• using R Under development (unstable) (2025-11-05 r88988)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     Debian clang version 19.1.7 (7)     Debian flang-new version 19.1.7 (7)
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8
• checking for file ‘phenofit/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘phenofit’ version ‘0.3.10’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [2s/2s] OK
• 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 ‘phenofit’ can be installed ... OK See the install log for details.
• used C compiler: ‘Debian clang version 19.1.7 (7)’
• used C++ compiler: ‘Debian clang version 19.1.7 (7)’
• checking package directory ... OK
• checking for future file timestamps ... 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/4s] OK
• checking whether the package can be loaded with stated dependencies ... [2s/3s] OK
• checking whether the package can be unloaded cleanly ... [2s/3s] OK
• checking whether the namespace can be loaded with stated dependencies ... [2s/3s] OK
• checking whether the namespace can be unloaded cleanly ... [2s/4s] OK
• checking loading without being on the library search path ... [3s/4s] OK
• checking whether startup messages can be suppressed ... [2s/4s] 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/38s] OK
• checking Rd files ... [1s/1s] 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 ... 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/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 $(LAPACK_LIBS) ... OK
• checking use of PKG_*FLAGS in Makefiles ... OK
• checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
• checking pragmas in C/C++ headers and code ... OK
• checking compilation flags used ... OK
• checking compiled code ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [20s/24s] ERROR Running examples in ‘phenofit-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: roughFit > ### Title: Rough fitting > ### Aliases: roughFit > ### Keywords: internal > > ### ** Examples > > data("CA_NS6") > d <- CA_NS6 > > nptperyear <- 23 > INPUT <- check_input(d$t, d$y, d$w, + QC_flag = d$QC_flag, + nptperyear = nptperyear, south = FALSE, + maxgap = nptperyear / 4, alpha = 0.02, wmin = 0.2 + ) > # plot_input(INPUT) > > wFUN <- "wTSM" > # all year as a whole > options = list(rFUN = "smooth_wWHIT", wFUN = wFUN, lambda = 10) > brks <- season(INPUT, lambda = 10) > plot_season(INPUT, brks, d) > > brks2 = season_input(INPUT, options) > all.equal(brks2, brks) [1] TRUE > > c(d_fit, info_peak) %<-% roughFit(INPUT) > d_season = find_season.peaks(d_fit, info_peak) > > c(t, ypred) %<-% d_fit[, .(t, ziter2)] > d_season = find_season.default(ypred, t) > all.equal(brks$dt, d_season) [1] TRUE > > # opt <- .options$season > # brks$fit - d_fit # function passed test > > # curve fitting by year > brks_mov <- season_mov(INPUT, + options = list( + rFUN = "smooth_wWHIT", wFUN = wFUN, + lambda = 10, + r_min = 0.05, ypeak_min = 0.05, + verbose = TRUE + ) + )   [season_mov] running 1 ... iloop = 1: lambda = 10.0, ntrough_PerYear = 0.00, npeak_PerYear = 0.00 iloop = 2: lambda = 5.0, ntrough_PerYear = 0.00, npeak_PerYear = 0.00 iloop = 3: lambda = 2.5, ntrough_PerYear = 0.00, npeak_PerYear = 0.00   [season_mov] running 2 ... iloop = 1: lambda = 10.0, ntrough_PerYear = 0.00, npeak_PerYear = 0.00 iloop = 2: lambda = 5.0, ntrough_PerYear = 0.00, npeak_PerYear = 0.00 iloop = 3: lambda = 2.5, ntrough_PerYear = 0.00, npeak_PerYear = 0.00   [season_mov] running 3 ... iloop = 1: lambda = 10.0, ntrough_PerYear = 0.00, npeak_PerYear = 0.00 iloop = 2: lambda = 5.0, ntrough_PerYear = 0.00, npeak_PerYear = 0.00 iloop = 3: lambda = 2.5, ntrough_PerYear = 0.00, npeak_PerYear = 0.00   [season_mov] running 4 ... iloop = 1: lambda = 10.0, ntrough_PerYear = 0.00, npeak_PerYear = 0.00 iloop = 2: lambda = 5.0, ntrough_PerYear = 