Aaron Lun
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/BiocNeighbors |
| Branch: RELEASE_3_8 |
| Last Commit: e252fc0 |
| Last Changed Date: 2018-10-30 11:42:09 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:53:38 -0400 (Tue, 16 Apr 2019).
| Package 139/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| BiocNeighbors 1.0.0 Aaron Lun
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: BiocNeighbors |
| Version: 1.0.0 |
| Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:BiocNeighbors.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings BiocNeighbors_1.0.0.tar.gz |
| StartedAt: 2019-04-15 22:28:51 -0400 (Mon, 15 Apr 2019) |
| EndedAt: 2019-04-15 22:30:52 -0400 (Mon, 15 Apr 2019) |
| EllapsedTime: 121.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BiocNeighbors.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:BiocNeighbors.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings BiocNeighbors_1.0.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/BiocNeighbors.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.0.0’
* 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 ... 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
* 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 7.06 0 7.065
* 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 NOTE
See
‘/home/biocbuild/bbs-3.8-bioc/meat/BiocNeighbors.Rcheck/00check.log’
for details.
BiocNeighbors.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL BiocNeighbors
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘BiocNeighbors’ ...
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppAnnoy/include" -I/usr/local/include -fpic -g -O2 -Wall -c annoy_stubs.cpp -o annoy_stubs.o
In file included from annoy_stubs.cpp:5:0:
query_annoy.h: In function ‘SEXPREC* query_annoy(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
query_annoy.h:12:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (size_t(Query.nrow())!=Ndim) {
^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppAnnoy/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-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppAnnoy/include" -I/usr/local/include -fpic -g -O2 -Wall -c find_neighbors.cpp -o find_neighbors.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppAnnoy/include" -I/usr/local/include -fpic -g -O2 -Wall -c init.cpp -o init.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppAnnoy/include" -I/usr/local/include -fpic -g -O2 -Wall -c kmknn.cpp -o kmknn.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppAnnoy/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-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppAnnoy/include" -I/usr/local/include -fpic -g -O2 -Wall -c query_neighbors.cpp -o query_neighbors.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppAnnoy/include" -I/usr/local/include -fpic -g -O2 -Wall -c utils.cpp -o utils.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o BiocNeighbors.so annoy_stubs.o find_kmknn.o find_neighbors.o init.o kmknn.o query_kmknn.o query_neighbors.o utils.o -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/library/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
* DONE (BiocNeighbors)
BiocNeighbors.Rcheck/tests/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
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)
Loading required package: BiocParallel
> test_check("BiocNeighbors")
══ testthat results ═══════════════════════════════════════════════════════════
OK: 1145 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
44.396 1.172 61.093
BiocNeighbors.Rcheck/BiocNeighbors-Ex.timings
| name | user | system | elapsed | |
| AnnoyIndex | 0.668 | 0.004 | 0.672 | |
| AnnoyParam | 0.012 | 0.000 | 0.011 | |
| KmknnIndex | 0.228 | 0.004 | 0.256 | |
| KmknnParam | 0.000 | 0.000 | 0.002 | |
| buildAnnoy | 0.628 | 0.004 | 0.635 | |
| buildKmknn | 0.280 | 0.004 | 0.284 | |
| buildNNIndex | 0.828 | 0.000 | 0.828 | |
| findAnnoy | 2.052 | 0.004 | 2.058 | |
| findKNN | 7.060 | 0.000 | 7.065 | |
| findKmknn | 1.340 | 0.012 | 1.380 | |
| findNeighbors | 1.160 | 0.004 | 1.164 | |
| queryAnnoy | 0.808 | 0.000 | 0.811 | |
| queryKNN | 1.912 | 0.008 | 1.925 | |
| queryKmknn | 0.464 | 0.000 | 0.487 | |
| queryNeighbors | 0.332 | 0.000 | 0.332 | |