- using R Under development (unstable) (2024-03-15 r86142)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
gcc-13 (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
- running under: Fedora Linux 36 (Workstation Edition)
- using session charset: UTF-8
- using option ‘--no-stop-on-test-error’
- checking for file ‘netgwas/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘netgwas’ version ‘1.14.2’
- 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
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- checking whether package ‘netgwas’ can be installed ... [17s/21s] OK
See the install log for details.
- checking package 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
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- checking dependencies in R code ... OK
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- checking R code for possible problems ... [29s/35s] OK
- checking Rd files ... NOTE
checkRd: (-1) CviCol.Rd:15: Lost braces; missing escapes or markup?
15 | The \emph{Arabidopsis thaliana} genotype data is derived from a RIL cross between Columbia-0 (Col-0) and the Cape Verde Island (Cvi-0), where 367 individuals were genotyped for 90 genetic markers. This is a diploid population with three possible genotpe states \code{(k = 3)}, where the genotypes coded as {0, 1, 2}, where 0 and 2 represent the homozygous genotypes and 1 defines the heterozygous genotype. \cr
| ^
checkRd: (-1) cal.pos.Rd:25: Lost braces; missing escapes or markup?
25 | If \code{pop.typ = "RILn"} the number of generations of selfing is limited to 20 to ensure sensible input. The constructed object is returned as a R/qtl \code{cross} object with the appropriate class structure. For \code{"RILn"} populations the constructed object is given the class {"bcsft"} by using the \pkg{qtl} package conversion function \code{convert2bcsft} with arguments \code{F.gen = n} and \code{BC.gen = 0}. For \code{"ARIL"} populations the constructed object is given the class \code{"riself"}.
| ^
checkRd: (-1) netgwas2cross.Rd:21: Lost braces; missing escapes or markup?
21 | If \code{pop.typ = "RILn"} the number of generations of selfing is limited to 20 to ensure sensible input. The constructed object is returned as a R/qtl \code{cross} object with the appropriate class structure. For \code{"RILn"} populations the constructed object is given the class {"bcsft"} by using the \pkg{qtl} package conversion function \code{convert2bcsft} with arguments \code{F.gen = n} and \code{BC.gen = 0}. For \code{"ARIL"} populations the constructed object is given the class \code{"riself"}.
| ^
checkRd: (-1) simGeno.Rd:26: Lost braces
26 | code{con.dist = "Mt"}. The default value is 3.}
| ^
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- checking for unstated dependencies in examples ... OK
- checking contents of ‘data’ directory ... OK
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- checking examples ... [35s/44s] OK
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [36s/46s] OK
Running ‘testthat.R’ [35s/45s]
- checking PDF version of manual ... [9s/13s] 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