##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CARNIVAL.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CARNIVAL_2.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/CARNIVAL.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CARNIVAL/DESCRIPTION’ ... OK
* this is package ‘CARNIVAL’ version ‘2.19.0’
* 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 code 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
checkSolverPathInSystem: no visible global function definition for
  ‘searchForSolver’
convergenceTextToTable: no visible binding for global variable ‘.’
convergenceTextToTable: no visible binding for global variable ‘Gap’
convergenceTextToTable: no visible binding for global variable
  ‘Objective’
convergenceTextToTable: no visible binding for global variable ‘Best
  Bound’
convergenceTextToTable: no visible binding for global variable ‘index’
createInternalDataRepresentation: no visible global function definition
  for ‘buildDataVector’
createInternalDataRepresentation: no visible global function definition
  for ‘createVariables’
exportIlpSolutionFromSolutionMatrix: no visible binding for global
  variable ‘nodes’
exportIlpSolutionFromSolutionMatrix: no visible binding for global
  variable ‘nodesValue’
exportIlpSolutionFromSolutionMatrix: no visible binding for global
  variable ‘solution’
exportIlpSolutionFromSolutionMatrix: no visible binding for global
  variable ‘Node2Value’
exportIlpSolutionFromSolutionMatrix: no visible binding for global
  variable ‘edgesUpValue’
exportIlpSolutionFromSolutionMatrix: no visible binding for global
  variable ‘edgesDownValue’
exportIlpSolutionFromSolutionMatrix: no visible binding for global
  variable ‘presents’
exportIlpSolutionFromSolutionMatrix: no visible binding for global
  variable ‘Node1’
exportIlpSolutionFromSolutionMatrix: no visible binding for global
  variable ‘Sign’
exportIlpSolutionFromSolutionMatrix: no visible binding for global
  variable ‘Node2’
exportIlpSolutionFromSolutionMatrix: no visible binding for global
  variable ‘Activity’
exportIlpSolutionFromSolutionMatrix: no visible binding for global
  variable ‘nodesType’
exportIlpSolutionFromSolutionMatrix: no visible binding for global
  variable ‘zeroActivity’
exportIlpSolutionFromSolutionMatrix: no visible binding for global
  variable ‘activityUp’
exportIlpSolutionFromSolutionMatrix: no visible binding for global
  variable ‘activityDown’
exportIlpSolutionFromSolutionMatrix: no visible binding for global
  variable ‘UpAct’
exportIlpSolutionFromSolutionMatrix: no visible binding for global
  variable ‘DownAct’
getSolutionMatrixGurobi: no visible global function definition for
  ‘read.csv2’
parseCplexLog: no visible binding for global variable ‘.’
prepareForCarnivalRun: no visible global function definition for
  ‘createLpFormulation’
processSolution: no visible global function definition for
  ‘exportIlpSolutionResultFromXml’
sendTaskToSolver: no visible global function definition for
  ‘transformVariables’
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’
Undefined global functions or variables:
  . Activity Best Bound DownAct Gap Node1 Node2 Node2Value Objective
  Sign Solutions UpAct activityDown activityUp buildDataVector
  createLpFormulation createVariables edgesDownValue edgesUpValue
  exportIlpSolutionResultFromXml index nodes nodesType nodesValue
  presents read.csv2 read.delim searchForSolver solution ticks
  transformVariables zeroActivity
Consider adding
  importFrom("utils", "read.csv2", "read.delim")
to your NAMESPACE file.
* 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 R/sysdata.rda ... 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 ... 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
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/CARNIVAL.Rcheck/00check.log’
for details.

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘CARNIVAL’ ...
** this is package ‘CARNIVAL’ version ‘2.19.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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)

R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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")
sh: NA/cplex: No such file or directory
sh: /tmp/RtmpGFcJJU/fileb3ab4a3cbbed: No such file or directory
Test run finished successfully.

