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This page was generated on 2023-03-20 11:06:09 -0400 (Mon, 20 Mar 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.2 (2022-10-31) -- "Innocent and Trusting" 4516
palomino4Windows Server 2022 Datacenterx644.2.2 (2022-10-31 ucrt) -- "Innocent and Trusting" 4295
lconwaymacOS 12.5.1 Montereyx86_644.2.2 (2022-10-31) -- "Innocent and Trusting" 4324
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 lconway


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? 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 1112/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mbkmeans 1.14.0  (landing page)
Davide Risso
Snapshot Date: 2023-03-17 14:00:04 -0400 (Fri, 17 Mar 2023)
git_url: https://git.bioconductor.org/packages/mbkmeans
git_branch: RELEASE_3_16
git_last_commit: c048655
git_last_commit_date: 2022-11-01 11:19:36 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 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
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: mbkmeans
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:mbkmeans.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings mbkmeans_1.14.0.tar.gz
StartedAt: 2023-03-17 21:11:00 -0400 (Fri, 17 Mar 2023)
EndedAt: 2023-03-17 21:16:00 -0400 (Fri, 17 Mar 2023)
EllapsedTime: 300.0 seconds
RetCode: 0
Status:   OK  
CheckDir: mbkmeans.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:mbkmeans.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings mbkmeans_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/mbkmeans.Rcheck’
* using R version 4.2.2 (2022-10-31)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.14.0’
* 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 ... 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.16-bioc/meat/mbkmeans.Rcheck/00check.log’
for details.



Installation output

mbkmeans.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL mbkmeans
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘mbkmeans’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/ClusterR/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/ClusterR/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c mini_batch.cpp -o mini_batch.o
In file included from mini_batch.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/armadillo:26:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/armadillo_bits/config.hpp:338:11: warning: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed [-W#pragma-messages]
  #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed")
          ^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/armadillo_bits/config.hpp:343:13: warning: INFO: suggest to use ARMA_WARN_LEVEL option instead [-W#pragma-messages]
    #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead")
            ^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/armadillo_bits/config.hpp:346:11: warning: INFO: see the documentation for details [-W#pragma-messages]
  #pragma message ("INFO: see the documentation for details")
          ^
In file included from mini_batch.cpp:3:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/ClusterR/include/ClusterRHeader.h:926:14: warning: variable 'status' set but not used [-Wunused-but-set-variable]
        bool status;
             ^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/ClusterR/include/ClusterRHeader.h:1601:14: warning: variable 'status' set but not used [-Wunused-but-set-variable]
        bool status;
             ^
5 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o mbkmeans.so RcppExports.o mini_batch.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.2/Resources/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 4.2.2 (2022-10-31) -- "Innocent and Trusting"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 
119.730  36.340 157.208 

Example timings

mbkmeans.Rcheck/mbkmeans-Ex.timings

nameusersystemelapsed
blocksize0.0000.0010.001
compute_wcss0.0000.0010.002
mbkmeans0.6030.0240.631
mini_batch0.0000.0000.001
predict_mini_batch0.0040.0010.005
predict_mini_batch_r0.0190.0030.023