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This page was generated on 2021-09-24 15:05:40 -0400 (Fri, 24 Sep 2021).

CHECK results for BiocNeighbors on nebbiolo1

To the developers/maintainers of the BiocNeighbors package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BiocNeighbors.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
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raw results

Package 165/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocNeighbors 1.10.0  (landing page)
Aaron Lun
Snapshot Date: 2021-09-23 04:50:12 -0400 (Thu, 23 Sep 2021)
git_url: https://git.bioconductor.org/packages/BiocNeighbors
git_branch: RELEASE_3_13
git_last_commit: c6779d6
git_last_commit_date: 2021-05-19 12:36:35 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: BiocNeighbors
Version: 1.10.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:BiocNeighbors.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings BiocNeighbors_1.10.0.tar.gz
StartedAt: 2021-09-23 08:59:26 -0400 (Thu, 23 Sep 2021)
EndedAt: 2021-09-23 09:03:57 -0400 (Thu, 23 Sep 2021)
EllapsedTime: 271.1 seconds
RetCode: 0
Status:   OK  
CheckDir: BiocNeighbors.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:BiocNeighbors.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings BiocNeighbors_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/BiocNeighbors.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.10.0’
* 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  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
* 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 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 ... 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
findNeighbors-functions 6.068  0.508   6.586
findNeighbors-methods   5.531  0.004   5.535
findKNN-methods         5.294  0.027   5.325
* 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-3.13-bioc/meat/BiocNeighbors.Rcheck/00check.log’
for details.



Installation output

BiocNeighbors.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL BiocNeighbors
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘BiocNeighbors’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/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/bbs-3.13-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-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-3.13-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_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/bbs-3.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.13-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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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")
[ FAIL 0 | WARN 488 | SKIP 0 | PASS 3516 ]
> 
> proc.time()
   user  system elapsed 
108.065   6.223 184.058 

Example timings

BiocNeighbors.Rcheck/BiocNeighbors-Ex.timings

nameusersystemelapsed
AnnoyIndex0.3890.0160.405
AnnoyParam0.0140.0000.014
BiocNeighbors-raw-index1.4140.0041.418
BiocNeighbors-ties0.0120.0000.013
ExhaustiveIndex0.0170.0000.018
ExhaustiveParam0.0020.0000.003
HnswIndex0.7830.0040.788
HnswParam0.0070.0000.008
KmknnIndex0.1890.0600.249
KmknnParam0.0040.0000.004
VptreeIndex0.0250.0040.030
VptreeParam0.0020.0000.002
buildAnnoy0.3480.0030.352
buildExhaustive0.0090.0000.009
buildHnsw0.7930.0000.794
buildIndex0.5220.0080.530
buildKmknn0.1820.0000.182
buildVptree0.0120.0040.017
findKNN-functions4.0560.0244.081
findKNN-methods5.2940.0275.325
findMutualNN0.0250.0030.029
findNeighbors-functions6.0680.5086.586
findNeighbors-methods5.5310.0045.535
queryKNN-functions2.0390.0172.055
queryKNN-methods1.5090.0021.511
queryNeighbors-functions0.4190.0040.423
queryNeighbors-methods0.8880.0040.892