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CHECK report for BiocNeighbors on tokay2

This page was generated on 2019-10-16 12:41:51 -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: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BiocNeighbors.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings BiocNeighbors_1.2.0.tar.gz
StartedAt: 2019-10-16 02:12:44 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 02:21:16 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 512.0 seconds
RetCode: 0
Status:  OK  
CheckDir: BiocNeighbors.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BiocNeighbors.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings BiocNeighbors_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/BiocNeighbors.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/BiocNeighbors/libs/i386/BiocNeighbors.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/BiocNeighbors/libs/x64/BiocNeighbors.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (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. 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
findKNN      7.68   0.05    7.72
find-methods 6.59   0.81    7.41
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
        user system elapsed
findKNN  5.1      0    5.09
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/BiocNeighbors.Rcheck/00check.log'
for details.



Installation output

BiocNeighbors.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/BiocNeighbors_1.2.0.tar.gz && rm -rf BiocNeighbors.buildbin-libdir && mkdir BiocNeighbors.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BiocNeighbors.buildbin-libdir BiocNeighbors_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL BiocNeighbors_1.2.0.zip && rm BiocNeighbors_1.2.0.tar.gz BiocNeighbors_1.2.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 56104  100 56104    0     0   840k      0 --:--:-- --:--:-- --:--:--  944k

install for i386

* installing *source* package 'BiocNeighbors' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppHNSW/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c annoy.cpp -o annoy.o
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include/annoylib.h:42:0,
                 from annoy.h:17,
                 from annoy.cpp:1:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include/mman.h: In function 'void* mmap(void*, size_t, int, int, int, off_t)':
C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include/mman.h:102:48: warning: right shift count >= width of type
                     (DWORD)0 : (DWORD)((off >> 32) & 0xFFFFFFFFL);
                                                ^
C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include/mman.h:111:52: warning: right shift count >= width of type
                     (DWORD)0 : (DWORD)((maxSize >> 32) & 0xFFFFFFFFL);
                                                    ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppHNSW/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c build_annoy.cpp -o build_annoy.o
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include/annoylib.h:42:0,
                 from annoy.h:17,
                 from build_annoy.cpp:2:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include/mman.h: In function 'void* mmap(void*, size_t, int, int, int, off_t)':
C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include/mman.h:102:48: warning: right shift count >= width of type
                     (DWORD)0 : (DWORD)((off >> 32) & 0xFFFFFFFFL);
                                                ^
C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include/mman.h:111:52: warning: right shift count >= width of type
                     (DWORD)0 : (DWORD)((maxSize >> 32) & 0xFFFFFFFFL);
                                                    ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppHNSW/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c build_hnsw.cpp -o build_hnsw.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppHNSW/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c build_vptree.cpp -o build_vptree.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppHNSW/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c distances.cpp -o distances.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppHNSW/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c find_annoy.cpp -o find_annoy.o
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include/annoylib.h:42:0,
                 from annoy.h:17,
                 from find_annoy.cpp:2:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include/mman.h: In function 'void* mmap(void*, size_t, int, int, int, off_t)':
C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include/mman.h:102:48: warning: right shift count >= width of type
                     (DWORD)0 : (DWORD)((off >> 32) & 0xFFFFFFFFL);
                                                ^
C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include/mman.h:111:52: warning: right shift count >= width of type
                     (DWORD)0 : (DWORD)((maxSize >> 32) & 0xFFFFFFFFL);
                                                    ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppHNSW/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c find_hnsw.cpp -o find_hnsw.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppHNSW/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c find_kmknn.cpp -o find_kmknn.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppHNSW/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c find_vptree.cpp -o find_vptree.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppHNSW/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c hnsw.cpp -o hnsw.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppHNSW/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c init.cpp -o init.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppHNSW/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c kmknn.cpp -o kmknn.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppHNSW/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c neighbor_queue.cpp -o neighbor_queue.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppHNSW/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c query_annoy.cpp -o query_annoy.o
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include/annoylib.h:42:0,
                 from annoy.h:17,
                 from query_annoy.cpp:2:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include/mman.h: In function 'void* mmap(void*, size_t, int, int, int, off_t)':
C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include/mman.h:102:48: warning: right shift count >= width of type
                     (DWORD)0 : (DWORD)((off >> 32) & 0xFFFFFFFFL);
                                                ^
C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include/mman.h:111:52: warning: right shift count >= width of type
                     (DWORD)0 : (DWORD)((maxSize >> 32) & 0xFFFFFFFFL);
                                                    ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppHNSW/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c query_hnsw.cpp -o query_hnsw.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppHNSW/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c query_kmknn.cpp -o query_kmknn.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppHNSW/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c query_vptree.cpp -o query_vptree.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppHNSW/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c range_find_kmknn.cpp -o range_find_kmknn.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppHNSW/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c range_find_vptree.cpp -o range_find_vptree.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppHNSW/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c range_query_kmknn.cpp -o range_query_kmknn.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppHNSW/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c range_query_vptree.cpp -o range_query_vptree.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppHNSW/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c utils.cpp -o utils.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppHNSW/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c vptree.cpp -o vptree.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o BiocNeighbors.dll tmp.def 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 -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/BiocNeighbors.buildbin-libdir/00LOCK-BiocNeighbors/00new/BiocNeighbors/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'BiocNeighbors'
    finding HTML links ... done
    AnnoyIndex                              html  
    AnnoyParam                              html  
    BiocNeighborIndex                       html  
    BiocNeighborParam                       html  
    BiocNeighbors-algorithms                html  
    BiocNeighbors-raw-index                 html  
    BiocNeighbors-ties                      html  
    HnswIndex                               html  
    HnswParam                               html  
    KmknnIndex                              html  
    KmknnParam                              html  
    VptreeIndex                             html  
    VptreeParam                             html  
    buildAnnoy                              html  
    buildHnsw                               html  
    buildIndex                              html  
    buildKmknn                              html  
    buildVptree                             html  
    find-methods                            html  
    finding level-2 HTML links ... done

