbors |
| Branch: master |
| Last Commit: 94fa697 |
| Last Changed Date: 2019-02-12 06:18:56 -0400 (Tue, 12 Feb 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 13:37:11 -0400 (Tue, 09 Apr 2019).
| Package 144/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| BiocNeighbors 1.1.12 Aaron Lun
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK |
| Package: BiocNeighbors |
| Version: 1.1.12 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BiocNeighbors.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BiocNeighbors_1.1.12.tar.gz |
| StartedAt: 2019-04-08 23:29:39 -0400 (Mon, 08 Apr 2019) |
| EndedAt: 2019-04-08 23:33:47 -0400 (Mon, 08 Apr 2019) |
| EllapsedTime: 247.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BiocNeighbors.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BiocNeighbors.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BiocNeighbors_1.1.12.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/BiocNeighbors.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiocNeighbors/DESCRIPTION’ ... OK
* this is package ‘BiocNeighbors’ version ‘1.1.12’
* 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 ... 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 ... 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 compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
findKNN 6.223 0.063 6.355
* 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: 1 NOTE
See
‘/Users/biocbuild/bbs-3.9-bioc/meat/BiocNeighbors.Rcheck/00check.log’
for details.
BiocNeighbors.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL BiocNeighbors ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘BiocNeighbors’ ... ** libs clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppHNSW/include" -I/usr/local/include -fPIC -Wall -g -O2 -c annoy.cpp -o annoy.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppHNSW/include" -I/usr/local/include -fPIC -Wall -g -O2 -c build_annoy.cpp -o build_annoy.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppHNSW/include" -I/usr/local/include -fPIC -Wall -g -O2 -c build_hnsw.cpp -o build_hnsw.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppHNSW/include" -I/usr/local/include -fPIC -Wall -g -O2 -c build_vptree.cpp -o build_vptree.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppHNSW/include" -I/usr/local/include -fPIC -Wall -g -O2 -c distances.cpp -o distances.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppHNSW/include" -I/usr/local/include -fPIC -Wall -g -O2 -c find_annoy.cpp -o find_annoy.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppHNSW/include" -I/usr/local/include -fPIC -Wall -g -O2 -c find_hnsw.cpp -o find_hnsw.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppHNSW/include" -I/usr/local/include -fPIC -Wall -g -O2 -c find_kmknn.cpp -o find_kmknn.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppHNSW/include" -I/usr/local/include -fPIC -Wall -g -O2 -c find_vptree.cpp -o find_vptree.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppHNSW/include" -I/usr/local/include -fPIC -Wall -g -O2 -c hnsw.cpp -o hnsw.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppHNSW/include" -I/usr/local/include -fPIC -Wall -g -O2 -c init.cpp -o init.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppHNSW/include" -I/usr/local/include -fPIC -Wall -g -O2 -c kmknn.cpp -o kmknn.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppHNSW/include" -I/usr/local/include -fPIC -Wall -g -O2 -c neighbor_queue.cpp -o neighbor_queue.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppHNSW/include" -I/usr/local/include -fPIC -Wall -g -O2 -c query_annoy.cpp -o query_annoy.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppHNSW/include" -I/usr/local/include -fPIC -Wall -g -O2 -c query_hnsw.cpp -o query_hnsw.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppHNSW/include" -I/usr/local/include -fPIC -Wall -g -O2 -c query_kmknn.cpp -o query_kmknn.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppHNSW/include" -I/usr/local/include -fPIC -Wall -g -O2 -c query_vptree.cpp -o query_vptree.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppHNSW/include" -I/usr/local/include -fPIC -Wall -g -O2 -c range_find_kmknn.cpp -o range_find_kmknn.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppHNSW/include" -I/usr/local/include -fPIC -Wall -g -O2 -c range_find_vptree.cpp -o range_find_vptree.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppHNSW/include" -I/usr/local/include -fPIC -Wall -g -O2 -c range_query_kmknn.cpp -o range_query_kmknn.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppHNSW/include" -I/usr/local/include -fPIC -Wall -g -O2 -c range_query_vptree.cpp -o range_query_vptree.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppHNSW/include" -I/usr/local/include -fPIC -Wall -g -O2 -c utils.cpp -o utils.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppAnnoy/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppHNSW/include" -I/usr/local/include -fPIC -Wall -g -O2 -c vptree.cpp -o vptree.o clang++ -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/usr/local/lib -o BiocNeighbors.so annoy.o build_annoy.o build_hnsw.o build_vptree.o distances.o find_annoy.o find_hnsw.o find_kmknn.o find_vptree.o hnsw.o init.o kmknn.o neighbor_queue.o query_annoy.o query_hnsw.o query_kmknn.o query_vptree.o range_find_kmknn.o range_find_vptree.o range_query_kmknn.o range_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/3.6/Resources/library/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 * DONE (BiocNeighbors)
BiocNeighbors.Rcheck/tests/testthat.Rout
R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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")
══ testthat results ═══════════════════════════════════════════════════════════
OK: 2507 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
105.230 6.782 144.809
BiocNeighbors.Rcheck/BiocNeighbors-Ex.timings
| name | user | system | elapsed | |
| AnnoyIndex | 0.496 | 0.021 | 0.529 | |
| AnnoyParam | 0.009 | 0.000 | 0.009 | |
| BiocNeighbors-raw-index | 2.691 | 0.014 | 2.738 | |
| BiocNeighbors-ties | 0.007 | 0.000 | 0.008 | |
| HnswIndex | 1.114 | 0.011 | 1.134 | |
| HnswParam | 0.005 | 0.000 | 0.006 | |
| KmknnIndex | 0.481 | 0.014 | 0.501 | |
| KmknnParam | 0.005 | 0.001 | 0.006 | |
| VptreeIndex | 0.042 | 0.001 | 0.045 | |
| VptreeParam | 0.002 | 0.001 | 0.002 | |
| buildAnnoy | 0.463 | 0.018 | 0.497 | |
| buildHnsw | 1.015 | 0.009 | 1.037 | |
| buildIndex | 0.654 | 0.025 | 0.683 | |
| buildKmknn | 0.213 | 0.007 | 0.219 | |
| buildVptree | 0.024 | 0.002 | 0.027 | |
| find-methods | 4.819 | 0.083 | 4.948 | |
| findKNN | 6.223 | 0.063 | 6.355 | |
| findNeighbors | 2.594 | 0.017 | 2.653 | |
| query-methods | 2.372 | 0.058 | 2.453 | |
| queryKNN | 1.916 | 0.059 | 1.991 | |
| queryNeighbors | 0.705 | 0.007 | 0.723 | |
| rangeFind-methods | 2.513 | 0.008 | 2.547 | |
| rangeQuery-methods | 0.403 | 0.004 | 0.410 | |