* using log directory 'd:/Rcompile/CRANpkg/local/4.7/phenofit.Rcheck' * using R Under development (unstable) (2026-10-24 r90762 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 14.3.0 GNU Fortran (GCC) 14.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * current time: 2026-10-26 00:03:17 UTC * checking for file 'phenofit/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'phenofit' version '0.3.11' * package encoding: UTF-8 * 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 hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'phenofit' can be installed ... OK * used C compiler: 'gcc.exe (GCC) 14.3.0' * used C++ compiler: 'g++.exe (GCC) 14.3.0' * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... 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 ... [3s] OK * checking whether the package can be loaded with stated dependencies ... [2s] OK * checking whether the package can be unloaded cleanly ... [2s] OK * checking whether the namespace can be loaded with stated dependencies ... [2s] OK * checking whether the namespace can be unloaded cleanly ... [3s] OK * checking loading without being on the library search path ... [2s] OK * checking whether startup messages can be suppressed ... [2s] 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 ... [17s] OK * checking Rd files ... [2s] OK * checking Rd metadata ... 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] OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * 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 pragmas in C/C++ headers and code ... OK * checking compiled code ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... [30s] OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... [55s] ERROR Running 'testthat.R' [55s] Running the tests in 'tests/testthat.R' failed. Complete output: > library(testthat) > library(phenofit) > > test_check("phenofit") Attaching package: 'data.table' The following object is masked from 'package:base': %notin% Saving _problems/test-PhenoExtract-25.R List of 5 $ AG : tibble [6 × 8] (S3: tbl_df/tbl/data.frame) $ Beck : tibble [6 × 7] (S3: tbl_df/tbl/data.frame) $ Elmore: tibble [6 × 8] (S3: tbl_df/tbl/data.frame) $ Gu : tibble [6 × 10] (S3: tbl_df/tbl/data.frame) $ Zhang : tibble [6 × 8] (S3: tbl_df/tbl/data.frame) NULL # A tibble: 6 × 8 flag t0 mn mx rsp a3 rau a5 1 1999_1 -135. 0.201 0.636 0.00932 2.85 0.00852 2 2 2000_1 189. 0.238 0.635 0.0126 2.47 0.00801 3.21 3 2001_1 569. 0.252 0.626 0.0108 2.96 0.00950 2.96 4 2002_1 892. 0.253 0.614 0.0159 2 0.00724 3.08 5 2003_1 1268. 0.236 0.577 0.0121 2.88 0.00723 2.88 6 2004_1 1676. 0.202 0.576 0.00839 2.81 0.00980 3.52 Saving _problems/test-PhenoExtract-53.R meth R2 NSE R RMSE pvalue n_sim 1: AG 0.9986908 0.9985845 0.9993452 9.940385e-03 4.489925e-65 46 2: Beck 1.0000000 1.0000000 1.0000000 4.931510e-10 0.000000e+00 46 3: Elmore 1.0000000 1.0000000 1.0000000 3.945072e-10 0.000000e+00 46 4: Gu 1.0000000 1.0000000 1.0000000 5.218882e-11 0.000000e+00 46 5: Zhang 1.0000000 1.0000000 1.0000000 5.529113e-06 8.044939e-208 46 $AG formula: mn + (mx - mn) * exp(-((t0 - t) * rsp)^a3) formula: mn + (mx - mn) * exp(-((t - t0) * rau)^a5) pars: t0 mn mx rsp a3 rau a5 nlminb 149.8926 0.1020656 0.7095242 0.009389263 6 0.009367765 6 warning: solve(): system is singular; attempting approx solution warning: solve(): system is close to singular; rcond: 1.65502e-16; attempting approx solution warning: solve(): system is close to singular; rcond: 2.19427e-17; attempting approx solution warning: solve(): system is close to singular; rcond: 1.65502e-16; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is close to singular; rcond: 1.33432e-17; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is close to singular; rcond: 2.38811e-17; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is close to singular; rcond: 2.03034e-17; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is close to singular; rcond: 1.33432e-17; attempting approx solution warning: solve(): system is close to singular; rcond: 3.31005e-17; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is close to singular; rcond: 3.08395e-17; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is close to singular; rcond: 2.36432e-17; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is close to singular; rcond: 6.97437e-18; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is close to singular; rcond: 1.85037e-16; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is close to singular; rcond: 2.80681e-17; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is close to singular; rcond: 5.43896e-17; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is close to singular; rcond: 2.38811e-17; attempting approx solution warning: solve(): system is close to singular; rcond: 3.05447e-17; attempting approx solution warning: solve(): system is close to singular; rcond: 2.11109e-17; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is close to singular; rcond: 6.04329e-17; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is close to singular; rcond: 1.85037e-16; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is close to singular; rcond: 2.80681e-17; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is close to singular; rcond: 5.43896e-17; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is close to singular; rcond: 3.31005e-17; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is close to singular; rcond: 2.38811e-17; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is close to singular; rcond: 3.31005e-17; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is close to singular; rcond: 2.38811e-17; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is close to singular; rcond: 1.94249e-17; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is close to singular; rcond: 3.84957e-17; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is close to singular; rcond: 3.31005e-17; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is close to singular; rcond: 8.58712e-17; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is close to singular; rcond: 2.38811e-17; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is close to singular; rcond: 2.09346e-17; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is close to singular; rcond: 3.82199e-17; attempting approx solution warning: solve(): system is close to singular; rcond: 2.38705e-17; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is close to singular; rcond: 2.38811e-17; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is close to singular; rcond: 5.88785e-17; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is close to singular; rcond: 1.85037e-16; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is close to singular; rcond: 7.40149e-17; attempting approx solution warning: solve(): system is close to singular; rcond: 6.20634e-17; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is close to singular; rcond: 2.38811e-17; attempting approx solution warning: solve(): system is close to singular; rcond: 3.05447e-17; attempting approx solution warning: solve(): system is close to singular; rcond: 2.11109e-17; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is close to singular; rcond: 5.43896e-17; attempting approx solution warning: solve(): system is close to singular; rcond: 4.38854e-17; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is close to singular; rcond: 1.00786e-16; attempting approx solution warning: solve(): system is close to singular; rcond: 1.46031e-17; attempting approx solution warning: solve(): system is close to singular; rcond: 5.02097e-17; attempting approx solution warning: solve(): system is close to singular; rcond: 1.25524e-17; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is close to singular; rcond: 3.31005e-17; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is close to singular; rcond: 3.31005e-17; attempting approx solution [ FAIL 2 | WARN 2 | SKIP 0 | PASS 68 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-PhenoExtract.R:23:1'): (code run outside of `test_that()`) ─── Expected `{ ... }` to run silently. Actual noise: warnings. ── Failure ('test-PhenoExtract.R:50:5'): get_pheno.fFIT works ────────────────── Expected `{ ... }` to run silently. Actual noise: warnings. [ FAIL 2 | WARN 2 | SKIP 0 | PASS 68 ] Error: ! Test failures. Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [32s] OK * checking PDF version of manual ... [23s] OK * checking HTML version of manual ... [6s] OK * DONE Status: 1 ERROR