    findKNN                                 html  
    findNeighbors                           html  
    query-methods                           html  
    queryKNN                                html  
    queryNeighbors                          html  
    rangeFind-methods                       html  
    rangeQuery-methods                      html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'BiocNeighbors' ...
** libs
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppHNSW/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c annoy.cpp -o annoy.o
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include/annoylib.h:42:0,
                 from annoy.h:17,
                 from annoy.cpp:1:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include/mman.h: In function 'void* mmap(void*, size_t, int, int, int, off_t)':
C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include/mman.h:102:48: warning: right shift count >= width of type
                     (DWORD)0 : (DWORD)((off >> 32) & 0xFFFFFFFFL);
                                                ^
C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include/mman.h:111:52: warning: right shift count >= width of type
                     (DWORD)0 : (DWORD)((maxSize >> 32) & 0xFFFFFFFFL);
                                                    ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppHNSW/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c build_annoy.cpp -o build_annoy.o
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include/annoylib.h:42:0,
                 from annoy.h:17,
                 from build_annoy.cpp:2:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include/mman.h: In function 'void* mmap(void*, size_t, int, int, int, off_t)':
C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include/mman.h:102:48: warning: right shift count >= width of type
                     (DWORD)0 : (DWORD)((off >> 32) & 0xFFFFFFFFL);
                                                ^
C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include/mman.h:111:52: warning: right shift count >= width of type
                     (DWORD)0 : (DWORD)((maxSize >> 32) & 0xFFFFFFFFL);
                                                    ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppHNSW/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c build_hnsw.cpp -o build_hnsw.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppHNSW/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c build_vptree.cpp -o build_vptree.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppHNSW/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c distances.cpp -o distances.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppHNSW/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c find_annoy.cpp -o find_annoy.o
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include/annoylib.h:42:0,
                 from annoy.h:17,
                 from find_annoy.cpp:2:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include/mman.h: In function 'void* mmap(void*, size_t, int, int, int, off_t)':
C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include/mman.h:102:48: warning: right shift count >= width of type
                     (DWORD)0 : (DWORD)((off >> 32) & 0xFFFFFFFFL);
                                                ^
C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include/mman.h:111:52: warning: right shift count >= width of type
                     (DWORD)0 : (DWORD)((maxSize >> 32) & 0xFFFFFFFFL);
                                                    ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppHNSW/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c find_hnsw.cpp -o find_hnsw.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppHNSW/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c find_kmknn.cpp -o find_kmknn.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppHNSW/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c find_vptree.cpp -o find_vptree.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppHNSW/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c hnsw.cpp -o hnsw.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppHNSW/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c init.cpp -o init.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppHNSW/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c kmknn.cpp -o kmknn.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppHNSW/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c neighbor_queue.cpp -o neighbor_queue.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppHNSW/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c query_annoy.cpp -o query_annoy.o
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include/annoylib.h:42:0,
                 from annoy.h:17,
                 from query_annoy.cpp:2:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include/mman.h: In function 'void* mmap(void*, size_t, int, int, int, off_t)':
C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include/mman.h:102:48: warning: right shift count >= width of type
                     (DWORD)0 : (DWORD)((off >> 32) & 0xFFFFFFFFL);
                                                ^
C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include/mman.h:111:52: warning: right shift count >= width of type
                     (DWORD)0 : (DWORD)((maxSize >> 32) & 0xFFFFFFFFL);
                                                    ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppHNSW/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c query_hnsw.cpp -o query_hnsw.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppHNSW/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c query_kmknn.cpp -o query_kmknn.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppHNSW/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c query_vptree.cpp -o query_vptree.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppHNSW/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c range_find_kmknn.cpp -o range_find_kmknn.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppHNSW/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c range_find_vptree.cpp -o range_find_vptree.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppHNSW/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c range_query_kmknn.cpp -o range_query_kmknn.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppHNSW/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c range_query_vptree.cpp -o range_query_vptree.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppHNSW/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c utils.cpp -o utils.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppAnnoy/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppHNSW/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c vptree.cpp -o vptree.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o BiocNeighbors.dll tmp.def 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 -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/BiocNeighbors.buildbin-libdir/BiocNeighbors/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BiocNeighbors' as BiocNeighbors_1.2.0.zip
* DONE (BiocNeighbors)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'BiocNeighbors' successfully unpacked and MD5 sums checked