Attaching package: 'dplyr'

The following object is masked from 'package:testthat':

    matches

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

The following names changed in the network:
  user.defined.id mapped.id
1             I*1       I_1
2             N2-       N2_
3            <N1>     X_N1_
The following names changed in the network:
  user.defined.id mapped.id
1            *N*1     X_N_1
2             N+2       N_2
3             M1:       M1_
4             M1*       M1_
The following node names maps to the same ID:
  user.defined.id mapped.id
3             M1:       M1_
4             M1*       M1_
The following names changed in the network:
  user.defined.id mapped.id
1             I*1       I_1
2             N2-       N2_
3            <N1>     X_N1_
The following names changed in the network:
  user.defined.id mapped.id
1            *N*1     X_N_1
2             N+2       N_2
3             M1:       M1_
--- Start of the CARNIVAL pipeline ---
20:54:21 19.10.2025 Carnival flavour: vanilla
20:54:21 19.10.2025 Generating variables for lp problem
20:54:21 19.10.2025 Done: generating variables for lp problem
Saving preprocessed data.
Done: saving parsed data: ./test_model1/test5//parsedData_t20_54_21d19_10_2025n92.RData
20:54:21 19.10.2025 Generating formulation for LP problem
20:54:21 19.10.2025 Done: generating formulation for LP problem.
Saving LP file
Done: Saving LP file: ./test_model1/test5//lpFile_t20_54_21d19_10_2025n92.lp
20:54:21 19.10.2025 Solving LP problem
Parsing .lp file for lpSolve
Rows: 174 Columns: 1
-- Column specification --------------------------------------------------------
Delimiter: ","
chr (1): X1

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Done: parsing .lp file for lpSolve
20:54:22 19.10.2025 Done: solving LP problem.
20:54:22 19.10.2025 Getting the solution matrix
20:54:22 19.10.2025 Done: getting the solution matrix.
20:54:22 19.10.2025 Exporting solution matrix
20:54:22 19.10.2025 Done: exporting solution matrix.
Cleaning intermediate files
Done: cleaning
20:54:22 19.10.2025 All tasks finished.

--- End of the CARNIVAL pipeline --- 

 
--- Start of the CARNIVAL pipeline ---
20:54:22 19.10.2025 Carnival flavour: inverse
Perturbations are not provided, all parents nodes are added as potential perturbations.
20:54:22 19.10.2025 Generating variables for lp problem
20:54:22 19.10.2025 Done: generating variables for lp problem
Saving preprocessed data.
Done: saving parsed data: /Users/biocbuild/bbs-3.22-bioc/meat/CARNIVAL.Rcheck/tests/testthat/work_lpsolve/work_lpsolve//parsedData_t20_54_22d19_10_2025n86.RData
20:54:22 19.10.2025 Generating formulation for LP problem
20:54:22 19.10.2025 Done: generating formulation for LP problem.
Saving LP file
Done: Saving LP file: /Users/biocbuild/bbs-3.22-bioc/meat/CARNIVAL.Rcheck/tests/testthat/work_lpsolve/work_lpsolve//lpFile_t20_54_22d19_10_2025n86.lp
20:54:22 19.10.2025 Solving LP problem
Parsing .lp file for lpSolve
Rows: 142 Columns: 1
-- Column specification --------------------------------------------------------
Delimiter: ","
chr (1): X1

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Done: parsing .lp file for lpSolve
20:54:22 19.10.2025 Done: solving LP problem.
20:54:22 19.10.2025 Getting the solution matrix
20:54:22 19.10.2025 Done: getting the solution matrix.
20:54:22 19.10.2025 Exporting solution matrix
20:54:22 19.10.2025 Done: exporting solution matrix.
Cleaning intermediate files
Done: cleaning
20:54:22 19.10.2025 All tasks finished.

