* using log directory ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/lgcp.Rcheck’
* using R Under development (unstable) (2025-02-23 r87804)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 19.1.7 (1+b1)
    Debian flang-new version 19.1.7 (1+b1)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘lgcp/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘lgcp’ version ‘2.0’
* 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 serialization versions ... OK
* checking whether package ‘lgcp’ can be installed ... OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-clang/lgcp-00install.html' for details.
* 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 ... [13s/16s] OK
* checking whether the package can be loaded with stated dependencies ... [12s/15s] OK
* checking whether the package can be unloaded cleanly ... [13s/16s] OK
* checking whether the namespace can be loaded with stated dependencies ... [13s/15s] OK
* checking whether the namespace can be unloaded cleanly ... [13s/16s] OK
* checking loading without being on the library search path ... [12s/16s] OK
* checking whether startup messages can be suppressed ... [13s/16s] 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 ... [107s/136s] OK
* checking Rd files ... [2s/4s] NOTE
checkRd: (-1) GaussianPrior.Rd:24: Lost braces
    24 | \link{LogGaussianPrior}, link{PriorSpec.list}
       |                              ^
checkRd: (-1) LogGaussianPrior.Rd:24: Lost braces
    24 | \link{GaussianPrior}, link{PriorSpec.list}
       |                           ^
checkRd: (-1) initialiseAMCMC.Rd:20: Lost braces
    20 | lgcp vignette, code{vignette("lgcp")}, for further details on writing adaptive MCMC schemes.
       |                    ^
checkRd: (-1) lgcpPredictAggregateSpatialPlusPars.Rd:120: Lost braces
   120 | link{chooseCellWidth}, \link{getpolyol}, \link{guessinterp}, \link{getZmat},
       |     ^
checkRd: (-1) lgcpPredictMultitypeSpatialPlusPars.Rd:112: Lost braces
   112 | link{chooseCellWidth}, \link{getpolyol}, \link{guessinterp}, \link{getZmat},
       |     ^
checkRd: (-1) lgcpPredictSpatialPlusPars.Rd:107: Lost braces
   107 | link{chooseCellWidth}, \link{getpolyol}, \link{guessinterp}, \link{getZmat},
       |     ^
checkRd: (-1) lgcpPredictSpatioTemporalPlusPars.Rd:128: Lost braces
   128 | link{chooseCellWidth}, \link{getpolyol}, \link{guessinterp}, \link{getZmat},
       |     ^
checkRd: (-1) spatialAtRisk.Rd:61: Lost braces
    61 | \link{selectObsWindow} \link{lgcpPredict}, link{lgcpSim}, \link{spatialAtRisk.default}, \link{spatialAtRisk.fromXYZ}, \link{spatialAtRisk.im}, \link{spatialAtRisk.function}, \link{spatialAtRisk.SpatialGridDataFrame}, \link{spatialAtRisk.SpatialPolygonsDataFrame}, \link{spatialAtRisk.bivden}
       |                                                ^
checkRd: (-1) spatialAtRisk.SpatialGridDataFrame.Rd:25: Lost braces
    25 | \link{lgcpPredict}, link{lgcpSim}, \link{spatialAtRisk.default}, \link{spatialAtRisk.fromXYZ}, \link{spatialAtRisk.im}, \link{spatialAtRisk.function}, \link{spatialAtRisk.SpatialPolygonsDataFrame}, \link{spatialAtRisk.bivden}
       |                         ^
checkRd: (-1) spatialAtRisk.SpatialPolygonsDataFrame.Rd:25: Lost braces
