| Back to Multiple platform build/check report for BioC 3.17 |
|
This page was generated on 2023-04-12 10:55:34 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the BiocNeighbors package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 180/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BiocNeighbors 1.17.1 (landing page) Aaron Lun
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | WARNINGS | ||||||||||
| Package: BiocNeighbors |
| Version: 1.17.1 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:BiocNeighbors.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings BiocNeighbors_1.17.1.tar.gz |
| StartedAt: 2023-04-12 04:56:27 -0400 (Wed, 12 Apr 2023) |
| EndedAt: 2023-04-12 05:02:04 -0400 (Wed, 12 Apr 2023) |
| EllapsedTime: 337.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: BiocNeighbors.Rcheck |
| Warnings: 2 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:BiocNeighbors.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings BiocNeighbors_1.17.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/BiocNeighbors.Rcheck’
* using R Under development (unstable) (2023-02-14 r83833)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
* running under: Ubuntu 20.04.6 LTS
* using session charset: UTF-8
* checking for file ‘BiocNeighbors/DESCRIPTION’ ... OK
* this is package ‘BiocNeighbors’ version ‘1.17.1’
* 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++ (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
installed size is 22.1Mb
sub-directories of 1Mb or more:
libs 21.2Mb
* 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/bbs-3.17-bioc/R/site-library/BiocNeighbors/libs/BiocNeighbors.so’:
Found ‘__sprintf_chk’, 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
findNeighbors-functions 6.324 0.512 6.836
findKNN-methods 5.572 0.120 5.692
findNeighbors-methods 5.474 0.008 5.482
* 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 ...
‘approx.Rmd’ using ‘UTF-8’... OK
‘exact.Rmd’ using ‘UTF-8’... OK
‘range.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 WARNINGs, 2 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/BiocNeighbors.Rcheck/00check.log’
for details.
BiocNeighbors.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL BiocNeighbors ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’ * installing *source* package ‘BiocNeighbors’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0’ using C++11 g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-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-3.17-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.17-bioc/R/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)
BiocNeighbors.Rcheck/tests/testthat.Rout
R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences"
Copyright (C) 2023 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 494 | SKIP 0 | PASS 3516 ]
[ FAIL 0 | WARN 494 | SKIP 0 | PASS 3516 ]
>
> proc.time()
user system elapsed
128.686 6.355 206.325
BiocNeighbors.Rcheck/BiocNeighbors-Ex.timings
| name | user | system | elapsed | |
| AnnoyIndex | 0.422 | 0.016 | 0.439 | |
| AnnoyParam | 0.013 | 0.000 | 0.013 | |
| BiocNeighbors-raw-index | 1.560 | 0.008 | 1.567 | |
| BiocNeighbors-ties | 0.013 | 0.000 | 0.012 | |
| ExhaustiveIndex | 0.013 | 0.004 | 0.017 | |
| ExhaustiveParam | 0.001 | 0.000 | 0.002 | |
| HnswIndex | 0.865 | 0.008 | 0.872 | |
| HnswParam | 0.007 | 0.000 | 0.007 | |
| KmknnIndex | 0.186 | 0.016 | 0.203 | |
| KmknnParam | 0.003 | 0.000 | 0.004 | |
| VptreeIndex | 0.034 | 0.000 | 0.034 | |
| VptreeParam | 0.002 | 0.000 | 0.002 | |
| buildAnnoy | 0.367 | 0.000 | 0.368 | |
| buildExhaustive | 0.008 | 0.000 | 0.009 | |
| buildHnsw | 0.812 | 0.000 | 0.813 | |
| buildIndex | 0.540 | 0.008 | 0.549 | |
| buildKmknn | 0.176 | 0.000 | 0.177 | |
| buildVptree | 0.021 | 0.000 | 0.021 | |
| findKNN-functions | 4.273 | 0.064 | 4.338 | |
| findKNN-methods | 5.572 | 0.120 | 5.692 | |
| findMutualNN | 0.033 | 0.016 | 0.049 | |
| findNeighbors-functions | 6.324 | 0.512 | 6.836 | |
| findNeighbors-methods | 5.474 | 0.008 | 5.482 | |
| queryKNN-functions | 1.937 | 0.040 | 1.978 | |
| queryKNN-methods | 1.549 | 0.044 | 1.594 | |
| queryNeighbors-functions | 0.421 | 0.016 | 0.437 | |
| queryNeighbors-methods | 0.924 | 0.024 | 0.949 | |