• using R Under development (unstable) (2026-09-16 r90549 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: 2026-09-17 21:50:35 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 See the install log for details.
• 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 ... [3s] 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 ... [1s] 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 ... [31s] OK
• checking for unstated dependencies in 'tests' ... OK
• checking tests ... [56s] 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     <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>   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      <char> <num> <num> <num> <num> <num> <num>   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 ... [33s] OK
• checking PDF version of manual ... [23s] OK
• checking HTML version of manual ... [7s] OK
• DONE

Status: 1 ERROR