* using log directory ‘/data/gannet/ripley/R/packages/tests-clang/vegan.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 ‘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 whether package ‘vegan’ can be installed ... [64s/85s] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/vegan-00install.html' for details.
* used C compiler: ‘clang version 18.1.4’
* used Fortran compiler: ‘flang-new version 18.1.4’
* 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... 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 ... [130s/154s] OK
* checking Rd files ... 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 ... NOTE
Undeclared package ‘coda’ in Rd xrefs
* 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 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 ... [61s/84s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [27s/44s] OK
  Running ‘aitchison-tests.R’
  Running ‘cca-object-tests.R’ [7s/17s]
  Comparing ‘cca-object-tests.Rout’ to ‘cca-object-tests.Rout.save’ ... OK
  Running ‘decostand-tests.R’
  Running ‘oecosimu-tests.R’
  Comparing ‘oecosimu-tests.Rout’ to ‘oecosimu-tests.Rout.save’ ... OK
  Running ‘vegan-tests.R’ [10s/14s]
  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 ... [49s/67s] OK
* checking PDF version of manual ... [30s/41s] OK
* checking HTML version of manual ... [24s/29s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 2 NOTEs