* using log directory ‘/srv/hornik/tmp/CRAN_pretest/refund.Rcheck’
* using R Under development (unstable) (2024-09-18 r87177)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 18.1.8 (9)
    Debian flang-new version 18.1.8 (9)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘refund/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘refund’ version ‘0.1-37’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [5s/6s] INFO
Maintainer: ‘Julia Wrobel <julia.wrobel@emory.edu>’
* 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 ‘refund’ can be installed ... [13s/13s] WARNING
Found the following significant warnings:
  Warning: S3 method ‘smooth.construct.peer.smooth.spec’ was declared in NAMESPACE but not found
See ‘/srv/hornik/tmp/CRAN_pretest/refund.Rcheck/00install.out’ for details.
* 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 ... [2s/2s] 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] NOTE
Warning: S3 method ‘smooth.construct.peer.smooth.spec’ was declared in NAMESPACE but not found

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... [2s/2s] 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 ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [28s/28s] OK
* checking Rd files ... [1s/1s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  af.Rd: bam, gamm, smooth.terms, s, t2, te, linear.functional.terms
  af_old.Rd: bam, gamm, s, t2, te, smooth.basisPar, fd,
    linear.functional.terms
  fgam.Rd: gam
  fosr.Rd: fd
  fosr.vs.Rd: grpreg
  fosr2s.Rd: fd
  fpc.Rd: bam, gamm
  lf.Rd: bam, gamm, smooth.terms, linear.functional.terms
  lf.vd.Rd: te, s, linear.functional.terms
  lf_old.Rd: bam, gamm, te, s, smooth.basisPar, fd,
    linear.functional.terms
  peer_old.Rd: lme
  pfr.Rd: gam, s, te, t2, bam, gamm, gamm4
  predict.fgam.Rd: predict.gam
  predict.pfr.Rd: predict.gam
  smooth.construct.fpc.smooth.spec.Rd: smooth.construct
  smooth.construct.pco.smooth.spec.Rd: gam
  smooth.construct.peer.smooth.spec.Rd: smooth.construct
  vis.fgam.Rd: levelplot, vis.gam, plot.gam
  vis.pfr.Rd: levelplot, vis.gam, plot.gam
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 ... [12s/12s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [55s/55s] ERROR
  Running ‘testthat.R’ [55s/55s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > library("refund")
  Warning message:
  S3 method 'smooth.construct.peer.smooth.spec' was declared in NAMESPACE but not found 
  > 
  > Sys.setenv(NOT_CRAN = "true")
  > test_check("refund")
  nbasis: 40 
  nbasis: 40 
  nbasis: 20 
  nbasis: 25 
  nbasis: 30 
  nbasis: 35 
  nbasis: 40 
  nbasis: 35 
  using seWithMean for  s(argvals.vec) .
  using seWithMean for  te(xte1,xte2) .
  using seWithMean for  s(argvals.vec) .
  using seWithMean for  te(xte1,xte2) .
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 42 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-peer.R:8:3'): peer with D2 penalty ─────────────────────────────
  Error in `UseMethod("smooth.construct")`: no applicable method for 'smooth.construct' applied to an object of class "peer.smooth.spec"
  Backtrace:
      ▆
   1. └─refund::pfr(pasat ~ peer(cca, pentype = "D"), data = DTI) at test-peer.R:8:3
   2.   ├─base::eval(newcall)
   3.   │ └─base::eval(newcall)
   4.   └─mgcv::gam(...)
   5.     ├─base::do.call(...)
   6.     └─mgcv:::gam.setup(...)
   7.       └─mgcv::smoothCon(...)
   8.         └─mgcv:::smooth.construct3(object, data, knots)
   9.           └─mgcv::smooth.construct(object, dk$data, dk$knots)
  ── Error ('test-peer.R:18:3'): peer with structured penalty works ──────────────
  Error in `UseMethod("smooth.construct")`: no applicable method for 'smooth.construct' applied to an object of class "peer.smooth.spec"
  Backtrace:
      ▆
   1. └─refund::pfr(...) at test-peer.R:18:3
   2.   ├─base::eval(newcall)
   3.   │ └─base::eval(newcall)
   4.   └─mgcv::gam(...)
   5.     ├─base::do.call(...)
   6.     └─mgcv:::gam.setup(...)
   7.       └─mgcv::smoothCon(...)
   8.         └─mgcv:::smooth.construct3(object, data, knots)
   9.           └─mgcv::smooth.construct(object, dk$data, dk$knots)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 42 ]
  Error: Test failures
  Execution halted
* checking PDF version of manual ... [6s/5s] OK
* checking HTML version of manual ... [4s/3s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR, 1 WARNING, 2 NOTEs