* using log directory ‘/srv/hornik/tmp/CRAN/coco.Rcheck’
* using R Under development (unstable) (2024-07-20 r86909)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 18.1.8 (1+b1)
    Debian flang-new version 18.1.8 (1+b1)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘coco/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘coco’ version ‘0.1’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [2s/2s] ERROR
Maintainer: ‘Federico Blasi <federico.blasi@math.uzh.ch>’

New submission

Conflicting package names (submitted: coco, existing: CoCo [CRAN archive])

Non-FOSS package license (`use_gpl3_license()`)

Possibly misspelled words in DESCRIPTION:
  Nonstationary (3:49)
  nonstationary (13:43)

The Title field should be in title case. Current version is:
  ‘Covariate-based Covariance Functions For Nonstationary Gaussian Processes’
In title case that is:
  ‘Covariate-Based Covariance Functions for Nonstationary Gaussian Processes’

Size of tarball: 9261278 bytes
* 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 executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘coco’ can be installed ... [14s/14s] WARNING
Found the following significant warnings:
  Warning: /srv/hornik/tmp/CRAN/coco.Rcheck/00_pkg_src/coco/man/coco-package.Rd:13: unexpected UNKNOWN '\license'
  Warning: coco-package.Rd:13: All text must be in a section
See ‘/srv/hornik/tmp/CRAN/coco.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Debian clang version 18.1.8 (3)’
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... WARNING
Non-standard license specification:
  `use_gpl3_license()`
Standardizable: FALSE
Author field differs from that derived from Authors@R
  Author:    ‘Federico Blasi’
  Authors@R: ‘Federico Blasi [aut, cre], Reinhard Furrer [ctb]’

* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... WARNING
Vignettes with missing or empty \VignetteIndexEntry:
  coco.Rnw
See sections ‘The INDEX file’ and ‘Package subdirectories’ in the
‘Writing R Extensions’ manual.
* 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 whether startup messages can be suppressed ... [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
getBoundariesV3: no visible global function definition for ‘dist’
getCondNumber: no visible global function definition for ‘cov2cor’
plotOptimInfo: no visible global function definition for ‘par’
plot,coco: no visible global function definition for ‘par’
print,coco: no visible binding for global variable ‘number_mean’
print,coco: no visible binding for global variable ‘number_std.dev’
print,coco: no visible binding for global variable ‘number_scale’
print,coco: no visible binding for global variable ‘Inv.Hess’
Undefined global functions or variables:
  Inv.Hess cov2cor dist number_mean number_scale number_std.dev par
Consider adding
  importFrom("graphics", "par")
  importFrom("stats", "cov2cor", "dist")
to your NAMESPACE file.

Found if() conditions comparing class() to string:
File ‘coco/R/getFunctions.R’: if (class(x) == "coco") ...
File ‘coco/R/getFunctions.R’: if (class(coco.object) == "coco") ...
File ‘coco/R/getFunctions.R’: if (class(coco.object) == "coco") ...
Use inherits() (or maybe is()) instead.
* checking Rd files ... [0s/0s] WARNING
prepare_Rd: ./man/coco-package.Rd:13: unexpected UNKNOWN '\license'
prepare_Rd: coco-package.Rd:13: All text must be in a section
* checking Rd metadata ... WARNING
Rd files with duplicated alias 'coco':
  ‘coco-package.Rd’ ‘coco.Rd’
* checking Rd line widths ... NOTE
Rd file 'GetNeg2loglikelihoodProfile.Rd':
  \usage lines wider than 90 characters:
     GetNeg2loglikelihoodProfile(theta, par.pos, locs, x_covariates, smooth.limits, z, n, x_betas,lambda)

Rd file 'GetNeg2loglikelihoodTaper.Rd':
  \usage lines wider than 90 characters:
     GetNeg2loglikelihoodTaper(theta, par.pos, ref_taper, locs, x_covariates, smooth.limits, cholS, z, n, lambda)

Rd file 'GetNeg2loglikelihoodTaperProfile.Rd':
  \usage lines wider than 90 characters:
     GetNeg2loglikelihoodTaperProfile(theta, par.pos, ref_taper, locs, x_covariates, smooth.limits, cholS, z, n, lambda)

Rd file 'cocoOptim.Rd':
  \usage lines wider than 90 characters:
     cocoOptim(coco.object, boundaries = list(), ncores = parallel::detectCores(), optim.control, optim.type,...)

