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CHECK report for multiClust on malbec1

This page was generated on 2021-01-19 11:52:15 -0500 (Tue, 19 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE multiClust PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1176/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
multiClust 1.20.0
Nathan Lawlor
Snapshot Date: 2021-01-18 14:42:24 -0500 (Mon, 18 Jan 2021)
URL: https://git.bioconductor.org/packages/multiClust
Branch: RELEASE_3_12
Last Commit: 4aec467
Last Changed Date: 2020-10-27 11:09:35 -0500 (Tue, 27 Oct 2020)
malbec1 Linux (Ubuntu 18.04.5 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: multiClust
Version: 1.20.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:multiClust.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings multiClust_1.20.0.tar.gz
StartedAt: 2021-01-19 04:41:23 -0500 (Tue, 19 Jan 2021)
EndedAt: 2021-01-19 04:42:41 -0500 (Tue, 19 Jan 2021)
EllapsedTime: 78.2 seconds
RetCode: 0
Status:  OK 
CheckDir: multiClust.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:multiClust.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings multiClust_1.20.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/multiClust.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘multiClust/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘multiClust’ version ‘1.20.0’
* 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 ‘multiClust’ 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 ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
cluster_analysis 8.992  0.012   8.808
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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: OK


Installation output

multiClust.Rcheck/00install.out

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### Running command:
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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL multiClust
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘multiClust’ ...
** using staged installation
** 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 (multiClust)

Tests output

multiClust.Rcheck/tests/runTests.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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.

> BiocGenerics:::testPackage("multiClust")
Loading required package: amap


RUNIT TEST PROTOCOL -- Tue Jan 19 04:42:38 2021 
*********************************************** 
Number of test functions: 9 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
multiClust RUnit Tests - 9 test functions, 0 errors, 0 failures
Number of test functions: 9 
Number of errors: 0 
Number of failures: 0 
Warning message:
In `[.data.frame`(transinput, 1:probe_number, ) :
  NAs introduced by coercion
> 
> proc.time()
   user  system elapsed 
  3.628   0.188   3.948 

Example timings

multiClust.Rcheck/multiClust-Ex.timings

nameusersystemelapsed
WriteMatrixToFile0.0360.0000.037
avg_probe_exp0.6840.0280.913
cluster_analysis8.9920.0128.808
input_file0.1080.0000.110
nor.min.max0.0080.0000.006
number_clusters0.0960.0000.097
number_probes0.1520.0000.156
probe_ranking0.3720.0040.375
surv_analysis0.5160.0040.630