* using log directory ‘/srv/hornik/tmp/CRAN_pretest/fbkmr.Rcheck’
* using R Under development (unstable) (2024-12-10 r87437)
* 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 ‘fbkmr/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘fbkmr’ version ‘0.1.1’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [3s/3s] NOTE
Maintainer: ‘Junwei Lu <junweilu@hsph.harvard.edu>’

New submission
* 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 ‘fbkmr’ can be installed ... [6s/6s] WARNING
Found the following significant warnings:
  Note: possible error in 'postmeanhnew_wasp(fit = fit, ': unused argument (method = method) 
  Warning: replacing previous import ‘Matrix::image’ by ‘graphics::image’ when loading ‘fbkmr’
  Warning: replacing previous import ‘Matrix::cov2cor’ by ‘stats::cov2cor’ when loading ‘fbkmr’
  Warning: replacing previous import ‘Matrix::toeplitz’ by ‘stats::toeplitz’ when loading ‘fbkmr’
  Warning: replacing previous import ‘Matrix::update’ by ‘stats::update’ when loading ‘fbkmr’
  Warning: replacing previous import ‘Matrix::tail’ by ‘utils::tail’ when loading ‘fbkmr’
  Warning: replacing previous import ‘Matrix::head’ by ‘utils::head’ when loading ‘fbkmr’
See ‘/srv/hornik/tmp/CRAN_pretest/fbkmr.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking DESCRIPTION meta-information ... NOTE
License components which are templates and need '+ file LICENSE':
  MIT
* checking top-level files ... NOTE
Non-standard files/directories found at top level:
  ‘Makefile’ ‘Readme.md’ ‘Scalable_BKMR_arxiv.pdf’ ‘figs’
* 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 whether startup messages can be suppressed ... [1s/1s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... WARNING
'::' or ':::' imports not declared from:
  ‘dplyr’ ‘tidyr’ ‘truncnorm’
'library' or 'require' calls not declared from:
  ‘Matrix’ ‘lpSolve’
'library' or 'require' calls in package code:
  ‘Matrix’ ‘lpSolve’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [11s/11s] NOTE
kmbayes_Wasp: warning in kmbayes(y = y_i, Z = Z_i, X = X_i, Znew =
  Znew, iter = iter, knots = knots100, control.param = list(lambda.jump
  = rep(2.8, 1), mu.lambda = rep(15, 1), sigma.lambda = rep(8, 1)),
  verbose = F, varsel = varsel, sketch.type = "sub_sampling", p =
  ceiling(nrow(Z)/n_subset), n_subset = n_subset, indx = indx, Snum =
  1, est.h = FALSE, h.post.type = h.post.type, est.last.h = 1000):
  partial argument match of 'control.param' to 'control.params'
OverallRiskSummaries : preds.fun: possible error in
  postmeanhnew_wasp(fit = fit, y = y, Z = Z, X = X, Znew = znew, sel =
  sel, method = method): unused argument (method = method)
PredictorResponseBivar: no visible binding for global variable ‘j’
PredictorResponseUnivar: no visible binding for global variable ‘j’
SingVarIntSummary : preds.fun: possible error in postmeanhnew_wasp(fit
  = fit, y = y, Z = Z, X = X, Znew = znew, sel = sel, method = method):
  unused argument (method = method)
VarRiskSummary : preds.fun: possible error in postmeanhnew_wasp(fit =
  fit, y = y, Z = Z, X = X, Znew = znew, sel = sel, method = method):
  unused argument (method = method)
kmbayes_Wasp: no visible binding for global variable ‘i’
kmbayes_Wasp: no visible binding for global variable ‘h.post.type’
linear_prog_h: no visible binding for global variable ‘samp_1’
linear_prog_h: no visible binding for global variable ‘samp_2’
overall_dens: no visible global function definition for ‘gurobi’
overall_dens_h: no visible binding for global variable ‘result’
overall_dens_h: no visible binding for global variable ‘aOptSol’
sketching: no visible global function definition for ‘mvrnorm’
wasp_bayes: no visible binding for global variable ‘samp_1’
wasp_bayes: no visible binding for global variable ‘samp_2’
wasp_bayes: no visible binding for global variable ‘post_samp_1’
Undefined global functions or variables:
  aOptSol gurobi h.post.type i j mvrnorm post_samp_1 result samp_1
  samp_2

