Aaron Lun
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/BiocNeighbors |
| Branch: RELEASE_3_10 |
| Last Commit: 1fcb470 |
| Last Changed Date: 2020-02-29 00:44:32 -0400 (Sat, 29 Feb 2020) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:14:27 -0400 (Wed, 15 Apr 2020).
| Package 153/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| BiocNeighbors 1.4.2 Aaron Lun
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: BiocNeighbors |
| Version: 1.4.2 |
| Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:BiocNeighbors.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings BiocNeighbors_1.4.2.tar.gz |
| StartedAt: 2020-04-15 05:51:35 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 05:56:22 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 286.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: BiocNeighbors.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:BiocNeighbors.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings BiocNeighbors_1.4.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/BiocNeighbors.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.4.2’
* 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 ... WARNING
Found the following significant warnings:
kmknn.h:37:31: warning: ‘Kmknn<BNManhattan>::centers’ will be initialized after [-Wreorder]
kmknn.h:33:20: warning: ‘neighbor_queue Kmknn<BNManhattan>::nearest’ [-Wreorder]
kmknn.cpp:13:1: warning: when initialized here [-Wreorder]
kmknn.h:37:31: warning: ‘Kmknn<BNEuclidean>::centers’ will be initialized after [-Wreorder]
kmknn.h:33:20: warning: ‘neighbor_queue Kmknn<BNEuclidean>::nearest’ [-Wreorder]
See ‘/home/biocbuild/bbs-3.10-bioc/meat/BiocNeighbors.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
installed size is 10.4Mb
sub-directories of 1Mb or more:
libs 10.0Mb
* 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
findNeighbors 7.484 0.004 7.579
findKNN 6.064 0.020 6.097
rangeFind-methods 5.200 0.224 5.428
find-methods 5.396 0.004 5.467
* 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 WARNING, 2 NOTEs
See
‘/home/biocbuild/bbs-3.10-bioc/meat/BiocNeighbors.Rcheck/00check.log’
for details.
BiocNeighbors.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL BiocNeighbors
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘BiocNeighbors’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RcppAnnoy/include" -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RcppAnnoy/include" -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RcppAnnoy/include" -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RcppAnnoy/include" -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RcppAnnoy/include" -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RcppAnnoy/include" -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RcppAnnoy/include" -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RcppAnnoy/include" -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RcppAnnoy/include" -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RcppAnnoy/include" -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RcppAnnoy/include" -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RcppAnnoy/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RcppHNSW/include" -I/usr/local/include -fpic -g -O2 -Wall -c kmknn.cpp -o kmknn.o
In file included from kmknn.cpp:1:0:
kmknn.cpp: In instantiation of ‘Kmknn<Distance>::Kmknn(Rcpp::NumericMatrix, Rcpp::NumericMatrix, Rcpp::List, bool) [with Distance = BNManhattan; Rcpp::NumericMatrix = Rcpp::Matrix<14>; Rcpp::List = Rcpp::Vector<19>]’:
kmknn.cpp:218:16: required from here
kmknn.h:37:31: warning: ‘Kmknn<BNManhattan>::centers’ will be initialized after [-Wreorder]
const Rcpp::NumericMatrix centers;
^~~~~~~
kmknn.h:33:20: warning: ‘neighbor_queue Kmknn<BNManhattan>::nearest’ [-Wreorder]
neighbor_queue nearest;
^~~~~~~
kmknn.cpp:13:1: warning: when initialized here [-Wreorder]
Kmknn<Distance>::Kmknn(Rcpp::NumericMatrix ex, Rcpp::NumericMatrix cen, Rcpp::List info, bool warn_ties) :
^~~~~~~~~~~~~~~
In file included from kmknn.cpp:1:0:
kmknn.cpp: In instantiation of ‘Kmknn<Distance>::Kmknn(Rcpp::NumericMatrix, Rcpp::NumericMatrix, Rcpp::List, bool) [with Distance = BNEuclidean; Rcpp::NumericMatrix = Rcpp::Matrix<14>; Rcpp::List = Rcpp::Vector<19>]’:
kmknn.cpp:219:16: required from here
kmknn.h:37:31: warning: ‘Kmknn<BNEuclidean>::centers’ will be initialized after [-Wreorder]
const Rcpp::NumericMatrix centers;
^~~~~~~
kmknn.h:33:20: warning: ‘neighbor_queue Kmknn<BNEuclidean>::nearest’ [-Wreorder]
neighbor_queue nearest;
^~~~~~~
kmknn.cpp:13:1: warning: when initialized here [-Wreorder]
Kmknn<Distance>::Kmknn(Rcpp::NumericMatrix ex, Rcpp::NumericMatrix cen, Rcpp::List info, bool warn_ties) :
^~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RcppAnnoy/include" -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RcppAnnoy/include" -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RcppAnnoy/include" -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RcppAnnoy/include" -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RcppAnnoy/include" -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RcppAnnoy/include" -I"/home/biocbuild/bbs-3.10-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-3.10-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 find_annoy.o find_hnsw.o find_kmknn.o find_vptree.o hnsw.o kmknn.o query_annoy.o query_hnsw.o query_kmknn.o query_vptree.o utils.o vptree.o -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.10-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)
BiocNeighbors.Rcheck/tests/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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: 2876 | SKIPPED: 0 | WARNINGS: 34 | FAILED: 0 ]
>
> proc.time()
user system elapsed
120.468 4.236 183.251
BiocNeighbors.Rcheck/BiocNeighbors-Ex.timings
| name | user | system | elapsed | |
| AnnoyIndex | 0.508 | 0.020 | 0.541 | |
| AnnoyParam | 0.016 | 0.000 | 0.016 | |
| BiocNeighbors-raw-index | 2.040 | 0.004 | 2.047 | |
| BiocNeighbors-ties | 0.008 | 0.000 | 0.009 | |
| HnswIndex | 1.032 | 0.004 | 1.042 | |
| HnswParam | 0.000 | 0.000 | 0.004 | |
| KmknnIndex | 0.444 | 0.000 | 0.461 | |
| KmknnParam | 0.004 | 0.000 | 0.004 | |
| VptreeIndex | 0.028 | 0.000 | 0.029 | |
| VptreeParam | 0.004 | 0.000 | 0.002 | |
| buildAnnoy | 0.552 | 0.008 | 0.583 | |
| buildHnsw | 1.268 | 0.004 | 1.270 | |
| buildIndex | 0.824 | 0.004 | 0.829 | |
| buildKmknn | 0.264 | 0.000 | 0.264 | |
| buildVptree | 0.028 | 0.000 | 0.027 | |
| find-methods | 5.396 | 0.004 | 5.467 | |
| findKNN | 6.064 | 0.020 | 6.097 | |
| findNeighbors | 7.484 | 0.004 | 7.579 | |
| query-methods | 2.656 | 0.008 | 2.670 | |
| queryKNN | 1.820 | 0.012 | 1.839 | |
| queryNeighbors | 1.044 | 0.000 | 1.045 | |
| rangeFind-methods | 5.200 | 0.224 | 5.428 | |
| rangeQuery-methods | 0.376 | 0.004 | 0.380 | |