* using log directory 'd:/RCompile/CRANincoming/R-devel/SQMtools.Rcheck'
* using R Under development (unstable) (2025-06-03 r88266 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'SQMtools/DESCRIPTION' ... OK
* this is package 'SQMtools' version '1.7.1'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [12s] OK
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'SQMtools' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [31s] OK
* checking Rd files ... NOTE
checkRd: (-1) SQM_to_microeco.Rd:25: Lost braces
    25 | \item{count}{character. Either \code{"abund"} for raw abundances, \code{"percent"} for percentages, \code{"bases"} for raw base counts, \code{"cov"} for coverages, code{"cpm"} for coverages per million reads, \code{"tpm"} for TPM normalized values or \code{"copy_number"} for copy numbers (default \code{"abund"}). Note that a given count type might not available in this object (e.g. TPM or copy number in SQMlite objects originating from a SQM reads project).}
       |                                                                                                                                                                         ^
checkRd: (-1) SQM_to_phyloseq.Rd:25: Lost braces
    25 | \item{count}{character. Either \code{"abund"} for raw abundances, \code{"percent"} for percentages, \code{"bases"} for raw base counts, \code{"cov"} for coverages, code{"cpm"} for coverages per million reads, \code{"tpm"} for TPM normalized values or \code{"copy_number"} for copy numbers (default \code{"abund"}). Note that a given count type might not available in this object (e.g. TPM or copy number in SQMlite objects originating from a SQM reads project).}
       |                                                                                                                                                                         ^
* 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 examples ... [29s] OK
* checking PDF version of manual ... [23s] OK
* checking HTML version of manual ... OK
* DONE
Status: 1 NOTE