Davide Risso
| Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/mbkmeans |
| git_branch: devel |
| git_last_commit: a741aba |
| git_last_commit_date: 2023-10-24 11:12:38 -0400 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-28 11:40:55 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
| 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 1164/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| mbkmeans 1.19.0 (landing page) Davide Risso
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: mbkmeans |
| Version: 1.19.0 |
| Command: /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:mbkmeans.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings mbkmeans_1.19.0.tar.gz |
| StartedAt: 2024-03-28 06:55:27 -0000 (Thu, 28 Mar 2024) |
| EndedAt: 2024-03-28 07:09:02 -0000 (Thu, 28 Mar 2024) |
| EllapsedTime: 814.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: mbkmeans.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:mbkmeans.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings mbkmeans_1.19.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/mbkmeans.Rcheck’
* using R Under development (unstable) (2024-03-19 r86153)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mbkmeans/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mbkmeans’ version ‘1.19.0’
* 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
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* 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 ... 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 loading without being on the library search path ... 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 ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 5 NOTEs
See
‘/home/biocbuild/bbs-3.19-bioc/meat/mbkmeans.Rcheck/00check.log’
for details.
mbkmeans.Rcheck/00install.out
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###
### Running command:
###
### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD INSTALL mbkmeans
###
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* installing to library ‘/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library’
* installing *source* package ‘mbkmeans’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 10.3.1’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/ClusterR/include' -I/usr/local/include -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/ClusterR/include' -I/usr/local/include -fPIC -g -O2 -Wall -c mini_batch.cpp -o mini_batch.o
In file included from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/RcppArmadillo/include/armadillo:26,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from mini_batch.cpp:2:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/RcppArmadillo/include/armadillo_bits/config.hpp:321:86: note: ‘#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed’
321 | #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed")
| ^
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/RcppArmadillo/include/armadillo_bits/config.hpp:326:75: note: ‘#pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead’
326 | #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead")
| ^
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/RcppArmadillo/include/armadillo_bits/config.hpp:329:61: note: ‘#pragma message: INFO: see the documentation for details’
329 | #pragma message ("INFO: see the documentation for details")
| ^
In file included from mini_batch.cpp:3:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-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/R/R-4.4-devel-2024.03.20/site-library/ClusterR/include/ClusterRHeader.h:862:14: warning: variable ‘status’ set but not used [-Wunused-but-set-variable]
862 | bool status;
| ^~~~~~
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-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>]’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/ClusterR/include/ClusterRHeader.h:1601:70: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/ClusterR/include/ClusterRHeader.h:1530:14: warning: variable ‘status’ set but not used [-Wunused-but-set-variable]
1530 | bool status;
| ^~~~~~
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-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>]’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/ClusterR/include/ClusterRHeader.h:1635:70: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/ClusterR/include/ClusterRHeader.h:1530:14: warning: variable ‘status’ set but not used [-Wunused-but-set-variable]
g++ -std=gnu++11 -shared -L/home/biocbuild/R/R-4.4-devel-2024.03.20/lib -L/usr/local/lib -o mbkmeans.so RcppExports.o mini_batch.o -L/home/biocbuild/R/R-4.4-devel-2024.03.20/lib -lR
installing to /home/biocbuild/R/R-4.4-devel-2024.03.20/site-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)
mbkmeans.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
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
589.413 8.938 599.478
mbkmeans.Rcheck/mbkmeans-Ex.timings
| name | user | system | elapsed | |
| blocksize | 0 | 0 | 0 | |
| compute_wcss | 0.001 | 0.000 | 0.000 | |
| mbkmeans | 0.635 | 0.020 | 0.656 | |
| mini_batch | 0.001 | 0.000 | 0.001 | |
| predict_mini_batch | 0.005 | 0.000 | 0.005 | |
| predict_mini_batch_r | 0.008 | 0.000 | 0.009 | |