* using log directory ‘/data/gannet/ripley/R/packages/tests-Suggests/hyperSpec.Rcheck’ * using R Under development (unstable) (2022-05-26 r82405) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-stop-on-test-error’ * checking for file ‘hyperSpec/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘hyperSpec’ version ‘0.100.0’ * 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 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 ‘hyperSpec’ can be installed ... [25s/30s] 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 R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... 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 ... [33s/33s] OK * checking Rd files ... 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 ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking R/sysdata.rda ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [17s/17s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘unittests.R’ ERROR Running the tests in ‘tests/unittests.R’ failed. Complete output: > library (testthat) > test_check("hyperSpec") Loading required package: hyperSpec Loading required package: lattice Loading required package: grid Loading required package: ggplot2 Loading required package: xml2 Package hyperSpec, version 0.100.0 To get started, try vignette ("hyperspec") package?hyperSpec vignette (package = "hyperSpec") If you use this package please cite it appropriately. citation("hyperSpec") will give you the correct reference. The project homepage is http://hyperspec.r-forge.r-project.org [ FAIL 1 | WARN 0 | SKIP 62 | PASS 331 ] ══ Skipped tests ═══════════════════════════════════════════════════════════════ • TODO: implement (1) • empty test (4) • file import test files not installed (55) • no spc files with empty spectra available so far (1) • skip (1) ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure (???): non-increasing wavelength axis ─────────────────────────────── `plotmat(tmp)` produced warnings. [ FAIL 1 | WARN 0 | SKIP 62 | PASS 331 ] Deleting unused snapshots: • attached/plot-1-fill.svg • attached/plot-1-rev.svg • attached/plot-c.svg • attached/plot-depth.svg • attached/plot-map.svg • attached/plot-mat-contour.svg • attached/plot-mat.svg • attached/plot-spc.svg • attached/plot-spcmeansd.svg • attached/plot-spcprctile.svg • attached/plot-spcprctl5.svg • attached/plot-ts.svg • attached/plot-voronoi.svg • attached/plot.svg Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking re-building of vignette outputs ... [53s/53s] ERROR Error(s) in re-building vignettes: --- re-building ‘chondro.pdf.asis’ using asis --- finished re-building ‘chondro.pdf.asis’ --- re-building ‘fileio.pdf.asis’ using asis --- finished re-building ‘fileio.pdf.asis’ --- re-building ‘baseline.Rnw’ using Sweave Loading required package: lattice Loading required package: grid Loading required package: ggplot2 Loading required package: xml2 Package hyperSpec, version 0.100.0 To get started, try vignette ("hyperspec") package?hyperSpec vignette (package = "hyperSpec") If you use this package please cite it appropriately. citation("hyperSpec") will give you the correct reference. The project homepage is http://hyperspec.r-forge.r-project.org start: 300 support points Iteration 1: 146 support points Iteration 2: 85 support points Iteration 3: 44 support points Iteration 4: 26 support points Iteration 5: 12 support points Iteration 6: 7 support points Iteration 7: 2 support points Warning in max(x@wavelength) : no non-missing arguments to max; returning -Inf Warning in min(x@wavelength) : no non-missing arguments to min; returning Inf Warning in max(x@wavelength) : no non-missing arguments to max; returning -Inf Warning in min(x@wavelength) : no non-missing arguments to min; returning Inf Iteration 8: 0 support points spectrum 1: 2 support points, noise = 0.0, 8 iterations Fitting with npts.min = 15 start: 300 support points spectrum 1: 20 support points, noise = 0.0, 5 iterations Fitting with npts.min = 15 start: 300 support points spectrum 1: 26 support points, noise = 0.0, 5 iterations Fitting with npts.min = 15 start: 300 support points spectrum 1: 25 support points, noise = 0.0, 5 iterations Fitting with npts.min = 5 start: 100 support points spectrum 1: 99 support points, noise = 4.0, 2 iterations Fitting with npts.min = 15 start: 300 support points Iteration 1: 153 support points Iteration 2: 93 support points Iteration 3: 54 support points Iteration 4: 38 support points Iteration 5: 32 support points Iteration 6: 29 support points Iteration 7: 29 support points spectrum 1: 29 support points, noise = 15.0, 7 iterations Error: processing vignette 'baseline.Rnw' failed with diagnostics: chunk 20 Error in UseMethod("toBibtex") : no applicable method for 'toBibtex' applied to an object of class "NULL" --- failed re-building ‘baseline.Rnw’ --- re-building ‘flu.Rnw’ using Sweave Loading