* using log directory ‘/srv/hornik/tmp/CRAN_pretest/CoDaLoMic.Rcheck’
* using R Under development (unstable) (2024-12-07 r87428)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 19.1.1 (1)
    Debian flang-new version 19.1.1 (1)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘CoDaLoMic/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CoDaLoMic’ version ‘0.1.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [3s/3s] NOTE
Maintainer: ‘Irene Creus Martí <ircrmar@mat.upv.es>’

New submission

Possibly misspelled words in DESCRIPTION:
  Creus (7:191, 7:217, 7:246)
  Martí (7:197, 7:223, 7:252)
  Microbiome (3:45)
  al (7:206, 7:232, 7:261)
  et (7:203, 7:229, 7:258)
  microbiome (7:64)

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Irene", "Creus"),
                    family = "Martí",
                    role = c("aut", "cre"),
                    email = "ircrmar@mat.upv.es")
as necessary.

Package has a VignetteBuilder field but no prebuilt vignette index.
* checking package namespace information ... OK
* checking package dependencies ... INFO
Vignette dependency required without any vignettes: ‘knitr’
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking serialization versions ... OK
* checking whether package ‘CoDaLoMic’ can be installed ... [2s/2s] OK
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [0s/0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [0s/0s] OK
* checking use of S3 registration ... 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 ... [5s/5s] NOTE
Graphics: no visible binding for global variable ‘value’
Graphics: no visible binding for global variable ‘variable’
GraphicsPrediction: no visible binding for global variable ‘value’
GraphicsPrediction: no visible binding for global variable ‘variable’
GraphicsPredictionBPBM: no visible binding for global variable ‘value’
GraphicsPredictionBPBM: no visible binding for global variable
  ‘variable’
PCAbiplot: no visible binding for global variable ‘x’
PCAbiplot: no visible binding for global variable ‘y’
modelBPBM: no visible binding for global variable ‘ep’
modelBPBM: no visible global function definition for ‘inprod’
modelBPBM: no visible binding for global variable ‘a’
modelBPBM: no visible binding for global variable ‘vectorPB’
modelBPBM: no visible binding for global variable ‘BB’
modelBPBM: no visible global function definition for ‘pow’
modelBPBM: no visible binding for global variable ‘sdgamma’
Undefined global functions or variables:
  BB a ep inprod pow sdgamma value variable vectorPB x y
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 ... [0s/0s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... [21s/28s] ERROR
Running examples in ‘CoDaLoMic-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: PreparingTheData
> ### Title: Preparing dataset
> ### Aliases: PreparingTheData
> 
> ### ** Examples
> 
> 
> #Link to README file, a file with basic instructions for using the package.
> system.file("extdata", "README.pdf", package = "CoDaLoMic")
[1] "/srv/hornik/tmp/CRAN_pretest/CoDaLoMic.Rcheck/CoDaLoMic/extdata/README.pdf"
> 
> #On Windows, the PDF can be opened as follows:
> shell.exec(system.file("extdata", "README.pdf", package = "CoDaLoMic"))
Error in shell.exec(system.file("extdata", "README.pdf", package = "CoDaLoMic")) : 
  could not find function "shell.exec"
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
Estimate_Param_FBM         9.651  0.068   9.722
Estimate_Param_EstParmFunc 6.504  0.020   6.525
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [47s/90s] OK
  Running ‘testthat.R’ [47s/89s]
* checking PDF version of manual ... [4s/4s] WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! LaTeX Error: Unicode character − (U+2212)
               not set up for use with LaTeX.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
* checking PDF version of manual without index ... ERROR
* checking HTML version of manual ... [1s/1s] OK
* checking for non-standard things in the check directory ... NOTE
Found the following files/directories:
  ‘CoDaLoMic-manual.tex’
* checking for detritus in the temp directory ... OK
* DONE
Status: 2 ERRORs, 1 WARNING, 3 NOTEs