--- End of the CARNIVAL pipeline --- 

--- Start of the CARNIVAL pipeline ---
20:54:22 19.10.2025 Carnival flavour: vanilla
20:54:22 19.10.2025 Generating variables for lp problem
20:54:22 19.10.2025 Done: generating variables for lp problem
Saving preprocessed data.
Done: saving parsed data: ./test_model1/test1///parsedData_t20_54_22d19_10_2025n28.RData
20:54:22 19.10.2025 Generating formulation for LP problem
20:54:22 19.10.2025 Done: generating formulation for LP problem.
Saving LP file
Done: Saving LP file: ./test_model1/test1///lpFile_t20_54_22d19_10_2025n28.lp
20:54:22 19.10.2025 Solving LP problem
Parsing .lp file for lpSolve
Rows: 108 Columns: 1
-- Column specification --------------------------------------------------------
Delimiter: ","
chr (1): X1

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Done: parsing .lp file for lpSolve
20:54:22 19.10.2025 Done: solving LP problem.
20:54:22 19.10.2025 Getting the solution matrix
20:54:22 19.10.2025 Done: getting the solution matrix.
20:54:22 19.10.2025 Exporting solution matrix
20:54:22 19.10.2025 Done: exporting solution matrix.
Cleaning intermediate files
Done: cleaning
20:54:22 19.10.2025 All tasks finished.

--- End of the CARNIVAL pipeline --- 

--- Start of the CARNIVAL pipeline ---
20:54:22 19.10.2025 Carnival flavour: vanilla
20:54:22 19.10.2025 Generating variables for lp problem
20:54:22 19.10.2025 Done: generating variables for lp problem
Saving preprocessed data.
Done: saving parsed data: ./test_model1/test2///parsedData_t20_54_22d19_10_2025n14.RData
20:54:22 19.10.2025 Generating formulation for LP problem
20:54:22 19.10.2025 Done: generating formulation for LP problem.
Saving LP file
Done: Saving LP file: ./test_model1/test2///lpFile_t20_54_22d19_10_2025n14.lp
20:54:23 19.10.2025 Solving LP problem
Parsing .lp file for lpSolve
Rows: 108 Columns: 1
-- Column specification --------------------------------------------------------
Delimiter: ","
chr (1): X1

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Done: parsing .lp file for lpSolve
20:54:23 19.10.2025 Done: solving LP problem.
20:54:23 19.10.2025 Getting the solution matrix
20:54:23 19.10.2025 Done: getting the solution matrix.
20:54:23 19.10.2025 Exporting solution matrix
20:54:23 19.10.2025 Done: exporting solution matrix.
Cleaning intermediate files
Done: cleaning
20:54:23 19.10.2025 All tasks finished.

--- End of the CARNIVAL pipeline --- 

--- Start of the CARNIVAL pipeline ---
20:54:23 19.10.2025 Carnival flavour: vanilla
20:54:23 19.10.2025 Generating variables for lp problem
20:54:23 19.10.2025 Done: generating variables for lp problem
Saving preprocessed data.
Done: saving parsed data: ./test_model1/test3///parsedData_t20_54_23d19_10_2025n13.RData
20:54:23 19.10.2025 Generating formulation for LP problem
20:54:23 19.10.2025 Done: generating formulation for LP problem.
Saving LP file
Done: Saving LP file: ./test_model1/test3///lpFile_t20_54_23d19_10_2025n13.lp
20:54:23 19.10.2025 Solving LP problem
Parsing .lp file for lpSolve
Rows: 108 Columns: 1
-- Column specification --------------------------------------------------------
Delimiter: ","
chr (1): X1

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Done: parsing .lp file for lpSolve
20:54:23 19.10.2025 Done: solving LP problem.
20:54:23 19.10.2025 Getting the solution matrix
20:54:23 19.10.2025 Done: getting the solution matrix.
20:54:23 19.10.2025 Exporting solution matrix
20:54:23 19.10.2025 Done: exporting solution matrix.
Cleaning intermediate files
Done: cleaning
20:54:23 19.10.2025 All tasks finished.