0.00, npeak_PerYear = 0.00 iloop = 3: lambda = 2.5, ntrough_PerYear = 0.00, npeak_PerYear = 0.00   [season_mov] running 5 ... iloop = 1: lambda = 10.0, ntrough_PerYear = 0.00, npeak_PerYear = 0.00 iloop = 2: lambda = 5.0, ntrough_PerYear = 0.00, npeak_PerYear = 0.00 iloop = 3: lambda = 2.5, ntrough_PerYear = 0.00, npeak_PerYear = 0.00   [season_mov] running 6 ... iloop = 1: lambda = 10.0, ntrough_PerYear = 0.00, npeak_PerYear = 0.00 iloop = 2: lambda = 5.0, ntrough_PerYear = 0.00, npeak_PerYear = 0.00 iloop = 3: lambda = 2.5, ntrough_PerYear = 0.00, npeak_PerYear = 0.00   [season_mov] running 7 ... iloop = 1: lambda = 10.0, ntrough_PerYear = 0.00, npeak_PerYear = 0.00 iloop = 2: lambda = 5.0, ntrough_PerYear = 0.00, npeak_PerYear = 0.00 iloop = 3: lambda = 2.5, ntrough_PerYear = 0.00, npeak_PerYear = 0.00 > plot_season(INPUT, brks_mov) > > rfit <- brks2rfit(brks_mov) > r <- get_pheno(rfit) Error in `str_replace_all()`: ! Failed to apply `replacement` function. ℹ It must accept a character vector of any length. Caused by error in `rep()`: ! invalid 'times' argument Backtrace:      ▆   1. ├─phenofit::get_pheno(rfit)   2. ├─phenofit:::get_pheno.rfit(rfit)   3. │ └─... %>% set_names(dt$flag)   4. ├─dplyr::group_map(...)   5. ├─dplyr:::group_map.data.frame(...)   6. │ └─dplyr:::map2(chunks, group_keys, .f, ...)   7. │ └─base::mapply(.f, .x, .y, MoreArgs = list(...), SIMPLIFY = FALSE)   8. │ └─phenofit (local) `<fn>`(dots[[1L]][[1L]], dots[[2L]][[1L]])   9. │ └─phenofit:::PhenoDeriv.default(values, t, der1, IsPlot = FALSE)  10. │ └─phenofit::findpeaks(...)  11. │ └─xc %<>% str_replace_midzero()  12. ├─phenofit:::str_replace_midzero(.)  13. │ └─str_replace_all(x, "\\++0\\++", . %>% replace("+")) %>% ...  14. ├─stringr::str_replace_all(., "-+0-+", . %>% replace("-"))  15. │ └─stringr:::str_transform_all(string, pattern, replacement)  16. │ ├─base::withCallingHandlers(...)  17. │ └─magrittr (local) replacement(old_flat)  18. │ └─magrittr::freduce(value, `_function_list`)  19. │ ├─base::withVisible(function_list[[k]](value))  20. │ └─function_list[[k]](value)  21. │ └─phenofit (local) replace(., "-")  22. │ └─base::paste(rep(replacement, nchar(x)), collapse = "")  23. └─base::.handleSimpleError(...)  24. └─stringr (local) h(simpleError(msg, call))  25. └─cli::cli_abort(...)  26. └─rlang::abort(...) Execution halted
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [55s/64s] ERROR   Running ‘testthat.R’ [55s/63s] Running the tests in ‘tests/testthat.R’ failed. Complete output:   > library(testthat)   > library(phenofit)   >   > test_check("phenofit")   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        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 4.932917e-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 8.315171e-11 0.000000e+00 46   5: Zhang 1.0000000 1.0000000 1.0000000 5.529117e-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 singular (rcond: 1.65502e-16); attempting approx solution      warning: solve(): system is singular (rcond: 2.19427e-17); attempting approx solution      warning: solve(): system is 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 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 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 (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 singular (rcond: 1.33432e-17); attempting approx solution      warning: solve(): system is 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 singular (rcond: 3.08395e-17); attempting approx solution      warning: solve(): system is singular; attempting approx solution      warning: solve(): system is 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 singular (rcond: 6.97437e-18); attempting approx solution   [ FAIL 2 | WARN 2 | SKIP 0 | PASS 66 ]      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Error ('test-PhenoExtract.R:63:5'): get_pheno.rfit works ────────────────────   Error in `str_replace_all(x, "\\++0\\++", . %>% replace("+"))`: Failed to apply `replacement` function.   