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CHECK report for BiocNeighbors on malbec1

This page was generated on 2020-08-07 11:37:41 -0400 (Fri, 07 Aug 2020).

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 154/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocNeighbors 1.7.0
Aaron Lun
Snapshot Date: 2020-08-06 14:50:46 -0400 (Thu, 06 Aug 2020)
URL: https://git.bioconductor.org/packages/BiocNeighbors
Branch: master
Last Commit: 1dcfaf3
Last Changed Date: 2020-04-27 15:17:53 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BiocNeighbors
Version: 1.7.0
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_1.7.0.tar.gz
StartedAt: 2020-08-07 04:00:22 -0400 (Fri, 07 Aug 2020)
EndedAt: 2020-08-07 04:05:31 -0400 (Fri, 07 Aug 2020)
EllapsedTime: 308.3 seconds
RetCode: 0
Status:  OK 
CheckDir: BiocNeighbors.Rcheck
Warnings: 0

Command output

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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_1.7.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/BiocNeighbors.Rcheck’
* using R version 4.0.2 (2020-06-22)
* 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 ‘1.7.0’
* 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 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 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
rangeFind-methods 7.612  0.344   7.964
findKNN           7.480  0.012   7.502
findNeighbors     7.068  0.000   7.082
* 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.



Installation output

BiocNeighbors.Rcheck/00install.out

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###
### 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'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppAnnoy/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'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppAnnoy/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'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppAnnoy/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'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppAnnoy/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'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppAnnoy/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'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppAnnoy/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'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppAnnoy/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'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppAnnoy/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'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppAnnoy/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'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppAnnoy/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'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppAnnoy/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'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppAnnoy/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'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppAnnoy/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'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppAnnoy/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'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppAnnoy/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'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppAnnoy/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'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppAnnoy/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'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppAnnoy/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'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppAnnoy/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'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppAnnoy/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'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppAnnoy/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)

Tests output

BiocNeighbors.Rcheck/tests/testthat.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 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")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 3441 | SKIPPED: 0 | WARNINGS: 44 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
119.824   5.328 199.219 

Example timings

BiocNeighbors.Rcheck/BiocNeighbors-Ex.timings

nameusersystemelapsed
AnnoyIndex0.6000.0040.606
AnnoyParam0.0120.0000.012
BiocNeighbors-raw-index2.3720.0042.378
BiocNeighbors-ties0.0080.0000.006
ExhaustiveIndex0.0120.0040.017
ExhaustiveParam0.0040.0000.003
HnswIndex1.1840.0001.187
HnswParam0.0040.0000.005
KmknnIndex0.4560.0000.459
KmknnParam0.0000.0000.003
VptreeIndex0.0280.0000.028
VptreeParam0.0000.0000.002
buildAnnoy0.4160.0080.426
buildExhaustive0.0160.0000.015
buildHnsw1.2120.0001.212
buildIndex0.6160.0080.626
buildKmknn0.1960.0000.199
buildVptree0.0200.0000.018
find-methods4.9560.0124.975
findKNN7.4800.0127.502
findNeighbors7.0680.0007.082
query-methods2.2320.0042.235
queryKNN1.6240.0081.633
queryNeighbors0.8920.0000.892
rangeFind-methods7.6120.3447.964
rangeQuery-methods0.6000.0040.606