Tests output

BiocNeighbors.Rcheck/tests_i386/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 
 112.15   13.81  184.12 

BiocNeighbors.Rcheck/tests_x64/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-w64-mingw32/x64 (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 
 102.62   13.00  174.82 

Example timings

BiocNeighbors.Rcheck/examples_i386/BiocNeighbors-Ex.timings

nameusersystemelapsed
AnnoyIndex0.840.050.89
AnnoyParam0.020.000.01
BiocNeighbors-raw-index2.710.012.73
BiocNeighbors-ties0.020.000.02
HnswIndex2.140.822.95
HnswParam000
KmknnIndex0.430.000.43
KmknnParam0.020.000.02
VptreeIndex0.050.000.05
VptreeParam000
buildAnnoy0.790.030.82
buildHnsw2.200.793.00
buildIndex1.060.021.07
buildKmknn0.250.000.25
buildVptree0.030.000.03
find-methods6.590.817.41
findKNN7.680.057.72
findNeighbors3.220.003.22
query-methods4.150.784.94
queryKNN2.520.082.59
queryNeighbors0.610.040.66
rangeFind-methods2.70.02.7
rangeQuery-methods0.410.000.41

BiocNeighbors.Rcheck/examples_x64/BiocNeighbors-Ex.timings

nameusersystemelapsed
AnnoyIndex0.420.030.45
AnnoyParam0.020.000.02
BiocNeighbors-raw-index1.670.001.67
BiocNeighbors-ties000
HnswIndex1.160.471.62
HnswParam0.010.000.02
KmknnIndex0.320.000.31
KmknnParam000
VptreeIndex0.030.000.03
VptreeParam000
buildAnnoy0.390.000.39
buildHnsw1.190.531.72
buildIndex0.510.050.56
buildKmknn0.170.000.17
buildVptree0.020.000.02
find-methods4.340.554.89
findKNN5.100.005.09
findNeighbors3.080.003.08
query-methods2.370.422.81
queryKNN1.910.031.94
queryNeighbors0.610.000.61
rangeFind-methods1.860.001.86
rangeQuery-methods0.310.000.31