Package: mbkmeans

Version: 1.2.0

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:mbkmeans.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings mbkmeans_1.2.0.tar.gz

StartedAt: 2020-04-15 06:26:30 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 06:29:27 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 176.6 seconds

RetCode: 0

Status:  OK

CheckDir: mbkmeans.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:mbkmeans.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings mbkmeans_1.2.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/mbkmeans.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 ‘mbkmeans/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mbkmeans’ version ‘1.2.0’
* package encoding: UTF-8
* 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 ‘mbkmeans’ 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
* 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-3.10-bioc/meat/mbkmeans.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL mbkmeans
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘mbkmeans’ ...
** 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/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rhdf5lib/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/ClusterR/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/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rhdf5lib/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/ClusterR/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c mini_batch.cpp -o mini_batch.o
In file included from mini_batch.cpp:3:0:
/home/biocbuild/bbs-3.10-bioc/R/library/ClusterR/include/ClusterRHeader.h: In member function ‘arma::mat clustR::ClustHeader::KMEANS_arma(arma::mat&, int, int, bool, std::__cxx11::string, Rcpp::Nullable<Rcpp::Matrix<14> >, int)’:
/home/biocbuild/bbs-3.10-bioc/R/library/ClusterR/include/ClusterRHeader.h:837:14: warning: variable ‘status’ set but not used [-Wunused-but-set-variable]
         bool status;
              ^~~~~~
/home/biocbuild/bbs-3.10-bioc/R/library/ClusterR/include/ClusterRHeader.h: In member function ‘Rcpp::List clustR::ClustHeader::GMM_arma(arma::mat&, int, std::__cxx11::string, std::__cxx11::string, int, int, bool, double, int)’:
/home/biocbuild/bbs-3.10-bioc/R/library/ClusterR/include/ClusterRHeader.h:1433:14: warning: variable ‘status’ set but not used [-Wunused-but-set-variable]
         bool status;
              ^~~~~~
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.10-bioc/R/lib -L/usr/local/lib -o mbkmeans.so RcppExports.o mini_batch.o -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.10-bioc/R/library/00LOCK-mbkmeans/00new/mbkmeans/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 (mbkmeans)

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(mbkmeans)
> 
> test_check("mbkmeans")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 19 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  9.140   0.248   9.411 

name	user	system	elapsed
blocksize	0	0	0
compute_wcss	0.000	0.000	0.001
mbkmeans	0.540	0.004	0.548
mini_batch	0	0	0
predict_mini_batch	0.008	0.000	0.005