required package: lattice Loading required package: grid Loading required package: ggplot2 Loading required package: xml2 Package hyperSpec, version 0.100.0 To get started, try vignette ("hyperspec") package?hyperSpec vignette (package = "hyperSpec") If you use this package please cite it appropriately. citation("hyperSpec") will give you the correct reference. The project homepage is http://hyperspec.r-forge.r-project.org Read 362 items Read 362 items Read 362 items Read 362 items Read 362 items Read 362 items --- finished re-building ‘flu.Rnw’ --- re-building ‘hyperspec.Rnw’ using Sweave Loading required package: lattice Loading required package: grid Loading required package: ggplot2 Loading required package: xml2 Package hyperSpec, version 0.100.0 To get started, try vignette ("hyperspec") package?hyperSpec vignette (package = "hyperSpec") If you use this package please cite it appropriately. citation("hyperSpec") will give you the correct reference. The project homepage is http://hyperspec.r-forge.r-project.org Loading required namespace: mvtnorm Failed with error: ‘there is no package called ‘mvtnorm’’ Error: processing vignette 'hyperspec.Rnw' failed with diagnostics: chunk 18 Error in .rmmvnorm(n, mean@data$spc, sigma) : package 'mvtnorm' needed to generate multivariate normal random data. --- failed re-building ‘hyperspec.Rnw’ --- re-building ‘laser.Rnw’ using Sweave Loading required package: lattice Loading required package: grid Loading required package: ggplot2 Loading required package: xml2 Package hyperSpec, version 0.100.0 To get started, try vignette ("hyperspec") package?hyperSpec vignette (package = "hyperSpec") If you use this package please cite it appropriately. citation("hyperSpec") will give you the correct reference. The project homepage is http://hyperspec.r-forge.r-project.org Loading required package: rgl Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called ‘rgl’ Loading required package: rgl Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called ‘rgl’ --- finished re-building ‘laser.Rnw’ --- re-building ‘plotting.Rnw’ using Sweave Loading required package: lattice Loading required package: grid Loading required package: ggplot2 Loading required package: xml2 Package hyperSpec, version 0.100.0 To get started, try vignette ("hyperspec") package?hyperSpec vignette (package = "hyperSpec") If you use this package please cite it appropriately. citation("hyperSpec") will give you the correct reference. The project homepage is http://hyperspec.r-forge.r-project.org Warning in plotmat(flu) : package 'plotrix' not available: omitting legend. Warning in (function (object, model = spc ~ c, groups = NULL, func = NULL, : Intensity at first wavelengh only is used. Warning in hyperSpec:::.levelplot(x, data, ...) : Only first wavelength is used for plotting Warning in plotc(x, ...) : Intensity at first wavelengh only is used. Warning in plotmat(x, ...) : package 'plotrix' not available: omitting legend. Warning in plotmat(laser) : package 'plotrix' not available: omitting legend. Warning in (function (x, y, z, subscripts, at = pretty(z), ..., col.regions = regions$col, : 'x' values are not equispaced; output may be wrong Loading required namespace: plotrix Failed with error: ‘there is no package called ‘plotrix’’ Warning in hyperSpec:::.levelplot(x, data, ...) : Only first wavelength is used for plotting Warning in plotmat(x, ...) : package 'plotrix' not available: omitting legend. Warning in plotmat(laser, col = heat.colors(20)) : package 'plotrix' not available: omitting legend. Warning in plotmat(laser, y = "t") : package 'plotrix' not available: omitting legend. Warning in plotmat(laser, y = laser$t, ylab = labels(laser, "t")) : package 'plotrix' not available: omitting legend. Warning in plotmat(flu, col = matlab.dark.palette(20)) : package 'plotrix' not available: omitting legend. Loading required package: latticeExtra Attaching package: ‘latticeExtra’ The following object is masked from ‘package:ggplot2’: layer Warning in (function (x, y, z, subscripts, at = pretty(z), ..., col.regions = regions$col, : 'x' values are not equispaced; output may be wrong Warning in (function (x, y, z, subscripts, at = pretty(z), ..., col.regions = regions$col, : 'y' values are not equispaced; output may be wrong Loading required package: rgl Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called ‘rgl’ Warning: Using `as.character()` on a quosure is deprecated as of rlang 0.3.0. Please use `as_label()` or `as_name()` instead. This warning is displayed once per session. --- finished re-building ‘plotting.Rnw’ SUMMARY: processing the following files failed: ‘baseline.Rnw’ ‘hyperspec.Rnw’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 2 ERRORs See ‘/data/gannet/ripley/R/packages/tests-Suggests/hyperSpec.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 3:50.29, 197.97 + 18.25