- using R Under development (unstable) (2024-04-12 r86412)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
clang version 18.1.2
flang-new version 18.1.2
- running under: Fedora Linux 36 (Workstation Edition)
- using session charset: UTF-8
- using option ‘--no-stop-on-test-error’
- 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 ... [78s/102s] OK
See the install log 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 ... [17s/21s] OK
- checking whether the package can be loaded with stated dependencies ... [15s/18s] OK
- checking whether the package can be unloaded cleanly ... [16s/20s] OK
- checking whether the namespace can be loaded with stated dependencies ... [16s/21s] OK
- checking whether the namespace can be unloaded cleanly ... [16s/22s] OK
- checking loading without being on the library search path ... [16s/20s] OK
- checking whether startup messages can be suppressed ... [17s/20s] 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 ... [115s/140s] OK
- checking Rd files ... 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 ... [11s/12s] 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 ... [110s/137s] OK
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... OK
- checking PDF version of manual ... [19s/25s] OK
- checking HTML version of manual ... [13s/17s] OK
- checking for non-standard things in the check directory ... OK
- checking for detritus in the temp directory ... OK
- DONE
Status: 2 NOTEs