* using log directory ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/vegan.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 ‘vegan/DESCRIPTION’ ... OK * this is package ‘vegan’ version ‘2.6-4’ * 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 ‘vegan’ can be installed ... OK See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-clang/vegan-00install.html' for details. * used C compiler: ‘Debian clang version 18.1.4 (1)’ * used Fortran compiler: ‘Debian flang-new version 18.1.4 (1)’ * 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 ... [2s/4s] OK * checking whether the package can be loaded with stated dependencies ... [2s/3s] OK * checking whether the package can be unloaded cleanly ... [2s/3s] OK * checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK * checking whether the namespace can be unloaded cleanly ... [2s/2s] OK * checking loading without being on the library search path ... [2s/3s] OK * checking whether startup messages can be suppressed ... [2s/2s] 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 ... [128s/151s] OK * checking Rd files ... [6s/7s] NOTE checkRd: (-1) clamtest.Rd:91: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) clamtest.Rd:92: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) clamtest.Rd:93: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) clamtest.Rd:94-96: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) commsim.Rd:52: Lost braces in \itemize; meant \describe ? checkRd: (-1) commsim.Rd:53: Lost braces in \itemize; meant \describe ? checkRd: (-1) commsim.Rd:54: Lost braces in \itemize; meant \describe ? checkRd: (-1) commsim.Rd:55: Lost braces in \itemize; meant \describe ? checkRd: (-1) commsim.Rd:56: Lost braces in \itemize; meant \describe ? checkRd: (-1) commsim.Rd:57: Lost braces in \itemize; meant \describe ? checkRd: (-1) commsim.Rd:58: Lost braces in \itemize; meant \describe ? checkRd: (-1) commsim.Rd:59: Lost braces in \itemize; meant \describe ? checkRd: (-1) commsim.Rd:60: Lost braces in \itemize; meant \describe ? checkRd: (-1) commsim.Rd:61: Lost braces in \itemize; meant \describe ? checkRd: (-1) commsim.Rd:62: Lost braces in \itemize; meant \describe ? checkRd: (-1) commsim.Rd:63: Lost braces in \itemize; meant \describe ? checkRd: (-1) commsim.Rd:101-102: Lost braces in \itemize; meant \describe ? checkRd: (-1) commsim.Rd:104-105: Lost braces in \itemize; meant \describe ? checkRd: (-1) commsim.Rd:107-109: Lost braces in \itemize; meant \describe ? checkRd: (-1) commsim.Rd:111-113: Lost braces in \itemize; meant \describe ? checkRd: (-1) commsim.Rd:115-116: Lost braces in \itemize; meant \describe ? checkRd: (-1) commsim.Rd:118-121: Lost braces in \itemize; meant \describe ? checkRd: (-1) commsim.Rd:123-129: Lost braces in \itemize; meant \describe ? checkRd: (-1) commsim.Rd:131-138: Lost braces in \itemize; meant \describe ? checkRd: (-1) commsim.Rd:140-151: Lost braces in \itemize; meant \describe ? checkRd: (-1) commsim.Rd:153-161: Lost braces in \itemize; meant \describe ? checkRd: (-1) commsim.Rd:163-171: Lost braces in \itemize; meant \describe ? checkRd: (-1) commsim.Rd:188-190: Lost braces in \itemize; meant \describe ? checkRd: (-1) commsim.Rd:192-201: Lost braces in \itemize; meant \describe ? checkRd: (-1) commsim.Rd:221-228: Lost braces in \itemize; meant \describe ? checkRd: (-1) commsim.Rd:230-236: Lost braces in \itemize; meant \describe ? checkRd: (-1) commsim.Rd:238-243: Lost braces in \itemize; meant \describe ? checkRd: (-1) commsim.Rd:263-265: Lost braces in \itemize; meant \describe ? checkRd: (-1) commsim.Rd:267-268: Lost braces in \itemize; meant \describe ? checkRd: (-1) commsim.Rd:270-272: Lost braces in \itemize; meant \describe ? checkRd: (-1) commsim.Rd:274-276: Lost braces in \itemize; meant \describe ? checkRd: (-1) commsim.Rd:278-279: Lost braces in \itemize; meant \describe ? checkRd: (-1) commsim.Rd:281-282: Lost braces in \itemize; meant \describe ? checkRd: (-1) commsim.Rd:303-305: Lost braces in \itemize; meant \describe ? checkRd: (-1) commsim.Rd:307-309: Lost braces in \itemize; meant \describe ? checkRd: (-1) commsim.Rd:311-313: Lost braces in \itemize; meant \describe ? checkRd: (-1) commsim.Rd:315-318: Lost braces in \itemize; meant \describe ? checkRd: (-1) commsim.Rd:320-323: Lost braces in \itemize; meant \describe ? checkRd: (-1) commsim.Rd:325-328: Lost braces in \itemize; meant \describe ? checkRd: (-1) commsim.Rd:330-332: Lost braces in \itemize; meant \describe ? checkRd: (-1) commsim.Rd:334-336: Lost braces in \itemize; meant \describe ? checkRd: (-1) commsim.Rd:338-340: Lost braces in \itemize; meant \describe ? checkRd: (-1) eventstar.Rd:62-63: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) eventstar.Rd:64-65: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) eventstar.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) eventstar.Rd:67-70: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) nullmodel.Rd:147: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) nullmodel.Rd:148: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) nullmodel.Rd:149: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) nullmodel.Rd:150: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) nullmodel.Rd:151: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) nullmodel.Rd:152: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) nullmodel.Rd:153: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) nullmodel.Rd:154: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) nullmodel.Rd:155: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) nullmodel.Rd:156-157: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) nullmodel.Rd:158-160: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) nullmodel.Rd:161-163: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) raupcrick.Rd:94: Lost braces; missing escapes or markup? 94 | \code{\link{vegdist}} with {method = "raup"} implements a related | ^ checkRd: (-1) varpart.Rd:239-240: Lost braces in \itemize; meant \describe ? checkRd: (-1) varpart.Rd:241-242: Lost braces in \itemize; meant \describe ? checkRd: (-1) varpart.Rd:243: Lost braces in \itemize; meant \describe ? checkRd: (-1) varpart.Rd:244-247: Lost braces in \itemize; meant \describe ? * 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 ... [0s/1s] OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK * checking pragmas in C/C++ headers and code ... OK * checking compilation flags used ... OK * checking compiled code ... OK * checking usage of KIND in Fortran files ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [54s/65s] OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed ordipointlabel 3.761 0.003 5.022 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [22s/34s] OK Running ‘aitchison-tests.R’ [2s/3s] Running ‘cca-object-tests.R’ [6s/15s] Comparing ‘cca-object-tests.Rout’ to ‘cca-object-tests.Rout.save’ ... OK Running ‘decostand-tests.R’ [2s/3s] Running ‘oecosimu-tests.R’ [3s/3s] Comparing ‘oecosimu-tests.Rout’ to ‘oecosimu-tests.Rout.save’ ... OK Running ‘vegan-tests.R’ [8s/9s] Comparing ‘vegan-tests.Rout’ to ‘vegan-tests.Rout.save’ ... OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [38s/46s] OK * checking PDF version of manual ... [25s/29s] OK * checking HTML version of manual ... [21s/29s] OK * checking for non-standard things in the check directory ... OK * DONE Status: 1 NOTE