* using log directory ‘/srv/hornik/tmp/CRAN/fdesigns.Rcheck’
* using R Under development (unstable) (2024-06-18 r86781)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 18.1.5 (2)
    Debian flang-new version 18.1.5 (2)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘fdesigns/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘fdesigns’ version ‘1.0’
* checking CRAN incoming feasibility ... [3s/3s] NOTE
Maintainer: ‘Damianos Michaelides <dm3g15@soton.ac.uk>’

New submission

The Title field should be in title case. Current version is:
‘Optimal experimental designs for functional models depending on profile factors using the coordinate exchange algorithm’
In title case that is:
‘Optimal Experimental Designs for Functional Models Depending on Profile Factors using the Coordinate Exchange Algorithm’

The Date field is over a month old.

This build time stamp is over a month old.
* 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 serialization versions ... OK
* checking whether package ‘fdesigns’ can be installed ... [20s/20s] WARNING
Found the following significant warnings:
  fdesignscpp.cpp:25:9: warning: 'set_cerr_stream' is deprecated: this function does nothing; instead use ARMA_CERR_STREAM or ARMA_WARN_LEVEL; see documentation [-Wdeprecated-declarations]
  fdesignscpp.cpp:73:9: warning: 'set_cerr_stream' is deprecated: this function does nothing; instead use ARMA_CERR_STREAM or ARMA_WARN_LEVEL; see documentation [-Wdeprecated-declarations]
  fdesignscpp.cpp:131:9: warning: 'set_cerr_stream' is deprecated: this function does nothing; instead use ARMA_CERR_STREAM or ARMA_WARN_LEVEL; see documentation [-Wdeprecated-declarations]
  fdesignscpp.cpp:205:9: warning: 'set_cerr_stream' is deprecated: this function does nothing; instead use ARMA_CERR_STREAM or ARMA_WARN_LEVEL; see documentation [-Wdeprecated-declarations]
  fdesignscpp.cpp:276:9: warning: 'set_cerr_stream' is deprecated: this function does nothing; instead use ARMA_CERR_STREAM or ARMA_WARN_LEVEL; see documentation [-Wdeprecated-declarations]
  fdesignscpp.cpp:347:9: warning: 'set_cerr_stream' is deprecated: this function does nothing; instead use ARMA_CERR_STREAM or ARMA_WARN_LEVEL; see documentation [-Wdeprecated-declarations]
  Warning: fdesigns-package.Rd:26: All text must be in a section
  Warning: fdesigns-package.Rd:27: All text must be in a section
See ‘/srv/hornik/tmp/CRAN/fdesigns.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Debian clang version 18.1.6 (1)’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* 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 ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
* checking loading without being on the library search path ... [1s/1s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... WARNING
print:
  function(x, ...)
print.fglm:
  function(obj)

print:
  function(x, ...)
print.flm:
  function(obj)

summary:
  function(object, ...)
summary.fglm:
  function(obj)

summary:
  function(object, ...)
summary.flm:
  function(obj)

plot:
  function(x, ...)
plot.fglm:
  function(obj)

plot:
  function(x, ...)
plot.flm:
  function(obj)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [7s/7s] NOTE
fglm.ints: warning in bsalljcbpowercpp(t = tbounds, j = 0, nbs = lkxi,
  aposx = aposx, alldeg = dx[dx.ints == 1], allknotsx = allknotsxb, nx
  = nx.ints, nb = nb[q]): partial argument match of 'alldeg' to
  'alldegx'
fglm.intspols: warning in bsalljcbpowercpp(t = tbounds, j = 0, nbs =
  lkxi, aposx = aposx, alldeg = c(rep(dx[dxpols.coord],
  dx.pols[dxpols.coord])), allknotsx = allknotsxb, nx = nx.ints, nb =
  nb[h]): partial argument match of 'alldeg' to 'alldegx'
fglm.intspols: warning in bsalljcbpowercpp(t = tbounds, j = 0, nbs =
  lkxi, aposx = aposx, alldeg = dx[dx.ints == 1], allknotsx =
  allknotsxb, nx = nx.ints, nb = nb[q]): partial argument match of
  'alldeg' to 'alldegx'
flm.ce.ints: warning in bsalljcbpowercpp(t = t, j = 0, nbs = lkxi,
  aposx = aposx, alldeg = dx[dx.ints == 1], allknotsx = allknotsxb, nx
  = nx.ints, nb = nb[q]): partial argument match of 'alldeg' to
  'alldegx'
flm.ce.intspols: warning in bsalljcbpowercpp(t = t, j = 0, nbs = lkxi,
  aposx = aposx, alldeg = c(rep(dx[dxpols.coord],
  dx.pols[dxpols.coord])), allknotsx = allknotsxb, nx = nx.ints, nb =
  nb[h]): partial argument match of 'alldeg' to 'alldegx'
flm.ce.intspols: warning in bsalljcbpowercpp(t = t, j = 0, nbs = lkxi,
  aposx = aposx, alldeg = dx[dx.ints == 1], allknotsx = allknotsxb, nx
  = nx.ints, nb = nb[q]): partial argument match of 'alldeg' to
  'alldegx'
fglm.ints: no visible global function definition for ‘optim’
fglm.intspols: no visible global function definition for ‘optim’
fglm.me: no visible global function definition for ‘optim’
flm.ce.ints: no visible global function definition for ‘optim’
flm.ce.intspols: no visible global function definition for ‘optim’
flm.ce.me: no visible global function definition for ‘optim’
pfglm: no visible global function definition for ‘Vbsplinespp’
plot.fglm: no visible global function definition for ‘stepfun’
plot.fglm: no visible global function definition for ‘axis’
plot.flm: no visible global function definition for ‘stepfun’
plot.flm: no visible global function definition for ‘axis’
Undefined global functions or variables:
  Vbsplinespp axis optim stepfun
Consider adding
  importFrom("graphics", "axis")
  importFrom("stats", "optim", "stepfun")
to your NAMESPACE file.

