• using R Under development (unstable) (2024-11-15 r87338)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-14 (GCC) 14.2.0     GNU Fortran (GCC) 14.2.0
• running under: Fedora Linux 36 (Workstation Edition)
• using session charset: UTF-8
• using option ‘--no-stop-on-test-error’
• checking for file ‘selectiongain/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘selectiongain’ version ‘2.0.710’
• 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 ‘selectiongain’ can be installed ... [16s/50s] 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
• 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 ... [33s/76s] OK
• checking Rd files ... NOTE checkRd: (-1) SDselectiongain.Rd:25: Lost braces; missing escapes or markup?     25 | is the vector of variance components of genetic effect, genotype \eqn{\times} location interaction, genotype \eqn{\times} year interaction, genotype \eqn{\times} location \eqn{\times} year interaction and the plot error. When \code{VSCA} is specified, the VGCAandE refers to the general combining ability, otherwise it stands for genetic effect. The default value is {1,1,1,1,1}. Variances types listed in Longin et al. (2007) can be used. For example, \code{VGCAandE="VC2"} will set the value as {1,0.5,0.5,1,2}.}        | ^ checkRd: (-1) SDselectiongain.Rd:25: Lost braces; missing escapes or markup?     25 | is the vector of variance components of genetic effect, genotype \eqn{\times} location interaction, genotype \eqn{\times} year interaction, genotype \eqn{\times} location \eqn{\times} year interaction and the plot error. When \code{VSCA} is specified, the VGCAandE refers to the general combining ability, otherwise it stands for genetic effect. The default value is {1,1,1,1,1}. Variances types listed in Longin et al. (2007) can be used. For example, \code{VGCAandE="VC2"} will set the value as {1,0.5,0.5,1,2}.}        | ^ checkRd: (-1) SDselectiongain.Rd:28: Lost braces; missing escapes or markup?     28 | is the vector of variance components for specific combining ability. The default value is {0,0,0,0}. }        | ^ checkRd: (-1) SDselectiongain.Rd:31: Lost braces; missing escapes or markup?     31 | is the vector of variance components for line per se. The default value is {0,0,0,0,0}.}        | ^ checkRd: (-1) multistagecor.Rd:23: Lost braces; missing escapes or markup?     23 | \item{VGCAandE}{is the vector of variance components of genetic effect, genotype \eqn{\times} location interaction, genotype \eqn{\times} year interaction, genotype \eqn{\times} location \eqn{\times} year interaction and the plot error. When \code{VSCA} is specified, the VGCAandE refers to the general combining ability (hybrid breeding), otherwise it stands for genetic effect (line breeding). The default value is {1,1,1,1,1}. Variances types listed in Longin et al. (2007) can be used. For example, \code{VGCAandE="VC2"} will set the value as {1,0.5,0.5,1,2}. }        | ^ checkRd: (-1) multistagecor.Rd:23: Lost braces; missing escapes or markup?     23 | \item{VGCAandE}{is the vector of variance components of genetic effect, genotype \eqn{\times} location interaction, genotype \eqn{\times} year interaction, genotype \eqn{\times} location \eqn{\times} year interaction and the plot error. When \code{VSCA} is specified, the VGCAandE refers to the general combining ability (hybrid breeding), otherwise it stands for genetic effect (line breeding). The default value is {1,1,1,1,1}. Variances types listed in Longin et al. (2007) can be used. For example, \code{VGCAandE="VC2"} will set the value as {1,0.5,0.5,1,2}. }        | ^ checkRd: (-1) multistagecor.Rd:25: Lost braces; missing escapes or markup?     25 | \item{VSCA}{is the vector of variance components for specific combining ability (hybrid breeding). The default value is {0,0,0,0}. }        | ^ checkRd: (-1) multistagecor.Rd:27: Lost braces; missing escapes or markup?     27 | \item{VLine}{Only to be used if parental and testcross selection are performed in a breeding strategy, For an example see the paper "Wegenast, Longin... 2008. Hybrid maize breeding with doubled haploids. IV". If this strategy is implemented, then Vline correspond to the vector of variance components for the parents (line per se). The default value is {0,0,0,0,0}.}        | ^ checkRd: (-1) multistagecor.Rd:49: Lost braces; missing escapes or markup?     49 | \item{VGCAandE2}{In the case of simultaneos selection of two traits (index selection) it is the vector of variance components of genetic effect, genotype \eqn{\times} location interaction, genotype \eqn{\times} year interaction, genotype \eqn{\times} location \eqn{\times} year interaction and the plot error for the second trait. When \code{VSCA2} is specified, the VGCAandE refers to the general combining ability, otherwise it stands for genetic effect of the second trait. The default value is {0,0,0,0,0}, meaning no simultaneos selection of two traits.}        | ^ checkRd: (-1) multistagecor.Rd:51: Lost braces; missing escapes or markup?     51 | \item{VSCA2}{In the case of simultaneos selection of two traits (index selection) it is the vector of variance components for specific combining ability for the second trait. The default value is {0,0,0,0}. The default value is {0,0,0,0} }        | ^ checkRd: (-1) multistagecor.Rd:51: Lost braces; missing escapes or markup?     51 | \item{VSCA2}{In the case of simultaneos selection of two traits (index selection) it is the vector of variance components for specific combining ability for the second trait. The default value is {0,0,0,0}. The default value is {0,0,0,0} }        | ^ checkRd: (-1) multistageoptimum.grid.Rd:49: Lost braces; missing escapes or markup?     