--- End of the CARNIVAL pipeline --- 

--- Start of the CARNIVAL pipeline ---
20:54:23 19.10.2025 Carnival flavour: vanilla
20:54:23 19.10.2025 Generating variables for lp problem
20:54:23 19.10.2025 Done: generating variables for lp problem
Saving preprocessed data.
Done: saving parsed data: ./test_model1/test4///parsedData_t20_54_23d19_10_2025n14.RData
20:54:23 19.10.2025 Generating formulation for LP problem
20:54:23 19.10.2025 Done: generating formulation for LP problem.
Saving LP file
Done: Saving LP file: ./test_model1/test4///lpFile_t20_54_23d19_10_2025n14.lp
20:54:23 19.10.2025 Solving LP problem
Parsing .lp file for lpSolve
Rows: 121 Columns: 1
-- Column specification --------------------------------------------------------
Delimiter: ","
chr (1): X1

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Done: parsing .lp file for lpSolve
20:54:23 19.10.2025 Done: solving LP problem.
20:54:23 19.10.2025 Getting the solution matrix
20:54:23 19.10.2025 Done: getting the solution matrix.
20:54:23 19.10.2025 Exporting solution matrix
20:54:23 19.10.2025 Done: exporting solution matrix.
Cleaning intermediate files
Done: cleaning
20:54:23 19.10.2025 All tasks finished.

--- End of the CARNIVAL pipeline --- 

--- Start of the CARNIVAL pipeline ---
20:54:23 19.10.2025 Carnival flavour: vanilla
20:54:23 19.10.2025 Generating variables for lp problem
20:54:23 19.10.2025 Done: generating variables for lp problem
Saving preprocessed data.
Done: saving parsed data: ./test_model1/test5//parsedData_t20_54_23d19_10_2025n71.RData
20:54:23 19.10.2025 Generating formulation for LP problem
20:54:23 19.10.2025 Done: generating formulation for LP problem.
Saving LP file
Done: Saving LP file: ./test_model1/test5//lpFile_t20_54_23d19_10_2025n71.lp
20:54:23 19.10.2025 Solving LP problem
Parsing .lp file for lpSolve
Rows: 174 Columns: 1
-- Column specification --------------------------------------------------------
Delimiter: ","
chr (1): X1

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Done: parsing .lp file for lpSolve
20:54:23 19.10.2025 Done: solving LP problem.
20:54:23 19.10.2025 Getting the solution matrix
20:54:23 19.10.2025 Done: getting the solution matrix.
20:54:23 19.10.2025 Exporting solution matrix
20:54:23 19.10.2025 Done: exporting solution matrix.
Cleaning intermediate files
Done: cleaning
20:54:23 19.10.2025 All tasks finished.

--- End of the CARNIVAL pipeline --- 

--- Start of the CARNIVAL pipeline ---
20:54:24 19.10.2025 Carnival flavour: vanilla
20:54:24 19.10.2025 Generating variables for lp problem
20:54:24 19.10.2025 Done: generating variables for lp problem
Saving preprocessed data.
Done: saving parsed data: ./test_model1/testweight2///parsedData_t20_54_24d19_10_2025n41.RData
20:54:24 19.10.2025 Generating formulation for LP problem
20:54:24 19.10.2025 Done: generating formulation for LP problem.
Saving LP file
Done: Saving LP file: ./test_model1/testweight2///lpFile_t20_54_24d19_10_2025n41.lp
20:54:24 19.10.2025 Solving LP problem
Parsing .lp file for lpSolve
Rows: 108 Columns: 1
-- Column specification --------------------------------------------------------
Delimiter: ","
chr (1): X1

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Done: parsing .lp file for lpSolve
20:54:24 19.10.2025 Done: solving LP problem.
20:54:24 19.10.2025 Getting the solution matrix
20:54:24 19.10.2025 Done: getting the solution matrix.
20:54:24 19.10.2025 Exporting solution matrix
20:54:24 19.10.2025 Done: exporting solution matrix.
Cleaning intermediate files
Done: cleaning
20:54:24 19.10.2025 All tasks finished.

