Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:05:09 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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 CARNIVAL on nebbiolo2


To the developers/maintainers of the CARNIVAL package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CARNIVAL.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 247/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CARNIVAL 2.4.0  (landing page)
Olga Ivanova
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/CARNIVAL
git_branch: RELEASE_3_14
git_last_commit: c22da3e
git_last_commit_date: 2021-10-26 12:59:23 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: CARNIVAL
Version: 2.4.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:CARNIVAL.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings CARNIVAL_2.4.0.tar.gz
StartedAt: 2022-04-12 06:41:34 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 06:42:04 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 29.9 seconds
RetCode: 0
Status:   OK  
CheckDir: CARNIVAL.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:CARNIVAL.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings CARNIVAL_2.4.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/CARNIVAL.Rcheck’
* using R version 4.1.3 (2022-03-10)
* 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 ‘2.4.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 ... NOTE
Namespaces in Imports field not imported from:
  ‘methods’ ‘rmarkdown’
  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 ... NOTE
convergenceTextToTable: no visible binding for global variable ‘.’
convergenceTextToTable: no visible binding for global variable ‘Gap’
convergenceTextToTable: no visible global function definition for
  ‘across’
convergenceTextToTable: no visible global function definition for
  ‘everything’
convergenceTextToTable: no visible binding for global variable
  ‘Objective’
convergenceTextToTable: no visible binding for global variable ‘Best
  Bound’
convergenceTextToTable: no visible global function definition for ‘n’
convergenceTextToTable: no visible binding for global variable ‘index’
defaultCbcSolveCarnivalOptions: no visible binding for global variable
  ‘solverPath’
exportIlpSolutionResultFromXml: no visible global function definition
  for ‘is’
parseCplexLog: no visible binding for global variable ‘.’
prepareLPMatrixSingle: no visible global function definition for
  ‘error’
solveWithCbc: no visible global function definition for ‘read.csv2’
solveWithCplex: no visible global function definition for ‘read.delim’
timeStringToTable: no visible binding for global variable ‘.’
timeStringToTable: no visible binding for global variable ‘ticks’
timeStringToTable: no visible binding for global variable ‘Solutions’
timeStringToTable: no visible global function definition for ‘across’
timeStringToTable: no visible global function definition for
  ‘everything’
writeCplexCommandFileFromJson: no visible global function definition
  for ‘fromJSON’
Undefined global functions or variables:
  . Best Bound Gap Objective Solutions across error everything fromJSON
  index is n read.csv2 read.delim solverPath ticks
Consider adding
  importFrom("methods", "is")
  importFrom("utils", "read.csv2", "read.delim")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
prepare_Rd: checkData.Rd:23-25: Dropping empty section \value
prepare_Rd: checkOptionsValidity.Rd:14-16: Dropping empty section \value
prepare_Rd: defaultCbcSolveCarnivalOptions.Rd:12-14: Dropping empty section \value
prepare_Rd: defaultCplexSpecificOptions.Rd:12-14: Dropping empty section \value
prepare_Rd: defaultLpSolveCarnivalOptions.Rd:12-14: Dropping empty section \value
prepare_Rd: setCarnivalOptions.Rd:14-16: Dropping empty section \value
prepare_Rd: solveWithCbc.Rd:12-14: Dropping empty section \value
prepare_Rd: suggestedCbcSpecificOptions.Rd:12-14: Dropping empty section \value
prepare_Rd: suggestedCplexSpecificOptions.Rd:12-14: Dropping empty section \value
* 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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/CARNIVAL.Rcheck/00check.log’
for details.



Installation output

CARNIVAL.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL CARNIVAL
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-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


Example timings

CARNIVAL.Rcheck/CARNIVAL-Ex.timings

nameusersystemelapsed
checkOptionsValidity0.0010.0000.001
defaultCbcSolveCarnivalOptions0.0010.0000.001
defaultLpSolveCarnivalOptions000
generateLpFileCarnival0.0020.0000.002
runCARNIVAL0.0020.0000.001
runFromLpCarnival0.0010.0000.001
runInverseCarnival0.0010.0000.001
runVanillaCarnival0.0020.0000.001
setCarnivalOptions000
suggestedCbcSpecificOptions000
suggestedCplexSpecificOptions000