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This page was generated on 2022-03-18 11:07:56 -0400 (Fri, 18 Mar 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" 4334
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4097
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" 4083
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" 4134
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

CHECK results for mbkmeans on riesling1


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 1068/2090HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mbkmeans 1.11.0  (landing page)
Davide Risso
Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022)
git_url: https://git.bioconductor.org/packages/mbkmeans
git_branch: master
git_last_commit: 656214a
git_last_commit_date: 2021-10-26 12:50:45 -0400 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: mbkmeans
Version: 1.11.0
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:mbkmeans.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings mbkmeans_1.11.0.tar.gz
StartedAt: 2022-03-17 19:29:49 -0400 (Thu, 17 Mar 2022)
EndedAt: 2022-03-17 19:35:51 -0400 (Thu, 17 Mar 2022)
EllapsedTime: 361.7 seconds
RetCode: 0
Status:   OK  
CheckDir: mbkmeans.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:mbkmeans.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings mbkmeans_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/mbkmeans.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'mbkmeans/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'mbkmeans' version '1.11.0'
* 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 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 ... 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 for x64 is not available
File 'D:/biocbuild/bbs-3.15-bioc/R/library/mbkmeans/libs/x64/mbkmeans.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (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. 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
* 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: 2 NOTEs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/mbkmeans.Rcheck/00check.log'
for details.



Installation output

mbkmeans.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL mbkmeans
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'mbkmeans' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/ClusterR/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/ClusterR/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c mini_batch.cpp -o mini_batch.o
In file included from mini_batch.cpp:3:
D:/biocbuild/bbs-3.15-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)':
D:/biocbuild/bbs-3.15-bioc/R/library/ClusterR/include/ClusterRHeader.h:926:14: warning: variable 'status' set but not used [-Wunused-but-set-variable]
         bool status;
              ^~~~~~
D:/biocbuild/bbs-3.15-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)':
D:/biocbuild/bbs-3.15-bioc/R/library/ClusterR/include/ClusterRHeader.h:1522:14: warning: variable 'status' set but not used [-Wunused-but-set-variable]
         bool status;
              ^~~~~~
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o mbkmeans.dll tmp.def RcppExports.o mini_batch.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-mbkmeans/00new/mbkmeans/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'mbkmeans'
    finding HTML links ... done
    MbkmeansParam                           html  
    blocksize                               html  
    clusterRows                             html  
    compute_wcss                            html  
    mbkmeans                                html  
    mini_batch                              html  
    predict_mini_batch                      html  
    predict_mini_batch_r                    html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (mbkmeans)
Making 'packages.html' ... done

Tests output

mbkmeans.Rcheck/tests/testthat.Rout


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 29 ]
> 
> proc.time()
   user  system elapsed 
 130.34   92.14  223.06 

Example timings

mbkmeans.Rcheck/mbkmeans-Ex.timings

nameusersystemelapsed
blocksize000
compute_wcss000
mbkmeans0.440.030.47
mini_batch000
predict_mini_batch0.000.010.01
predict_mini_batch_r0.020.000.02