Found if() conditions comparing class() to string:
File ‘fbkmr/R/CompPostmeanHnew_wasp.R’: if (class(Znew) == "data.frame") ...
File ‘fbkmr/R/CompRisk_wasp.R’: if (class(Znew) == "data.frame") ...
File ‘fbkmr/R/InvestigatePrior_rm.R’: if (class(U) == "try-error") ...
File ‘fbkmr/R/SamplePred.R’: if (class(Znew) == "data.frame") ...
File ‘fbkmr/R/SamplePred.R’: if (class(Xnew) != "matrix") ...
Use inherits() (or maybe is()) instead.
* 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 ... WARNING
Functions or methods with usage in Rd file 'hello.Rd' but not in code:
  ‘hello’

Codoc mismatches from Rd file 'skmbayes.Rd':
skmbayes
  Code: function(Z, X, y, n_subset = 1, n_samp = 200, iter = 1000,
                 varsel = FALSE, est.h = TRUE, Znew = NULL, file_path =
                 NULL, save_loc = FALSE, ...)
  Docs: function(Z, X, y, n_subset = 1, n_samp = 200, iter = 1000,
                 varsel = FALSE, est.h = TRUE, Znew = NULL, file_path =
                 NULL, save_loc = FALSE, linprog = TRUE, ...)
  Argument names in docs not in code:
    linprog
  Mismatches in argument names:
    Position: 12 Code: ... Docs: linprog

* checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'OverallRiskSummaries_wasp.Rd'
  ‘Z.q’

Undocumented arguments in Rd file 'SingVarRiskSummaries_wasp.Rd'
  ‘Z.q’

Undocumented arguments in Rd file 'kmbayes.Rd'
  ‘sketch.type’ ‘p’ ‘n_subset’ ‘indx’ ‘Snum’ ‘h.post.type’ ‘est.last.h’

Undocumented arguments in Rd file 'kmbayes_Wasp.Rd'
  ‘n_samp’ ‘save_loc’ ‘...’
Documented arguments not in \usage in Rd file 'kmbayes_Wasp.Rd':
  ‘family’ ‘id’ ‘verbose’ ‘starting.values’ ‘control.params’ ‘groups’
  ‘ztest’ ‘rmethod’

Documented arguments not in \usage in Rd file 'postmeanhnew_wasp.Rd':
  ‘method’

Undocumented arguments in Rd file 'skmbayes.Rd'
  ‘...’
Documented arguments not in \usage in Rd file 'skmbayes.Rd':
  ‘family’ ‘id’ ‘verbose’ ‘starting.values’ ‘control.params’ ‘groups’
  ‘knots’ ‘ztest’ ‘rmethod’

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.
S3 methods shown with full name in Rd file 'print.bkmrfit.Rd':
  ‘print.bkmrfit’

S3 methods shown with full name in Rd file 'summary.bkmrfit.Rd':
  ‘summary.bkmrfit’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... WARNING
Found the following file(s) containing GNU extensions:
  Makefile
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif, .NOTPARALLEL See section ‘Writing portable
packages’ in the ‘Writing R Extensions’ manual.
* checking include directives in Makefiles ... OK
* checking examples ... [1s/1s] ERROR
Running examples in ‘fbkmr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: hello
> ### Title: Hello, World!
> ### Aliases: hello
> 
> ### ** Examples
> 
> hello()
Error in hello() : could not find function "hello"
Execution halted
* checking PDF version of manual ... [3s/3s] OK
* checking HTML version of manual ... [1s/1s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR, 5 WARNINGs, 4 NOTEs