* using log directory ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/biomod2.Rcheck’ * using R Under development (unstable) (2024-04-27 r86487) * 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 ‘biomod2/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘biomod2’ version ‘4.2-4’ * 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 ‘biomod2’ can be installed ... OK See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-clang/biomod2-00install.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 ... [14s/16s] OK * checking whether the package can be loaded with stated dependencies ... [14s/16s] OK * checking whether the package can be unloaded cleanly ... [13s/14s] OK * checking whether the namespace can be loaded with stated dependencies ... [13s/16s] OK * checking whether the namespace can be unloaded cleanly ... [15s/20s] OK * checking loading without being on the library search path ... [14s/16s] OK * checking whether startup messages can be suppressed ... [14s/19s] 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 ... [99s/113s] OK * checking Rd files ... [2s/3s] NOTE checkRd: (-1) BIOMOD.stored.data.Rd:25: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD.stored.data.Rd:26-27: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD.stored.data.Rd:28: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD.stored.data.Rd:29-30: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD.stored.data.Rd:31-32: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD.stored.data.Rd:33-34: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_EnsembleForecasting.Rd:114-115: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_EnsembleForecasting.Rd:116-118: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_EnsembleForecasting.Rd:119-120: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_EnsembleForecasting.Rd:121-123: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_EnsembleModeling.Rd:167-168: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_EnsembleModeling.Rd:169-170: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_EnsembleModeling.Rd:171-172: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_EnsembleModeling.Rd:173-174: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_EnsembleModeling.Rd:175: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_EnsembleModeling.Rd:190-202: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_EnsembleModeling.Rd:203-206: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_EnsembleModeling.Rd:207-214: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_EnsembleModeling.Rd:215-220: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_EnsembleModeling.Rd:221-222: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_EnsembleModeling.Rd:229: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_EnsembleModeling.Rd:231-234: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_EnsembleModeling.Rd:236-243: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_EnsembleModeling.Rd:245-259: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_EnsembleModeling.Rd:261-276: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_EnsembleModeling.Rd:278-282: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_Modeling.Rd:321: Lost braces 321 | \code{\link[rpart]{rpart}}, code{\link[nnet]{nnet}}, | ^ checkRd: (-1) BIOMOD_ModelingOptions.Rd:70-86: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:77-78: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:79-81: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:87-90: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:91-95: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:96-97: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:124-126: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:127-142: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:134: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:135-137: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:143-144: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:145-149: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:150-151: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:152-160: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:170-171: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:173: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:180-181: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:182-186: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:187-191: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:192-193: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:194-195: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:202-203: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:213-214: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:223-239: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:230-231: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:232-234: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:240-242: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:253-254: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:266-267: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:269-273: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:275-280: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:282-287: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:289-294: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:296-298: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:300-301: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:303-304: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:306-307: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:307-308: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:310-311: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:313-314: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:316-317: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:317-319: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:321-323: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:325-327: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:329-332: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:334-336: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:338-340: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:342-344: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:346-348: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_ModelingOptions.Rd:350-352: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_Projection.Rd:110-111: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_Projection.Rd:112-113: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_Projection.Rd:114-117: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_Projection.Rd:118-119: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_Projection.Rd:120-122: Lost braces in \itemize; meant \describe ? checkRd: (-1) BIOMOD_RangeSize.