    25 | \link{lgcpPredict}, link{lgcpSim}, \link{spatialAtRisk.default}, \link{spatialAtRisk.fromXYZ}, \link{spatialAtRisk.im}, \link{spatialAtRisk.function}, \link{spatialAtRisk.SpatialGridDataFrame}, \link{spatialAtRisk.bivden}
       |                         ^
checkRd: (-1) spatialAtRisk.bivden.Rd:25: Lost braces
    25 | \link{lgcpPredict}, link{lgcpSim}, \link{spatialAtRisk.default}, \link{spatialAtRisk.fromXYZ}, \link{spatialAtRisk.im}, \link{spatialAtRisk.function}, \link{spatialAtRisk.SpatialGridDataFrame}, \link{spatialAtRisk.SpatialPolygonsDataFrame}
       |                         ^
checkRd: (-1) spatialAtRisk.default.Rd:26: Lost braces
    26 | \link{lgcpPredict}, link{lgcpSim}, \link{spatialAtRisk.fromXYZ}, \link{spatialAtRisk.im}, \link{spatialAtRisk.function}, \link{spatialAtRisk.SpatialGridDataFrame}, \link{spatialAtRisk.SpatialPolygonsDataFrame}, \link{spatialAtRisk.bivden}, \code{xvals}, \code{yvals}, \code{zvals}
       |                         ^
checkRd: (-1) spatialAtRisk.fromXYZ.Rd:30: Lost braces
    30 | \link{lgcpPredict}, link{lgcpSim}, \link{spatialAtRisk.default}, \link{spatialAtRisk.im}, \link{spatialAtRisk.function}, \link{spatialAtRisk.SpatialGridDataFrame}, \link{spatialAtRisk.SpatialPolygonsDataFrame}, \link{spatialAtRisk.bivden}
       |                         ^
checkRd: (-1) spatialAtRisk.function.Rd:30: Lost braces
    30 | \link{lgcpPredict}, link{lgcpSim}, \link{spatialAtRisk.default}, \link{spatialAtRisk.fromXYZ}, \link{spatialAtRisk.im}, \link{spatialAtRisk.SpatialGridDataFrame}, \link{spatialAtRisk.SpatialPolygonsDataFrame}, \link{spatialAtRisk.bivden}
       |                         ^
checkRd: (-1) spatialAtRisk.im.Rd:25: Lost braces
    25 | \link{lgcpPredict}, link{lgcpSim}, \link{spatialAtRisk.default}, \link{spatialAtRisk.fromXYZ}, \link{spatialAtRisk.function}, \link{spatialAtRisk.SpatialGridDataFrame}, \link{spatialAtRisk.SpatialPolygonsDataFrame}, \link{spatialAtRisk.bivden}
       |                         ^
checkRd: (-1) spatialAtRisk.lgcpgrid.Rd:27: Lost braces
    27 | \link{lgcpPredict}, link{lgcpSim}, \link{spatialAtRisk.default}, \link{spatialAtRisk.fromXYZ}, \link{spatialAtRisk.im}, \link{spatialAtRisk.function}, \link{spatialAtRisk.SpatialGridDataFrame}, \link{spatialAtRisk.SpatialPolygonsDataFrame}
       |                         ^
checkRd: (-1) updateAMCMC.Rd:20: Lost braces
    20 | lgcp vignette, code{vignette("lgcp")}, for further details on writing adaptive MCMC schemes.
       |                    ^
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  density.stppp.Rd: density.ppp
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 ... [0s/0s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [13s/17s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [114s/141s] OK
  Running ‘adaptiveSchemesTest.R’ [13s/16s]
  Running ‘fromSPDFTest.R’ [13s/16s]
  Running ‘gridAverageTest.R’ [12s/14s]
  Running ‘gridSummaryTest.R’ [12s/15s]
  Running ‘iteratorTest.R’ [12s/15s]
  Running ‘lgcpMethodsTest.R’ [25s/32s]
  Running ‘mstpppClassTest.R’ [13s/16s]
  Running ‘stpppClassTest.R’ [13s/17s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [2s/3s] OK
* checking PDF version of manual ... [17s/22s] OK
* checking HTML version of manual ... [11s/20s] OK
* checking for non-standard things in the check directory ... OK
* DONE
Status: 2 NOTEs