* using log directory ‘/data/gannet/ripley/R/packages/tests-clang/lgcp.Rcheck’
* using R Under development (unstable) (2025-02-17 r87732)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
clang version 20.1.0-rc2
flang version 20.1.0-rc2
* running under: Fedora Linux 40 (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 ... [103s/123s] 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 ... [21s/26s] OK
* checking whether the package can be loaded with stated dependencies ... [20s/26s] OK
* checking whether the package can be unloaded cleanly ... [20s/24s] OK
* checking whether the namespace can be loaded with stated dependencies ... [20s/25s] OK
* checking whether the namespace can be unloaded cleanly ... [20s/26s] OK
* checking loading without being on the library search path ... [22s/27s] OK
* checking whether startup messages can be suppressed ... [20s/25s] 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 ... [178s/210s] 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 ... [20s/25s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [196s/242s] OK
Running ‘adaptiveSchemesTest.R’ [20s/25s]
Running ‘fromSPDFTest.R’ [21s/25s]
Running ‘gridAverageTest.R’ [20s/25s]
Running ‘gridSummaryTest.R’ [20s/24s]
Running ‘iteratorTest.R’ [20s/25s]
Running ‘lgcpMethodsTest.R’ [53s/67s]
Running ‘mstpppClassTest.R’ [21s/25s]
Running ‘stpppClassTest.R’ [21s/24s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... [25s/32s] OK
* checking HTML version of manual ... [18s/30s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 NOTE