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) BIOMOD_RangeSize.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) BIOMOD_RangeSize.Rd:32-33: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) BIOMOD_RangeSize.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) BIOMOD_RangeSize.Rd:35-36: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) BIOMOD_RangeSize.Rd:37-38: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) BIOMOD_RangeSize.Rd:39-40: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) BIOMOD_RangeSize.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) BIOMOD_RangeSize.Rd:42-43: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) BIOMOD_RangeSize.Rd:44-45: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) biomod2_ensemble_model.Rd:30: Lost braces in \itemize; meant \describe ? checkRd: (-1) biomod2_ensemble_model.Rd:31: Lost braces in \itemize; meant \describe ? checkRd: (-1) biomod2_ensemble_model.Rd:32: Lost braces in \itemize; meant \describe ? checkRd: (-1) biomod2_ensemble_model.Rd:33: Lost braces in \itemize; meant \describe ? checkRd: (-1) biomod2_ensemble_model.Rd:34: Lost braces in \itemize; meant \describe ? checkRd: (-1) biomod2_ensemble_model.Rd:35: Lost braces in \itemize; meant \describe ? checkRd: (-1) biomod2_ensemble_model.Rd:36: Lost braces in \itemize; meant \describe ? checkRd: (-1) biomod2_model.Rd:36: Lost braces in \itemize; meant \describe ? checkRd: (-1) biomod2_model.Rd:37: Lost braces in \itemize; meant \describe ? checkRd: (-1) biomod2_model.Rd:38: Lost braces in \itemize; meant \describe ? checkRd: (-1) biomod2_model.Rd:39: Lost braces in \itemize; meant \describe ? checkRd: (-1) biomod2_model.Rd:40: Lost braces in \itemize; meant \describe ? checkRd: (-1) biomod2_model.Rd:41: Lost braces in \itemize; meant \describe ? checkRd: (-1) biomod2_model.Rd:42: Lost braces in \itemize; meant \describe ? checkRd: (-1) biomod2_model.Rd:43-44: Lost braces in \itemize; meant \describe ? checkRd: (-1) biomod2_model.Rd:45: Lost braces in \itemize; meant \describe ? checkRd: (-1) biomod2_model.Rd:46: Lost braces in \itemize; meant \describe ? checkRd: (-1) bm_CVnnet.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) bm_CVnnet.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) bm_CVnnet.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) bm_FindOptimStat.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) bm_FindOptimStat.Rd:43-44: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) bm_FindOptimStat.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) bm_FindOptimStat.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) bm_FindOptimStat.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) bm_PlotEvalBoxplot.Rd:50: Lost braces in \itemize; meant \describe ? checkRd: (-1) bm_PlotEvalBoxplot.Rd:51-53: Lost braces in \itemize; meant \describe ? checkRd: (-1) bm_PlotEvalMean.Rd:58: Lost braces in \itemize; meant \describe ? checkRd: (-1) bm_PlotEvalMean.Rd:59: Lost braces in \itemize; meant \describe ? checkRd: (-1) bm_PlotEvalMean.Rd:60: Lost braces in \itemize; meant \describe ? checkRd: (-1) bm_PlotEvalMean.Rd:61: Lost braces in \itemize; meant \describe ? checkRd: (-1) bm_PlotResponseCurves.Rd:86: Lost braces in \itemize; meant \describe ? checkRd: (-1) bm_PlotVarImpBoxplot.Rd:45: Lost braces in \itemize; meant \describe ? checkRd: (-1) bm_PseudoAbsences.Rd:114: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) bm_PseudoAbsences.Rd:115: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) bm_PseudoAbsences.Rd:116: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) bm_PseudoAbsences.Rd:117-118: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) bm_RunModelsLoop.Rd:116: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) bm_RunModelsLoop.Rd:117: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) bm_RunModelsLoop.Rd:118: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) bm_RunModelsLoop.Rd:119: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) bm_RunModelsLoop.Rd:120-121: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) bm_RunModelsLoop.Rd:122-123: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) bm_VariablesImportance.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) bm_VariablesImportance.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) bm_VariablesImportance.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly * 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 ... NOTE Documented arguments not in \usage in Rd file 'predict2.em.Rd': ‘na.rm’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... [10s/11s] OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [92s/99s] OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed BIOMOD_RangeSize 9.190 0.083 9.708 bm_PlotRangeSize 8.960 0.080 9.307 BIOMOD.ensemble.models.out 5.736 0.095 6.721 BIOMOD.formated.data.PA 5.652 0.109 6.680 BIOMOD_EnsembleModeling 5.562 0.063 6.018 BIOMOD.projection.out 4.863 0.091 5.370 bm_PlotResponseCurves 4.551 0.051 5.122 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [4s/5s] OK * checking PDF version of manual ... [16s/18s] OK * checking HTML version of manual ... [10s/12s] OK * checking for non-standard things in the check directory ... OK * DONE Status: 2 NOTEs