Package: clustNet Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘clustNet.Rmd’ using rmarkdown Quitting from lines 23-33 [unnamed-chunk-1] (clustNet.Rmd) Error: processing vignette 'clustNet.Rmd' failed with diagnostics: sample_degseq() did not succeed in maxtry=20 iterations --- failed re-building ‘clustNet.Rmd’ SUMMARY: processing the following file failed: ‘clustNet.Rmd’ Error: Vignette re-building failed. Execution halted Package: phenofit Check: tests New result: ERROR Running ‘testthat.R’ [66s/67s] 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 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 1677. 0.202 0.576 0.00832 2.84 0.00990 3.48 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 1.389780e-09 0.000000e+00 46 3: Elmore 1.0000000 1.0000000 1.0000000 4.161813e-10 0.000000e+00 46 4: Gu 1.0000000 1.0000000 1.0000000 4.891365e-11 0.000000e+00 46 5: Zhang 1.0000000 1.0000000 1.0000000 5.529073e-06 8.043461e-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 warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 1.85037e-16); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 2.80681e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is 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 singular (rcond: 2.38811e-17); attempting approx solution warning: solve(): system is singular (rcond: 3.05447e-17); attempting approx solution warning: solve(): system is 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 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 singular (rcond: 1.85037e-16); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 2.80681e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is 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 (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 (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 (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: 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 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 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 singular (rcond: 3.31005e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is 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 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 (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 singular (rcond: 3.82199e-17); attempting approx solution warning: solve(): system is 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 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: 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 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 singular (rcond: 7.40149e-17); attempting approx solution warning: solve(): system is 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 singular (rcond: 2.38811e-17); attempting approx solution warning: solve(): system is singular (rcond: 3.05447e-17); attempting approx solution warning: solve(): system is 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 (rcond: 5.43896e-17); attempting approx solution warning: solve(): system is 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 singular (rcond: 1.00786e-16); attempting approx solution warning: solve(): system is singular (rcond: 1.46031e-17); attempting approx solution warning: solve(): system is singular (rcond: 5.02097e-17); attempting approx solution warning: solve(): system is 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 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: 3.31005e-17); attempting approx solution [ FAIL 1 | WARN 2 | SKIP 0 | PASS 69 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-curvefit.R:18:5'): curvefit works ──────────────────────────── all.equal(p1, p2, tolerance = 1e-06) is not TRUE `actual` is a character vector ('Component "Elmore": Component "mn": Mean relative difference: 1.990404e-06') `expected` is a logical vector (TRUE) [ FAIL 1 | WARN 2 | SKIP 0 | PASS 69 ] Error: Test failures Execution halted Package: Rcssplot Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘Rcssplot.Rnw’ using knitr Quitting from lines 122-132 [base_barplot] (Rcssplot.Rnw) Error: processing vignette 'Rcssplot.Rnw' failed with diagnostics: :2:1: unexpected input 1: par(mfrow = c(1, 3), mar = c(2, 6, 4.8, 2)) 2: << ^ --- failed re-building ‘Rcssplot.Rnw’ SUMMARY: processing the following file failed: ‘Rcssplot.Rnw’ Error: Vignette re-building failed. Execution halted Package: rerddapXtracto Check: examples New result: ERROR Running examples in ‘rerddapXtracto-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: rxtracto > ### Title: Extract environmental data along a trajectory from an 'ERDDAP™' > ### server using 'rerddap'. > ### Aliases: rxtracto > > ### ** Examples > > ## toy example to show use > ## but keep execution time down > ## > # dataInfo <- rerddap::info('erdHadISST') > ## > parameter <- 'sst' > xcoord <- c(-130.5) > ycoord <- c(40.5) > tcoord <- c('2006-01-16') > # extract <- rxtracto(dataInfo, parameter = parameter, xcoord = xcoord, > # ycoord = ycoord, tcoord= tcoord > # ) > ## > ## bathymetry example > ## 2-D example getting bathymetry > dataInfo <- rerddap::info('etopo360') Error in curl::curl_fetch_memory(x$url$url, handle = x$url$handle) : Timeout was reached [upwell.pfeg.noaa.gov]: Connection time-out Calls: ... -> crul_fetch -> -> raise_libcurl_error Execution halted Package: weyl Check: tests New result: ERROR Running ‘testthat.R’ [52s/52s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library("testthat") > test_check("weyl") Loading required package: weyl Checking test 1 ... Test 1 passed Checking test 2 ... Test 2 passed Checking test 3 ... Test 3 passed [ FAIL 1 | WARN 0 | SKIP 0 | PASS 154 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test_aaa.R:39:3'): Test suite aaa.R ─────────────────────────────── `A^-1` did not throw an error. Backtrace: ▆ 1. └─weyl (local) checker1(A1) at test_aaa.R:87:1 2. └─testthat::expect_error(A^-1) at test_aaa.R:39:3 [ FAIL 1 | WARN 0 | SKIP 0 | PASS 154 ] Error: Test failures Execution halted