- using R version 4.3.0 alpha (2023-03-31 r84137)
- using platform: x86_64-apple-darwin20 (64-bit)
- R was compiled by
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
GNU Fortran (GCC) 12.2.0
- running under: macOS Ventura 13.3
- using session charset: UTF-8
- 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 ... [10s/12s] OK
See the install log for details.
- 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 R files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... [1s/1s] OK
- checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
- checking whether the package can be unloaded cleanly ... [1s/1s] OK
- checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
- checking whether the namespace can be unloaded cleanly ... [1s/2s] OK
- checking loading without being on the library search path ... [1s/1s] OK
- checking startup messages can be suppressed ... [1s/1s] 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 ... [11s/14s] OK
- checking Rd files ... [1s/1s] NOTE
checkRd: (-1) palettes.Rd:25: Escaped LaTeX specials: \#
- 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/2s] 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 ... [12s/18s] OK
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [5s/6s] OK
Running ‘unittests.R’ [4s/6s]
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes in ‘inst/doc’ ... OK
- checking running R code from vignettes ... [137s/190s] OK
‘chondro.pdf.asis’ using ‘UTF-8’... [0s/0s] OK
‘fileio.pdf.asis’ using ‘UTF-8’... [0s/1s] OK
‘baseline.Rnw’ using ‘UTF-8’... [3s/4s] OK
‘flu.Rnw’ using ‘UTF-8’... [2s/3s] OK
‘hyperspec.Rnw’ using ‘UTF-8’... [17s/24s] OK
‘laser.Rnw’ using ‘UTF-8’... [3s/5s] OK
‘plotting.Rnw’ using ‘UTF-8’... [111s/154s] OK
- checking re-building of vignette outputs ... [265s/358s] NOTE
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:
Running 'texi2dvi' on 'baseline.tex' failed.
LaTeX errors:
! LaTeX Error: File `inputenx.sty' not found.
Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)
! Emergency stop.
<read *>
l.5 \DeclareUnicodeCharacter
{03BB}{\ensuremath{\lambda}}^^M
! ==> Fatal error occurred, no output PDF file produced!
--- 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
Error: processing vignette 'flu.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'flu.tex' failed.
LaTeX errors:
! LaTeX Error: File `inputenx.sty' not found.
Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)
! Emergency stop.
<read *>
l.5 \DeclareUnicodeCharacter
{03BB}{\ensuremath{\lambda}}^^M
! ==> Fatal error occurred, no output PDF file produced!
--- failed 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
Loading required package: MASS
Warning in predict.lda(lda, chondro) :
variable names in 'newdata' do not match those in 'object'
Warning in rm(chondro) : object 'chondro' not found
Loading required package: baseline
Attaching package: ‘baseline’
The following object is masked from ‘package:stats’:
getCall
Warning in scores[, , 1:10] %*% loadings[1:10] :
Dropping column(s) of y: filename, measurement
Error: processing vignette 'hyperspec.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'hyperspec.tex' failed.
LaTeX errors:
! LaTeX Error: File `inputenx.sty' not found.
Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)
! Emergency stop.
<read *>
l.8 \DeclareUnicodeCharacter
{03BB}{\ensuremath{\lambda}}^^M
! ==> Fatal error occurred, no output PDF file produced!
--- 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
plot chunk
Warning in rgl.snapshot("fig-3D.png", fmt = "png", top = TRUE) :
this build of rgl does not support snapshots
Error: processing vignette 'laser.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'laser.tex' failed.
LaTeX errors:
! LaTeX Error: File `inputenx.sty' not found.
Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)
! Emergency stop.
<read *>
l.6 \DeclareUnicodeCharacter
{03BB}{\ensuremath{\lambda}}^^M
! ==> Fatal error occurred, no output PDF file produced!
--- failed 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 (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 (function (x, y, z, subscripts = TRUE, at = pretty(z), points = TRUE, :
The 'use.tripack' argument is deprecated and ignored. See ?panel.voronoi
Warning in plotc(x, ...) : Intensity at first wavelengh only is used.
Warning in (function (x, y, z, subscripts, at = pretty(z), ..., col.regions = regions$col, :
'x' values are not equispaced; output may be wrong
Warning in (function (x, y, z, subscripts = TRUE, at = pretty(z), points = TRUE, :
The 'use.tripack' argument is deprecated and ignored. See ?panel.voronoi
Warning in hyperSpec:::.levelplot(x, data, ...) :
Only first wavelength is used for plotting
Loading required package: latticeExtra
Attaching package: ‘latticeExtra’
The following object is masked from ‘package:ggplot2’:
layer
Warning in (function (x, y, z, subscripts = TRUE, at = pretty(z), points = TRUE, :
The 'use.tripack' argument is deprecated and ignored. See ?panel.voronoi
Warning in (function (x, y, z, subscripts, at = pretty(z), ..., col.regions = regions$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
Warning in (function (x, y, z, subscripts = TRUE, at = pretty(z), points = TRUE, :
The 'use.tripack' argument is deprecated and ignored. See ?panel.voronoi
Loading required package: rgl
Warning in rgl.snapshot("fig-3D.png", fmt = "png", top = TRUE) :
this build of rgl does not support snapshots
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 every 8 hours.
Error: processing vignette 'plotting.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'plotting.tex' failed.
LaTeX errors:
! LaTeX Error: File `inputenx.sty' not found.
Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)
! Emergency stop.
<read *>
l.7 \DeclareUnicodeCharacter
{03BB}{\ensuremath{\lambda}}^^M
! ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘plotting.Rnw’
SUMMARY: processing the following files failed:
‘baseline.Rnw’ ‘flu.Rnw’ ‘hyperspec.Rnw’ ‘laser.Rnw’ ‘plotting.Rnw’
Error: Vignette re-building failed.
Execution halted
- checking PDF version of manual ... [7s/10s] OK
- DONE
Status: 2 NOTEs
- using check arguments '--no-clean-on-error '