* using log directory ‘/data/gannet/ripley/R/packages/tests-clang/PGRdup.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 ‘PGRdup/DESCRIPTION’ ... OK
* this is package ‘PGRdup’ version ‘0.2.3.9’
* 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 ‘PGRdup’ can be installed ... [16s/21s] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/PGRdup-00install.html' for details.
* used C compiler: ‘clang 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 ... [23s/30s] OK
* checking Rd files ... NOTE
checkRd: (-1) GN1000.Rd:8: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GN1000.Rd:8: Lost braces
     8 |   columns(fields): \itemize{ \item{CommonName}{ : }{Common name} 
       |                                                    ^
checkRd: (-1) GN1000.Rd:9: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GN1000.Rd:9: Lost braces
     9 |   \item{BotanicalName}{ : }{Botanical name} \item{NationalID}{ : }{NBPGR 
       |                            ^
checkRd: (-1) GN1000.Rd:9-10: Lost braces
     9 |   \item{BotanicalName}{ : }{Botanical name} \item{NationalID}{ : }{NBPGR 
       |                                                                   ^
checkRd: (-1) GN1000.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GN1000.Rd:10: Lost braces
    10 |   National identifier} \item{CollNo}{ : }{Collector number} \item{DonorID}{ :
       |                                          ^
checkRd: (-1) GN1000.Rd:10-11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GN1000.Rd:11: Lost braces
    11 |   }{Donor ID} \item{OtherID1}{ : }{Other ID field 1} \item{OtherID2}{ : 
       |    ^
checkRd: (-1) GN1000.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GN1000.Rd:11: Lost braces
    11 |   }{Donor ID} \item{OtherID1}{ : }{Other ID field 1} \item{OtherID2}{ : 
       |                                   ^
checkRd: (-1) GN1000.Rd:11-12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GN1000.Rd:12: Lost braces
    12 |   }{Other ID field 2} \item{BioStatus}{ : }{Biological status}
       |    ^
checkRd: (-1) GN1000.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GN1000.Rd:12: Lost braces
    12 |   }{Other ID field 2} \item{BioStatus}{ : }{Biological status}
       |                                            ^
checkRd: (-1) GN1000.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GN1000.Rd:13: Lost braces
    13 |   \item{SourceCountry}{ : }{Country of origin} \item{TransferYear}{ : }{Year
       |                            ^
checkRd: (-1) GN1000.Rd:13-14: Lost braces
    13 |   \item{SourceCountry}{ : }{Country of origin} \item{TransferYear}{ : }{Year
       |                                                                        ^
checkRd: (-1) ReviewProbDup.Rd:35: Lost braces
    35 | \item{insert.blanks}{logical. If \code{TRUE}, inserts a row of /code{NAs}
       |                                                                     ^
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [76s/87s] OK
* checking PDF version of manual ... [9s/14s] OK
* checking HTML version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 NOTE