Rd file 'cocoSim.Rd':
  \usage lines wider than 90 characters:
     cocoSim(coco.object, pars, n, seed, standardize, type = 'classic', sim.type = NULL, cond.info = NULL)

These lines will be truncated in the PDF manual.
* checking Rd cross-references ... WARNING
Missing link or links in Rd file 'GetNeg2loglikelihood.Rd':
  ‘1’

Missing link or links in Rd file 'GetNeg2loglikelihoodProfile.Rd':
  ‘1’

Missing link or links in Rd file 'GetNeg2loglikelihoodTaper.Rd':
  ‘1’

Missing link or links in Rd file 'GetNeg2loglikelihoodTaperProfile.Rd':
  ‘1’

See section 'Cross-references' in the 'Writing R Extensions' manual.

Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  GetNeg2loglikelihood.Rd: 1
  GetNeg2loglikelihoodProfile.Rd: 1
  GetNeg2loglikelihoodTaper.Rd: 1
  GetNeg2loglikelihoodTaperProfile.Rd: 1
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘cov_rns’ ‘cov_rns_classic’ ‘cov_rns_classic_prod_smooth’
  ‘cov_rns_pred’ ‘cov_rns_taper_optimized_predict_range’
  ‘cov_rns_taper_optimized_range’ ‘holes’ ‘stripes’ ‘x’
Undocumented data sets:
  ‘holes’ ‘stripes’
Undocumented S4 methods:
  generic 'plot' and siglist 'coco'
  generic 'print' and siglist 'coco'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from Rd file 'getBoundariesV2.Rd':
getBoundariesV2
  Code: function(coco.object, mean.limits, std.dev.limits,
                 scale.limits, aniso.limits, tilt.limits,
                 smooth.limits, nugget.limits)
  Docs: function(coco.object, lower.value, upper.value)
  Argument names in code not in docs:
    mean.limits std.dev.limits scale.limits aniso.limits tilt.limits
    smooth.limits nugget.limits
  Argument names in docs not in code:
    lower.value upper.value
  Mismatches in argument names:
    Position: 2 Code: mean.limits Docs: lower.value
    Position: 3 Code: std.dev.limits Docs: upper.value

Codoc mismatches from Rd file 'getBoundariesV3.Rd':
getBoundariesV3
  Code: function(coco.object, mean.limits, global.lower,
                 std.dev.max.effects, scale.max.effects,
                 aniso.max.effects, tilt.max.effects,
                 smooth.max.effects, nugget.max.effects)
  Docs: function(coco.object, ...)
  Argument names in code not in docs:
    mean.limits global.lower std.dev.max.effects scale.max.effects
    aniso.max.effects tilt.max.effects smooth.max.effects
    nugget.max.effects
  Argument names in docs not in code:
    ...
  Mismatches in argument names:
    Position: 2 Code: mean.limits Docs: ...

Codoc mismatches from Rd file 'getHessian.Rd':
getHessian
  Code: function(coco.object, ncores = parallel::detectCores() - 1, eps
                 = .Machine$double.eps^(1/4))
  Docs: function(coco.object, ncores = 2, eps =
                 .Machine$double.eps^(1/4))
  Mismatches in argument default values:
    Name: 'ncores' Code: parallel::detectCores() - 1 Docs: 2

* checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'getBoundariesV2.Rd'
  ‘lower.value’ ‘upper.value’
Documented arguments not in \usage in Rd file 'getBoundariesV2.Rd':
  ‘param.limits’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... NOTE
Argument items with no description in Rd file 'getBoundariesV3.Rd':
  ‘...’
* 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 ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
              old_size new_size compress
  holes.rda      213Kb    183Kb       xz
  stripes.rda    853Kb    751Kb       xz
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... WARNING
  ‘gs+qpdf’ made some significant size reductions:
     compacted ‘coco.pdf’ from 8622Kb to 629Kb
  consider running tools::compactPDF(gs_quality = "ebook") on these files,
  or build the source package with --compact-vignettes=both
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [0s/0s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [2s/2s] OK
* checking PDF version of manual ... [3s/3s] OK
* checking HTML version of manual ... [0s/0s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR, 11 WARNINGs, 3 NOTEs