--- End of the CARNIVAL pipeline --- 

--- Start of the CARNIVAL pipeline ---
20:54:24 19.10.2025 Carnival flavour: vanilla
20:54:24 19.10.2025 Generating variables for lp problem
20:54:24 19.10.2025 Done: generating variables for lp problem
Saving preprocessed data.
Done: saving parsed data: ./test_model1/testweight3///parsedData_t20_54_24d19_10_2025n91.RData
20:54:24 19.10.2025 Generating formulation for LP problem
20:54:24 19.10.2025 Done: generating formulation for LP problem.
Saving LP file
Done: Saving LP file: ./test_model1/testweight3///lpFile_t20_54_24d19_10_2025n91.lp
20:54:24 19.10.2025 Solving LP problem
Parsing .lp file for lpSolve
Rows: 108 Columns: 1
-- Column specification --------------------------------------------------------
Delimiter: ","
chr (1): X1

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Done: parsing .lp file for lpSolve
20:54:24 19.10.2025 Done: solving LP problem.
20:54:24 19.10.2025 Getting the solution matrix
20:54:24 19.10.2025 Done: getting the solution matrix.
20:54:24 19.10.2025 Exporting solution matrix
20:54:24 19.10.2025 Done: exporting solution matrix.
Cleaning intermediate files
Done: cleaning
20:54:24 19.10.2025 All tasks finished.

--- End of the CARNIVAL pipeline --- 

--- Start of the CARNIVAL pipeline ---
20:54:24 19.10.2025 Carnival flavour: vanilla
20:54:24 19.10.2025 Generating variables for lp problem
20:54:24 19.10.2025 Done: generating variables for lp problem
Saving preprocessed data.
Done: saving parsed data: ./test_model1/testweight4///parsedData_t20_54_24d19_10_2025n45.RData
20:54:24 19.10.2025 Generating formulation for LP problem
20:54:24 19.10.2025 Done: generating formulation for LP problem.
Saving LP file
Done: Saving LP file: ./test_model1/testweight4///lpFile_t20_54_24d19_10_2025n45.lp
20:54:24 19.10.2025 Solving LP problem
Parsing .lp file for lpSolve
Rows: 108 Columns: 1
-- Column specification --------------------------------------------------------
Delimiter: ","
chr (1): X1

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Done: parsing .lp file for lpSolve
20:54:24 19.10.2025 Done: solving LP problem.
20:54:24 19.10.2025 Getting the solution matrix
20:54:24 19.10.2025 Done: getting the solution matrix.
20:54:24 19.10.2025 Exporting solution matrix
20:54:24 19.10.2025 Done: exporting solution matrix.
Cleaning intermediate files
Done: cleaning
20:54:24 19.10.2025 All tasks finished.

--- End of the CARNIVAL pipeline --- 

[ FAIL 0 | WARN 0 | SKIP 14 | PASS 135 ]

══ Skipped tests (14) ══════════════════════════════════════════════════════════
• !file.exists(cbcPath) is TRUE (1): 'test-set_solver_path.R:19:5'
• file.exists(cbcPath) is not TRUE (4): 'test_cbc_small_models.R:78:5',
  'test_cbc_small_models.R:131:5', 'test_cbc_small_models.R:185:5',
  'test_cbc_small_models.R:278:5'
• file.exists(cplexPath) is not TRUE (5): 'test_cplex_small_models.R:82:5',
  'test_cplex_small_models.R:136:5', 'test_cplex_small_models.R:194:5',
  'test_cplex_small_models.R:288:5', 'test_inverseCarnival.R:131:5'
• file.exists(gurobiPath) is not TRUE (4): 'test_gurobi_small_models.R:82:5',
  'test_gurobi_small_models.R:134:5', 'test_gurobi_small_models.R:188:5',
  'test_gurobi_small_models.R:279:5'

[ FAIL 0 | WARN 0 | SKIP 14 | PASS 135 ]
> 
> proc.time()
   user  system elapsed 
  5.022   0.553   5.699