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This page was generated on 2024-06-11 15:40 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
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

Package 1147/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mbkmeans 1.21.0  (landing page)
Davide Risso
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/mbkmeans
git_branch: devel
git_last_commit: 8980ffa
git_last_commit_date: 2024-04-30 11:13:46 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for mbkmeans on palomino4

To the developers/maintainers of the mbkmeans package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: mbkmeans
Version: 1.21.0
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:mbkmeans.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings mbkmeans_1.21.0.tar.gz
StartedAt: 2024-06-10 04:51:27 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 05:00:04 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 517.0 seconds
RetCode: 0
Status:   OK  
CheckDir: mbkmeans.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:mbkmeans.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings mbkmeans_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/mbkmeans.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'mbkmeans/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'mbkmeans' version '1.21.0'
* 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
* used C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 'F:/biocbuild/bbs-3.20-bioc/R/library/mbkmeans/libs/x64/mbkmeans.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

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
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  'F:/biocbuild/bbs-3.20-bioc/meat/mbkmeans.Rcheck/00check.log'
for details.


Installation output

mbkmeans.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL mbkmeans
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'mbkmeans' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
using C++11
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhdf5lib/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/beachmat/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/ClusterR/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhdf5lib/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/beachmat/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/ClusterR/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c mini_batch.cpp -o mini_batch.o
In file included from F:/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include/armadillo:26,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:29,
                 from mini_batch.cpp:2:
F:/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include/armadillo_bits/config.hpp:326:86: note: '#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed'
  326 |   #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed")
      |                                                                                      ^
F:/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include/armadillo_bits/config.hpp:331:75: note: '#pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead'
  331 |     #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead")
      |                                                                           ^
F:/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include/armadillo_bits/config.hpp:334:61: note: '#pragma message: INFO: see the documentation for details'
  334 |   #pragma message ("INFO: see the documentation for details")
      |                                                             ^
In file included from mini_batch.cpp:3:
F:/biocbuild/bbs-3.20-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)':
F:/biocbuild/bbs-3.20-bioc/R/library/ClusterR/include/ClusterRHeader.h:862:14: warning: variable 'status' set but not used [-Wunused-but-set-variable]
  862 |         bool status;
      |              ^~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/ClusterR/include/ClusterRHeader.h: In instantiation of 'T clustR::ClustHeader::GMM_arma_covariance_type(T, arma::mat&, int, std::string, std::string, int, int, bool, double, int) [with T = arma::gmm_priv::gmm_full<double>; arma::mat = arma::Mat<double>; std::string = std::__cxx11::basic_string<char>]':
F:/biocbuild/bbs-3.20-bioc/R/library/ClusterR/include/ClusterRHeader.h:1592:65:   required from here
F:/biocbuild/bbs-3.20-bioc/R/library/ClusterR/include/ClusterRHeader.h:1530:14: warning: variable 'status' set but not used [-Wunused-but-set-variable]
 1530 |         bool status;
      |              ^~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/ClusterR/include/ClusterRHeader.h: In instantiation of 'T clustR::ClustHeader::GMM_arma_covariance_type(T, arma::mat&, int, std::string, std::string, int, int, bool, double, int) [with T = arma::gmm_priv::gmm_diag<double>; arma::mat = arma::Mat<double>; std::string = std::__cxx11::basic_string<char>]':
F:/biocbuild/bbs-3.20-bioc/R/library/ClusterR/include/ClusterRHeader.h:1626:65:   required from here
F:/biocbuild/bbs-3.20-bioc/R/library/ClusterR/include/ClusterRHeader.h:1530:14: warning: variable 'status' set but not used [-Wunused-but-set-variable]
g++ -shared -s -static-libgcc -o mbkmeans.dll tmp.def RcppExports.o mini_batch.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-mbkmeans/00new/mbkmeans/libs/x64
** 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
** 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 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 
 140.04   27.85  168.21 

Example timings

mbkmeans.Rcheck/mbkmeans-Ex.timings

nameusersystemelapsed
blocksize000
compute_wcss000
mbkmeans0.611.271.93
mini_batch000
predict_mini_batch0.030.030.07
predict_mini_batch_r0.020.020.03