Found the following calls to attach():
File ‘fdesigns/R/fglm_InteractionsPolynomials_mclapply.R’:
  attach(d)
File ‘fdesigns/R/flm_InteractionsPolynomials_mclapply.R’:
  attach(d)
See section ‘Good practice’ in ‘?attach’.
* checking Rd files ... [0s/0s] WARNING
prepare_Rd: fdesigns-package.Rd:26: All text must be in a section
prepare_Rd: fdesigns-package.Rd:27: All text must be in a section
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Error: 35: Tag \link not expected in code block
Execution halted
These lines will be truncated in the PDF manual.
* checking Rd cross-references ... WARNING
Unknown package ‘<pkg>’ in Rd xrefs
Missing link or links in Rd file 'P.Rd':
  ‘[fdesigns]{I}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Functions or methods with usage in Rd file 'plotfglm.Rd' but not in code:
  ‘plot’

Functions or methods with usage in Rd file 'plotflm.Rd' but not in code:
  ‘plot’

Functions or methods with usage in Rd file 'printfglm.Rd' but not in code:
  ‘print’ ‘summary’

Functions or methods with usage in Rd file 'printflm.Rd' but not in code:
  ‘print’ ‘summary’

Functions or methods with usage in Rd file 'summaryfglm.Rd' but not in code:
  ‘print’ ‘summary’

Functions or methods with usage in Rd file 'summaryflm.Rd' but not in code:
  ‘print’ ‘summary’

Codoc mismatches from Rd file 'pflm.Rd':
pflm
  Code: function(formula, nsd = 1, mc.cores = 1, npf, tbounds, nruns,
                 startd = NULL, dx, knotsx, pars, db, knotsb = NULL,
                 criterion = c("A", "D"), lambda = 0, dlbound = -1,
                 dubound = 1, tol = 1e-04, progress = FALSE)
  Docs: function(formula, nsd = 1, mc.cores = 1, npf, tbounds, nruns,
                 startd = NULL, dx, knotsx, pars, db, knotsb = NULL,
                 lambda = 0, criterion = c("A", "D"), tol = 1e-04,
                 dlbound = -1, dubound = 1, progress = FALSE)
  Mismatches in argument names (first 3):
    Position: 13 Code: criterion Docs: lambda
    Position: 14 Code: lambda Docs: criterion
    Position: 15 Code: dlbound Docs: tol

* checking Rd \usage sections ... WARNING
Objects in \usage without \alias in Rd file 'plotfglm.Rd':
  ‘plot’

Objects in \usage without \alias in Rd file 'plotflm.Rd':
  ‘plot’

Objects in \usage without \alias in Rd file 'printfglm.Rd':
  ‘print’ ‘summary’

Objects in \usage without \alias in Rd file 'printflm.Rd':
  ‘print’ ‘summary’

Objects in \usage without \alias in Rd file 'summaryfglm.Rd':
  ‘print’ ‘summary’

Objects in \usage without \alias in Rd file 'summaryflm.Rd':
  ‘print’ ‘summary’

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
Auto-generated content requiring editing in Rd file 'fdesigns-package.Rd':
  \details: ‘...o use the package, including the most important functions ~~’
  \references: ‘~~ Literature or other references for background information ~~’
  \seealso: ‘~~ Optional links to other man pages, e.g. ~~ ~~ \code{\link...’
* checking for unstated dependencies in examples ... ERROR
Warning: parse error in file 'fdesigns-Ex.R':
57:11: unexpected symbol
56: 
57: ~~ simple examples
              ^
** will not attempt to run examples
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking examples ... SKIPPED
* 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, 6 WARNINGs, 5 NOTEs