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This page was generated on 2021-12-03 13:04:52 -0500 (Fri, 03 Dec 2021).

CHECK results for mbkmeans on nebbiolo2

To the developers/maintainers of the mbkmeans package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/mbkmeans.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1064/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mbkmeans 1.10.0  (landing page)
Davide Risso
Snapshot Date: 2021-12-02 01:55:06 -0500 (Thu, 02 Dec 2021)
git_url: https://git.bioconductor.org/packages/mbkmeans
git_branch: RELEASE_3_14
git_last_commit: 1503619
git_last_commit_date: 2021-10-26 12:50:45 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 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: mbkmeans
Version: 1.10.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:mbkmeans.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings mbkmeans_1.10.0.tar.gz
StartedAt: 2021-12-02 07:50:14 -0500 (Thu, 02 Dec 2021)
EndedAt: 2021-12-02 07:55:18 -0500 (Thu, 02 Dec 2021)
EllapsedTime: 304.0 seconds
RetCode: 0
Status:   OK  
CheckDir: mbkmeans.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:mbkmeans.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings mbkmeans_1.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/mbkmeans.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘1.10.0’
* 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 ... NOTE
  installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
* 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 ... NOTE
Namespace in Imports field not imported from: ‘S4Vectors’
  All declared Imports should be used.
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/mbkmeans.Rcheck/00check.log’
for details.



Installation output

mbkmeans.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL mbkmeans
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘mbkmeans’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/beachmat/include' -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/beachmat/include' -I'/home/biocbuild/bbs-3.14-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:
/home/biocbuild/bbs-3.14-bioc/R/library/ClusterR/include/ClusterRHeader.h: In member function ‘arma::mat clustR::ClustHeader::KMEANS_arma(arma::mat&, int, int, bool, std::string, Rcpp::Nullable<Rcpp::Matrix<14> >, int)’:
/home/biocbuild/bbs-3.14-bioc/R/library/ClusterR/include/ClusterRHeader.h:850:14: warning: variable ‘status’ set but not used [-Wunused-but-set-variable]
  850 |         bool status;
      |              ^~~~~~
/home/biocbuild/bbs-3.14-bioc/R/library/ClusterR/include/ClusterRHeader.h: In member function ‘Rcpp::List clustR::ClustHeader::GMM_arma(arma::mat&, int, std::string, std::string, int, int, bool, double, int)’:
/home/biocbuild/bbs-3.14-bioc/R/library/ClusterR/include/ClusterRHeader.h:1446:14: warning: variable ‘status’ set but not used [-Wunused-but-set-variable]
 1446 |         bool status;
      |              ^~~~~~
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.14-bioc/R/lib -L/usr/local/lib -o mbkmeans.so RcppExports.o mini_batch.o -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-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)

Tests output

mbkmeans.Rcheck/tests/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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(mbkmeans)
> 
> test_check("mbkmeans")
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 29 ]
> 
> proc.time()
   user  system elapsed 
143.167  23.717 166.872 

Example timings

mbkmeans.Rcheck/mbkmeans-Ex.timings

nameusersystemelapsed
blocksize000
compute_wcss0.0010.0000.000
mbkmeans0.7240.0120.736
mini_batch000
predict_mini_batch0.0040.0000.004
predict_mini_batch_r0.0110.0000.011