ℹ It must accept a character vector of any length.   Caused by error in `rep()`:   ! invalid 'times' argument   Backtrace:        ▆     1. ├─phenofit::get_pheno(rfit) at test-PhenoExtract.R:63:5     2. ├─phenofit:::get_pheno.rfit(rfit)     3. │ └─... %>% set_names(dt$flag)     4. ├─dplyr::group_map(...)     5. ├─dplyr:::group_map.data.frame(...)     6. │ └─dplyr:::map2(chunks, group_keys, .f, ...)     7. │ └─base::mapply(.f, .x, .y, MoreArgs = list(...), SIMPLIFY = FALSE)     8. │ └─phenofit (local) `<fn>`(dots[[1L]][[4L]], dots[[2L]][[4L]])     9. │ └─phenofit:::PhenoDeriv.default(values, t, der1, IsPlot = FALSE)    10. │ └─phenofit::findpeaks(...)    11. │ └─xc %<>% str_replace_midzero()    12. ├─phenofit:::str_replace_midzero(.)    13. │ ├─str_replace_all(x, "\\++0\\++", . %>% replace("+")) %>% ...    14. │ └─stringr::str_replace_all(x, "\\++0\\++", . %>% replace("+"))    15. │ └─stringr:::str_transform_all(string, pattern, replacement)    16. │ ├─base::withCallingHandlers(...)    17. │ └─magrittr (local) replacement(old_flat)    18. │ └─magrittr::freduce(value, `_function_list`)    19. │ ├─base::withVisible(function_list[[k]](value))    20. │ └─function_list[[k]](value)    21. │ └─phenofit (local) replace(., "+")    22. │ └─base::paste(rep(replacement, nchar(x)), collapse = "")    23. ├─stringr::str_replace_all(., "-+0-+", . %>% replace("-"))    24. │ └─stringr:::str_transform_all(string, pattern, replacement)    25. │ └─stringr::str_locate_all(string, pattern)    26. │ └─stringr:::check_lengths(string, pattern)    27. │ └─vctrs::vec_size_common(...)    28. └─base::.handleSimpleError(...)    29. └─stringr (local) h(simpleError(msg, call))    30. └─cli::cli_abort(...)    31. └─rlang::abort(...)   ── Error ('test-season.R:34:5'): `season` with smooth_wSG ──────────────────────   Error in `str_replace_all(., "-+0-+", . %>% replace("-"))`: Failed to apply `replacement` function.   ℹ It must accept a character vector of any length.   Caused by error in `rep()`:   ! invalid 'times' argument   Backtrace:        ▆     1. ├─testthat::expect_silent(brks <- do.call(season, param)) at test-season.R:34:5     2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)     3. │ ├─testthat (local) .capture(...)     4. │ │ ├─withr::with_output_sink(...)     5. │ │ │ └─base::force(code)     6. │ │ ├─base::withCallingHandlers(...)     7. │ │ └─base::withVisible(code)     8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))     9. ├─base::do.call(season, param)    10. ├─phenofit (local) `<fn>`(...)    11. │ └─phenofit:::findpeaks_season(...)    12. │ └─phenofit::findpeaks(...)    13. │ └─xc %<>% str_replace_midzero()    14. ├─phenofit:::str_replace_midzero(.)    15. │ └─str_replace_all(x, "\\++0\\++", . %>% replace("+")) %>% ...    16. ├─stringr::str_replace_all(., "-+0-+", . %>% replace("-"))    17. │ └─stringr:::str_transform_all(string, pattern, replacement)    18. │ ├─base::withCallingHandlers(...)    19. │ └─magrittr (local) replacement(old_flat)    20. │ └─magrittr::freduce(value, `_function_list`)    21. │ ├─base::withVisible(function_list[[k]](value))    22. │ └─function_list[[k]](value)    23. │ └─phenofit (local) replace(., "-")    24. │ └─base::paste(rep(replacement, nchar(x)), collapse = "")    25. └─base::.handleSimpleError(...)    26. └─stringr (local) h(simpleError(msg, call))    27. └─cli::cli_abort(...)    28. └─rlang::abort(...)      [ FAIL 2 | WARN 2 | SKIP 0 | PASS 66 ]   Error: Test failures   Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [34s/44s] OK
• checking PDF version of manual ... [10s/13s] OK
• checking HTML version of manual ... [4s/7s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 2 ERRORs