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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:combi.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings combi_1.16.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/combi.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘combi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘combi’ version ‘1.16.0’
* 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 ‘combi’ 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘DBI’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
  .C("spline_value", ..., PACKAGE = "cobs")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
addLink: no visible binding for global variable ‘species’
convPlot: no visible binding for global variable ‘Iteration’
convPlot: no visible binding for global variable ‘Value’
convPlot: no visible binding for global variable ‘Variable’
convPlot: no visible binding for global variable ‘Colour’
inflPlot: no visible binding for global variable ‘h’
inflPlot: no visible binding for global variable ‘LatentVariable’
inflPlot: no visible binding for global variable ‘value’
Undefined global functions or variables:
  Colour Iteration LatentVariable Value Variable h species value
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    7.       └─combi:::estIndepModel(...)
    8.         ├─base::suppressWarnings(...)
    9.         │ └─base::withCallingHandlers(...)
   10.         └─combi:::estMeanVarTrend(...)
   11.           └─stats::optimize(...)
   12.             └─stats (local) `<fn>`(-16.5139598160924)
   13.               └─combi (local) f(arg, ...)
   14.                 ├─base::suppressWarnings(...)
   15.                 │ └─base::withCallingHandlers(...)
   16.                 └─cobs::cobs(...)
   17.                   └─cobs::drqssbc2(...)
  
  [ FAIL 1 | WARN 13 | SKIP 0 | PASS 19 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/combi.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL combi
###
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* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘combi’ ...
** using staged installation
** R
** data
** 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 (combi)

R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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(combi)
Loading required package: DBI
> test_check("combi")
[ FAIL 1 | WARN 13 | SKIP 0 | PASS 19 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-combiinput.R:30:5'): combi runs when NAs present in data matrix
          and allowMissingess = TRUE ──
Error in `drqssbc2(x, y, w, pw = pw, knots = knots, degree = degree, Tlambda = if (select.lambda) lambdaSet else lambda, 
    constraint = constraint, ptConstr = ptConstr, maxiter = maxiter, 
    trace = trace - 1, nrq, nl1, neqc, niqc, nvar, tau = tau, 
    select.lambda = select.lambda, give.pseudo.x = keep.x.ps, 
    rq.tol = rq.tol, tol.0res = tol.0res, print.warn = print.warn)`: The problem is degenerate for the range of lambda specified.
Backtrace:
     ▆
  1. ├─testthat::expect_s3_class(...) at test-combiinput.R:30:5
  2. │ └─testthat::quasi_label(enquo(object), arg = "object")
  3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
  4. └─combi::combi(...)
  5.   └─base::lapply(...)
  6.     └─combi (local) FUN(X[[i]], ...)
  7.       └─combi:::estIndepModel(...)
  8.         ├─base::suppressWarnings(...)
  9.         │ └─base::withCallingHandlers(...)
 10.         └─combi:::estMeanVarTrend(...)
 11.           └─stats::optimize(...)
 12.             └─stats (local) `<fn>`(-16.5139598160924)
 13.               └─combi (local) f(arg, ...)
 14.                 ├─base::suppressWarnings(...)
 15.                 │ └─base::withCallingHandlers(...)
 16.                 └─cobs::cobs(...)
 17.                   └─cobs::drqssbc2(...)

[ FAIL 1 | WARN 13 | SKIP 0 | PASS 19 ]
Error: Test failures
Execution halted