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CHECK report for BiocNeighbors on malbec2

This page was generated on 2019-10-16 12:15:15 -0400 (Wed, 16 Oct 2019).

Package 147/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocNeighbors 1.2.0
Aaron Lun
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/BiocNeighbors
Branch: RELEASE_3_9
Last Commit: f754c63
Last Changed Date: 2019-05-02 11:54:12 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BiocNeighbors
Version: 1.2.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:BiocNeighbors.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings BiocNeighbors_1.2.0.tar.gz
StartedAt: 2019-10-16 00:05:38 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 00:08:58 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 200.2 seconds
RetCode: 0
Status:  OK 
CheckDir: BiocNeighbors.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:BiocNeighbors.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings BiocNeighbors_1.2.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/BiocNeighbors.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.2.0’
* 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 13.6Mb
  sub-directories of 1Mb or more:
    libs  13.2Mb
* 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      5.429  0.004   5.434
find-methods 5.345  0.020   5.503
* 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-3.9-bioc/meat/BiocNeighbors.Rcheck/00check.log’
for details.



Installation output

BiocNeighbors.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL BiocNeighbors
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘BiocNeighbors’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppHNSW/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c init.cpp -o init.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppHNSW/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c neighbor_queue.cpp -o neighbor_queue.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppHNSW/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c range_find_kmknn.cpp -o range_find_kmknn.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppHNSW/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c range_find_vptree.cpp -o range_find_vptree.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppHNSW/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c range_query_kmknn.cpp -o range_query_kmknn.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppHNSW/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c range_query_vptree.cpp -o range_query_vptree.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/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 -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-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 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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: 2503 | SKIPPED: 0 | WARNINGS: 34 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 92.285   3.400 125.410 

Example timings

BiocNeighbors.Rcheck/BiocNeighbors-Ex.timings

nameusersystemelapsed
AnnoyIndex0.6320.0160.649
AnnoyParam0.0140.0000.014
BiocNeighbors-raw-index2.4220.0002.422
BiocNeighbors-ties0.0070.0000.007
HnswIndex1.0980.0001.098
HnswParam0.0030.0000.003
KmknnIndex0.3010.0080.309
KmknnParam0.0030.0000.003
VptreeIndex0.0250.0000.026
VptreeParam0.0020.0000.002
buildAnnoy0.3500.0040.354
buildHnsw1.0400.0031.043
buildIndex0.7460.0080.755
buildKmknn0.2460.0000.245
buildVptree0.0240.0000.025
find-methods5.3450.0205.503
findKNN5.4290.0045.434
findNeighbors2.3540.0002.354
query-methods2.4080.0162.425
queryKNN2.0600.0122.072
queryNeighbors0.6520.0000.652
rangeFind-methods2.2170.0002.217
rangeQuery-methods0.3140.0000.314