* using log directory ‘/data/gannet/ripley/R/packages/tests-clang/lgcp.Rcheck’ * using R Under development (unstable) (2024-04-24 r86484) * using platform: x86_64-pc-linux-gnu * R was compiled by clang version 18.1.4 flang-new version 18.1.4 * running under: Fedora Linux 36 (Workstation Edition) * using session charset: UTF-8 * using option ‘--no-stop-on-test-error’ * 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 whether package ‘lgcp’ can be installed ... [101s/118s] OK See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/lgcp-00install.html' 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 code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [20s/23s] OK * checking whether the package can be loaded with stated dependencies ... [18s/20s] OK * checking whether the package can be unloaded cleanly ... [19s/21s] OK * checking whether the namespace can be loaded with stated dependencies ... [19s/22s] OK * checking whether the namespace can be unloaded cleanly ... [21s/24s] OK * checking loading without being on the library search path ... [19s/23s] OK * checking whether startup messages can be suppressed ... [20s/22s] 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 ... [172s/202s] OK * checking Rd files ... 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 ... 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 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 ... [21s/23s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [188s/223s] OK Running ‘adaptiveSchemesTest.R’ [20s/22s] Running ‘fromSPDFTest.R’ [20s/24s] Running ‘gridAverageTest.R’ [19s/24s] Running ‘gridSummaryTest.R’ [19s/24s] Running ‘iteratorTest.R’ [20s/24s] Running ‘lgcpMethodsTest.R’ [50s/59s] Running ‘mstpppClassTest.R’ [20s/26s] Running ‘stpppClassTest.R’ [19s/21s] * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... [25s/34s] OK * checking HTML version of manual ... [19s/33s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 NOTE