* using log directory ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/hsdar.Rcheck’ * using R version 4.3.0 beta (2023-04-08 r84203) * 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 ‘hsdar/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘hsdar’ version ‘1.0.4’ * 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 ‘hsdar’ can be installed ... [57s/76s] OK See 'https://www.r-project.org/nosvn/R.check/r-oldrel-macos-x86_64/hsdar-00install.html' for details. * used C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’ * used Fortran compiler: ‘GNU Fortran (GCC) 12.2.0’ * used SDK: ‘MacOSX11.3.sdk’ * checking installed package size ... NOTE installed size is 7.2Mb sub-directories of 1Mb or more: R 3.0Mb doc 2.5Mb * 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 ... [8s/10s] OK * checking whether the package can be loaded with stated dependencies ... [7s/10s] OK * checking whether the package can be unloaded cleanly ... [7s/10s] OK * checking whether the namespace can be loaded with stated dependencies ... [7s/10s] OK * checking whether the namespace can be unloaded cleanly ... [7s/10s] OK * checking loading without being on the library search path ... [7s/9s] OK * checking startup messages can be suppressed ... [8s/10s] 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 ... [27s/37s] OK * checking Rd files ... [9s/12s] NOTE checkRd: (-1) attributes_speclib.Rd:73: Escaped LaTeX specials: \$ checkRd: (-1) get_reflectance.Rd:34: 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 ... [8s/11s] 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 compiled code ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [21s/29s] OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... [23s/31s] OK ‘Hsdar-intro.Rnw’ using ‘CP1252’... [22s/31s] OK ‘References.Rnw’ using ‘CP1252’... [0s/0s] OK * checking re-building of vignette outputs ... [36s/48s] NOTE Error(s) in re-building vignettes: --- re-building ‘Hsdar-intro.Rnw’ using Sweave Loading required package: raster Loading required package: sp Loading required package: rgdal Please note that rgdal will be retired during 2023, plan transition to sf/stars/terra functions using GDAL and PROJ at your earliest convenience. See https://r-spatial.org/r/2022/04/12/evolution.html and https://github.com/r-spatial/evolution rgdal: version: 1.6-5, (SVN revision 1199) Geospatial Data Abstraction Library extensions to R successfully loaded Loaded GDAL runtime: GDAL 3.5.3, released 2022/10/21 Path to GDAL shared files: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/rgdal/gdal GDAL does not use iconv for recoding strings. GDAL binary built with GEOS: TRUE Loaded PROJ runtime: Rel. 9.1.0, September 1st, 2022, [PJ_VERSION: 910] Path to PROJ shared files: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/rgdal/proj PROJ CDN enabled: FALSE Linking to sp version:1.6-0 To mute warnings of possible GDAL/OSR exportToProj4() degradation, use options("rgdal_show_exportToProj4_warnings"="none") before loading sp or rgdal. Loading required package: signal Attaching package: ‘signal’ The following object is masked from ‘package:raster’: resample The following objects are masked from ‘package:stats’: filter, poly Loading required package: caret Loading required package: ggplot2 Loading required package: lattice Loading required package: Boruta ################################### This is hsdar 1.0.4 To get citation entry type 'citation("hsdar")' ################################### Attaching package: ‘hsdar’ The following object is masked from ‘package:raster’: nbands Warning: Not a validObject(): no slot of name "srs" for this object of class "RasterBrick" Warning in points2grid(points, tolerance, round) : cell size from constant coordinate 3 possibly taken from other coordinate Warning: GDAL support is provided by the sf and terra packages among others Warning in checkhull(sh_cline, 1) : Mismatch of continuum line at wavelength = 2487 Maximum distance between continuum line & spectrum at Wavelength = 2495 --- finished re-building ‘Hsdar-intro.Rnw’ --- re-building ‘References.Rnw’ using Sweave Error: processing vignette 'References.Rnw' failed with diagnostics: Running 'texi2dvi' on 'References.tex' failed. BibTeX errors: The top-level auxiliary file: References.aux I couldn't open style file elsarticle-harv.bst ---line 86 of file References.aux : \bibstyle{elsarticle-harv : } I'm skipping whatever remains of this command I found no style file---while reading file References.aux --- failed re-building ‘References.Rnw’ SUMMARY: processing the following file failed: ‘References.Rnw’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... [9s/12s] OK * DONE Status: 3 NOTEs * using check arguments '--no-clean-on-error ' * elapsed time (check, wall clock): 7:26