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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CARNIVAL.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings CARNIVAL_2.5.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/CARNIVAL.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CARNIVAL/DESCRIPTION' ... OK
* this is package 'CARNIVAL' version '2.5.0'
* 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 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
  'D:/biocbuild/bbs-3.15-bioc/meat/CARNIVAL.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL CARNIVAL
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'CARNIVAL' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'CARNIVAL'
    finding HTML links ... done
    addPerturbationNodes                    html  
    checkCarnivalOptions                    html  
    checkData                               html  
    checkOptionsValidity                    html  
    checkPriorKnowledgeNetwork              html  
    createInternalDataRepresentation        html  
    defaultCbcSolveCarnivalOptions          html  
    defaultCplexCarnivalOptions             html  
    defaultCplexSpecificOptions             html  
    defaultLpSolveCarnivalOptions           html  
    generateLpFileCarnival                  html  
    getOptionsList                          html  
    getSupportedSolvers                     html  
    getSupportedSolversFunctions            html  
    isInputValidCarnival                    html  
    parseCplexLog                           html  
    prepareForCarnivalRun                   html  
    preprocessPriorKnowledgeNetwork         html  
    processSolution                         html  
    readOptions                             html  
    runCARNIVAL                             html  
    runFromLpCarnival                       html  
    runInverseCarnival                      html  
    runVanillaCarnival                      html  
    sendTaskToSolver                        html  
    setCarnivalOptions                      html  
    solveCarnival                           html  
    solveCarnivalFromLp                     html  
    solveWithCbc                            html  
    suggestedCbcSpecificOptions             html  
    suggestedCplexSpecificOptions           html  
    writeParsedData                         html  
** 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)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'msqrob2' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'omicRexposome' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'scp' is missing or broken
 done