* using log directory ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/gstat.Rcheck’ * using R Under development (unstable) (2024-04-29 r86495) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 18.1.4 (1) Debian flang-new version 18.1.4 (1) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘gstat/DESCRIPTION’ ... OK * this is package ‘gstat’ version ‘2.1-1’ * 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 serialization versions ... OK * checking whether package ‘gstat’ can be installed ... OK See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-clang/gstat-00install.html' for details. * used C compiler: ‘Debian clang version 18.1.4 (1)’ * 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 ... [1s/1s] OK * checking whether the package can be loaded with stated dependencies ... [1s/2s] OK * checking whether the package can be unloaded cleanly ... [1s/2s] OK * checking whether the namespace can be loaded with stated dependencies ... [1s/2s] OK * checking whether the namespace can be unloaded cleanly ... [1s/2s] OK * checking loading without being on the library search path ... [1s/2s] OK * checking whether startup messages can be suppressed ... [2s/2s] 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 ... [34s/40s] OK * checking Rd files ... [1s/2s] NOTE checkRd: (-1) jura.Rd:29: Lost braces; missing escapes or markup? 29 | \item{Cd}{ mg cadmium kg^{-1} topsoil } | ^ checkRd: (-1) jura.Rd:30: Lost braces; missing escapes or markup? 30 | \item{Co}{ mg cobalt kg^{-1} topsoil } | ^ checkRd: (-1) jura.Rd:31: Lost braces; missing escapes or markup? 31 | \item{Cr}{ mg chromium kg^{-1} topsoil } | ^ checkRd: (-1) jura.Rd:32: Lost braces; missing escapes or markup? 32 | \item{Cu}{ mg copper kg^{-1} topsoil } | ^ checkRd: (-1) jura.Rd:33: Lost braces; missing escapes or markup? 33 | \item{Ni}{ mg nickel kg^{-1} topsoil } | ^ checkRd: (-1) jura.Rd:34: Lost braces; missing escapes or markup? 34 | \item{Pb}{ mg lead kg^{-1} topsoil } | ^ checkRd: (-1) jura.Rd:35: Lost braces; missing escapes or markup? 35 | \item{Zn}{ mg zinc kg^{-1} topsoil } | ^ checkRd: (-1) variogramST.Rd:49: Lost braces; missing escapes or markup? 49 | time lag $t$, the pseudo cross variogram $(Z_i(s)-Z_{i+t}(s+h))^2$ is averaged over all time | ^ checkRd: (-1) variogramST.Rd:50: Lost braces; missing escapes or markup? 50 | lagged observation sets $Z_i$ and $Z_{i+t}$ available (weighted by the number of pairs involved). | ^ * 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 ... [2s/3s] OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in shell scripts ... 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 sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [19s/23s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [62s/75s] OK Running ‘allier.R’ [2s/2s] Comparing ‘allier.Rout’ to ‘allier.Rout.save’ ... OK Running ‘blockkr.R’ [2s/2s] Comparing ‘blockkr.Rout’ to ‘blockkr.Rout.save’ ... OK Running ‘covtable.R’ [2s/2s] Comparing ‘covtable.Rout’ to ‘covtable.Rout.save’ ... OK Running ‘cv.R’ [2s/3s] Comparing ‘cv.Rout’ to ‘cv.Rout.save’ ... OK Running ‘cv3d.R’ [2s/3s] Comparing ‘cv3d.Rout’ to ‘cv3d.Rout.save’ ... OK Running ‘fit.R’ [2s/2s] Comparing ‘fit.Rout’ to ‘fit.Rout.save’ ... OK Running ‘krige0.R’ [4s/4s] Comparing ‘krige0.Rout’ to ‘krige0.Rout.save’ ... OK Running ‘line.R’ [2s/3s] Comparing ‘line.Rout’ to ‘line.Rout.save’ ... OK Running ‘merge.R’ [2s/2s] Comparing ‘merge.Rout’ to ‘merge.Rout.save’ ... OK Running ‘na.action.R’ [2s/2s] Comparing ‘na.action.Rout’ to ‘na.action.Rout.save’ ... OK Running ‘rings.R’ [2s/3s] Comparing ‘rings.Rout’ to ‘rings.Rout.save’ ... OK Running ‘sim.R’ [2s/2s] Comparing ‘sim.Rout’ to ‘sim.Rout.save’ ... OK Running ‘stars.R’ [18s/21s] Comparing ‘stars.Rout’ to ‘stars.Rout.save’ ...16c16 < > crs = CRS("EPSG:28992") --- > > crs = CRS("+init=epsg:28992") 66c66 < > crs = CRS("EPSG:28992") --- > > crs = CRS("+init=epsg:28992") 107a108,110 > [4] "Attributes: < Component \"proj4string\": Attributes: < Names: 1 string mismatch > >" > [5] "Attributes: < Component \"proj4string\": Attributes: < Length mismatch: comparison on first 2 components > >" > [6] "Attributes: < Component \"proj4string\": Attributes: < Component 2: 1 string mismatch > >" 112a116,118 > Warning message: > In CPL_crs_from_input(x) : > GDAL Message 1: +init=epsg:XXXX syntax is deprecated. It might return a CRS with a non-EPSG compliant axis order. 115c121 < User input: Amersfoort / RD New --- > User input: +init=epsg:28992 142c148,149 < ID["EPSG",8807]]], --- > ID["EPSG",8807]], > ID["EPSG",19914]], 144c151 < AXIS["easting (X)",east, --- > AXIS["(E)",east, 146,147c153,155 < LENGTHUNIT["metre",1]], < AXIS["northing (Y)",north, --- > LENGTHUNIT["metre",1, > ID["EPSG",9001]]], > AXIS["(N)",north, 149c157,158 < LENGTHUNIT["metre",1]], --- > LENGTHUNIT["metre",1, > ID["EPSG",9001]]], 151c160 < SCOPE["Engineering survey, topographic mapping."], --- > SCOPE["unknown"], 153,154c162 < BBOX[50.75,3.2,53.7,7.22]], < ID["EPSG",28992]] --- > BBOX[50.75,3.2,53.7,7.22]]] 169a178,180 > [8] "Attributes: < Component 5: Attributes: < Names: 1 string mismatch > >" > [9] "Attributes: < Component 5: Attributes: < Length mismatch: comparison on first 2 components > >" > [10] "Attributes: < Component 5: Attributes: < Component 2: 1 string mismatch > >" 247c258 < time 1 4 2019-02-25 15:37:25 Universal 1 secs POSIXct --- > time 1 4 2019-02-25 15:37:25 UTC 1 secs POSIXct 419,420c430,431 < [1] "2019-02-25 15:37:26 Universal" "2019-02-25 15:37:27 Universal" < [3] "2019-02-25 15:37:28 Universal" "2019-02-25 15:37:29 Universal" --- > [1] "2019-02-25 15:37:26 UTC" "2019-02-25 15:37:27 UTC" > [3] "2019-02-25 15:37:28 UTC" "2019-02-25 15:37:29 UTC" 432,433c443,444 < y 1 4 -1.11e-16 -0.7 NA [y] < time 1 4 2019-02-25 15:37:25 Universal 1 secs POSIXct --- > y 1 4 -1.11022e-16 -0.7 NA [y] > time 1 4 2019-02-25 15:37:25 UTC 1 secs POSIXct Running ‘unproj.R’ [5s/6s] Comparing ‘unproj.Rout’ to ‘unproj.Rout.save’ ...60c60 < Spam version 2.10-0 (2023-10-23) is loaded. --- > Spam version 2.9-1 (2022-08-07) is loaded. 74c74 < Linking to GEOS 3.12.1, GDAL 3.8.4, PROJ 9.4.0; sf_use_s2() is TRUE --- > Linking to GEOS 3.11.1, GDAL 3.6.2, PROJ 9.1.1; sf_use_s2() is TRUE Running ‘variogram.R’ [2s/2s] Comparing ‘variogram.Rout’ to ‘variogram.Rout.save’ ... OK Running ‘vdist.R’ [2s/3s] Comparing ‘vdist.Rout’ to ‘vdist.Rout.save’ ... OK Running ‘windst.R’ [11s/13s] Comparing ‘windst.Rout’ to ‘windst.Rout.save’ ... OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [52s/61s] OK * checking PDF version of manual ... [9s/12s] OK * checking HTML version of manual ... [5s/6s] OK * checking for non-standard things in the check directory ... OK * DONE Status: 1 NOTE