##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:BiocNeighbors.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings BiocNeighbors_1.20.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/BiocNeighbors.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiocNeighbors/DESCRIPTION’ ... OK
* this is package ‘BiocNeighbors’ version ‘1.20.0’
* 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
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
  installed size is 20.2Mb
  sub-directories of 1Mb or more:
    libs  19.3Mb
* 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 loading without being on the library search path ... 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 ... WARNING
checkRd: (5) BiocNeighborIndex.Rd:24: \item in \describe must have non-empty label
checkRd: (5) BiocNeighborIndex.Rd:25: \item in \describe must have non-empty label
checkRd: (5) BiocNeighborIndex.Rd:26: \item in \describe must have non-empty label
checkRd: (5) BiocNeighborIndex.Rd:27: \item in \describe must have non-empty label
checkRd: (5) BiocNeighborParam.Rd:18: \item in \describe must have non-empty label
checkRd: (5) BiocNeighborParam.Rd:19: \item in \describe must have non-empty label
checkRd: (5) BiocNeighborParam.Rd:20: \item in \describe must have non-empty label
checkRd: (5) BiocNeighborParam.Rd:21: \item in \describe must have non-empty label
* 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 ... WARNING
Note: information on .o files is not available
File ‘/home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/libs/BiocNeighbors.so’:
  Found ‘sprintf’, possibly from ‘sprintf’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘BiocNeighbors-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: findNeighbors
> ### Title: Find all neighbors in range
> ### Aliases: findNeighbors findNeighbors-methods
> ###   findNeighbors,missing,missing-method
> ###   findNeighbors,missing,KmknnParam-method
> ###   findNeighbors,KmknnIndex,missing-method
> ###   findNeighbors,KmknnIndex,KmknnParam-method
> ###   findNeighbors,missing,VptreeParam-method
> ###   findNeighbors,VptreeIndex,missing-method
> ###   findNeighbors,VptreeIndex,VptreeParam-method
> 
> ### ** Examples
> 
> Y <- matrix(rnorm(100000), ncol=20)
> k.out <- findNeighbors(Y, threshold=3)
> a.out <- findNeighbors(Y, threshold=3, BNPARAM=VptreeParam())
> 
> k.dex <- buildKmknn(Y)
> k.out2 <- findNeighbors(Y, threshold=3, BNINDEX=k.dex)
> k.out3 <- findNeighbors(Y, threshold=3, BNINDEX=k.dex, BNPARAM=KmknnParam())
> 
> v.dex <- buildVptree(Y)
> v.out2 <- findNeighbors(Y, threshold=3, BNINDEX=v.dex)
> v.out3 <- findNeighbors(Y, threshold=3, BNINDEX=v.dex, BNPARAM=VptreeParam())
* 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 ERROR, 2 WARNINGs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/BiocNeighbors.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL BiocNeighbors
###
##############################################################################
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* installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’
* installing *source* package ‘BiocNeighbors’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 10.3.1’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppHNSW/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppHNSW/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c annoy.cpp -o annoy.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-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/R/R-4.3.1/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-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/R/R-4.3.1/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-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/R/R-4.3.1/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppHNSW/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c distances.cpp -o distances.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppHNSW/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c exhaustive.cpp -o exhaustive.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-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/R/R-4.3.1/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-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/R/R-4.3.1/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-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/R/R-4.3.1/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-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/R/R-4.3.1/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-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/R/R-4.3.1/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-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/R/R-4.3.1/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppHNSW/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c hnsw.cpp -o hnsw.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppHNSW/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c kmknn.cpp -o kmknn.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-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/R/R-4.3.1/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-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/R/R-4.3.1/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-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/R/R-4.3.1/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-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/R/R-4.3.1/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-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/R/R-4.3.1/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppHNSW/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c utils.cpp -o utils.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-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/R/R-4.3.1/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/R/R-4.3.1/lib -lR
installing to /home/biocbuild/R/R-4.3.1/site-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)

R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 494 | SKIP 2 | PASS 3289 ]

══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• out of sync with RcppAnnoy, skipping tests (2): 'test-find-annoy.R:5:1',
  'test-query-annoy.R:5:1'

[ FAIL 0 | WARN 494 | SKIP 2 | PASS 3289 ]
> 
> proc.time()
   user  system elapsed 
128.473  10.785 234.316