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CHECK report for CARNIVAL on malbec1

This page was generated on 2020-08-13 11:22:46 -0400 (Thu, 13 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE CARNIVAL PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 225/1885HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CARNIVAL 1.1.0
Enio Gjerga
Snapshot Date: 2020-08-12 14:52:00 -0400 (Wed, 12 Aug 2020)
URL: https://git.bioconductor.org/packages/CARNIVAL
Branch: master
Last Commit: 09ec937
Last Changed Date: 2020-04-27 15:36:20 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 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: CARNIVAL
Version: 1.1.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:CARNIVAL.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings CARNIVAL_1.1.0.tar.gz
StartedAt: 2020-08-13 07:22:09 -0400 (Thu, 13 Aug 2020)
EndedAt: 2020-08-13 07:25:29 -0400 (Thu, 13 Aug 2020)
EllapsedTime: 200.1 seconds
RetCode: 0
Status:  OK 
CheckDir: CARNIVAL.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:CARNIVAL.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings CARNIVAL_1.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/CARNIVAL.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CARNIVAL/DESCRIPTION’ ... OK
* this is package ‘CARNIVAL’ version ‘1.1.0’
* 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 ‘CARNIVAL’ 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 ... NOTE
Uniprot2GeneSymbol: no visible global function definition for
  ‘read.table’
WriteDOTfig: no visible global function definition for ‘read.table’
checkInputObj: no visible global function definition for ‘is’
checkMeasObj: no visible global function definition for ‘is’
checkNetwork: no visible global function definition for ‘is’
checkSolver: no visible global function definition for ‘is’
checkWeightObj: no visible global function definition for ‘is’
exportResultAllConditions: no visible global function definition for
  ‘exportResultAllConditionsCPLEX’
exportResultAllConditions: no visible global function definition for
  ‘exportResultAllConditionsCBC’
exportResultCBC: no visible global function definition for ‘is’
exportResultCPLEX: no visible binding for global variable ‘measurement’
exportResultCPLEX: no visible global function definition for
  ‘read.delim’
exportResultCPLEX: no visible global function definition for ‘is’
exportResultLPSolve: no visible global function definition for ‘is’
solveCARNIVAL: no visible binding for global variable ‘variables’
Undefined global functions or variables:
  exportResultAllConditionsCBC exportResultAllConditionsCPLEX is
  measurement read.delim read.table variables
Consider adding
  importFrom("methods", "is")
  importFrom("utils", "read.delim", "read.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/CARNIVAL.Rcheck/00check.log’
for details.



Installation output

CARNIVAL.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL CARNIVAL
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘CARNIVAL’ ...
** 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 (CARNIVAL)

Tests output

CARNIVAL.Rcheck/tests/testthat.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
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.

> library(testthat)
> library(CARNIVAL)
> 
> test_check("CARNIVAL")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 1 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 11.064   0.332  11.493 

Example timings

CARNIVAL.Rcheck/CARNIVAL-Ex.timings

nameusersystemelapsed
runCARNIVAL0.1720.0280.396