49 | \item{cost.nursery}{a vector of length two c([cost of producing a DH line],[cost of testing a DH in nursery]). The default value is {0,0}. }        | ^ checkRd: (-1) multistageoptimum.search.Rd:21: Lost braces; missing escapes or markup?     21 | \item{VGCAandE}{is the vector of variance components of genetic effect, genotype \eqn{\times} location interaction, genotype \eqn{\times} year interaction, genotype \eqn{\times} location \eqn{\times} year interaction and the plot error. When \code{VSCA} is specified, it refers to the general combining ability, otherwise it stands for genetic effect. The default value is {1,1,1,1,1}. Variances types listed in Longin et al. (2007) can be used. E.g., \code{VGCAandE="VC2"} will set the value as {1,0.5,0.5,1,2}. }        | ^ checkRd: (-1) multistageoptimum.search.Rd:21: Lost braces; missing escapes or markup?     21 | \item{VGCAandE}{is the vector of variance components of genetic effect, genotype \eqn{\times} location interaction, genotype \eqn{\times} year interaction, genotype \eqn{\times} location \eqn{\times} year interaction and the plot error. When \code{VSCA} is specified, it refers to the general combining ability, otherwise it stands for genetic effect. The default value is {1,1,1,1,1}. Variances types listed in Longin et al. (2007) can be used. E.g., \code{VGCAandE="VC2"} will set the value as {1,0.5,0.5,1,2}. }        | ^ checkRd: (-1) multistageoptimum.search.Rd:60: Lost braces; missing escapes or markup?     60 | \item{cost.nursery}{a vector of length two c([cost of producing a DH line],[cost of testing a DH in nursery]). The default value is {0,0}. }        | ^ checkRd: (-1) multistageoptimum.searchIndexT.Rd:21: Lost braces; missing escapes or markup?     21 | \item{VGCAandE}{is the vector of variance components of genetic effect, genotype \eqn{\times} location interaction, genotype \eqn{\times} year interaction, genotype \eqn{\times} location \eqn{\times} year interaction and the plot error. When \code{VSCA} is specified, it refers to the general combining ability, otherwise it stands for genetic effect. The default value is {1,1,1,1,1}. Variances types listed in Longin et al. (2007) can be used. E.g., \code{VGCAandE="VC2"} will set the value as {1,0.5,0.5,1,2}. }        | ^ checkRd: (-1) multistageoptimum.searchIndexT.Rd:21: Lost braces; missing escapes or markup?     21 | \item{VGCAandE}{is the vector of variance components of genetic effect, genotype \eqn{\times} location interaction, genotype \eqn{\times} year interaction, genotype \eqn{\times} location \eqn{\times} year interaction and the plot error. When \code{VSCA} is specified, it refers to the general combining ability, otherwise it stands for genetic effect. The default value is {1,1,1,1,1}. Variances types listed in Longin et al. (2007) can be used. E.g., \code{VGCAandE="VC2"} will set the value as {1,0.5,0.5,1,2}. }        | ^ checkRd: (-1) multistageoptimum.searchIndexT.Rd:60: Lost braces; missing escapes or markup?     60 | \item{cost.nursery}{a vector of length two c([cost of producing a DH line],[cost of testing a DH in nursery]). The default value is {0,0}. }        | ^ checkRd: (-1) multistageoptimum.searchIndexT.Rd:70: Lost braces; missing escapes or markup?     70 | \item{VGCAandE2}{In the case of simultaneos selection of two traits (index selection) it is the vector of variance components of genetic effect, genotype \eqn{\times} location interaction, genotype \eqn{\times} year interaction, genotype \eqn{\times} location \eqn{\times} year interaction and the plot error for the second trait. When \code{VSCA2} is specified, the VGCAandE refers to the general combining ability, otherwise it stands for genetic effect of the second trait. The default value is {0,0,0,0,0}, meaning no simultaneos selection of two traits.}        | ^ checkRd: (-1) multistageoptimum.searchIndexT.Rd:72: Lost braces; missing escapes or markup?     72 | \item{VSCA2}{In the case of simultaneos selection of two traits (index selection) it is the vector of variance components for specific combining ability for the second trait. The default value is {0,0,0,0}. }        | ^ checkRd: (-1) multistageoptimum.searchThreeS.Rd:22: Lost braces; missing escapes or markup?     22 | \item{VGCAandE}{is the vector of variance components of genetic effect, genotype \eqn{\times} location interaction, genotype \eqn{\times} year interaction, genotype \eqn{\times} location \eqn{\times} year interaction and the plot error. When \code{VSCA} is specified, it refers to the general combining ability, otherwise it stands for genetic effect. The default value is {1,1,1,1,1}. Variances types listed in Longin et al. (2007) can be used. E.g., \code{VGCAandE="VC2"} will set the value as {1,0.5,0.5,1,2}. }        | ^ checkRd: (-1) multistageoptimum.searchThreeS.Rd:22: Lost braces; missing escapes or markup?     22 | \item{VGCAandE}{is the vector of variance components of genetic effect, genotype \eqn{\times} location interaction, genotype \eqn{\times} year interaction, genotype \eqn{\times} location \eqn{\times} year interaction and the plot error. When \code{VSCA} is specified, it refers to the general combining ability, otherwise it stands for genetic effect. The default value is {1,1,1,1,1}. Variances types listed in Longin et al. (2007) can be used. E.g., \code{VGCAandE="VC2"} will set the value as {1,0.5,0.5,1,2}. }        | ^ checkRd: (-1) multistageoptimum.searchThreeS.Rd:69: Lost braces; missing escapes or markup?     69 | \item{cost.nursery}{a vector of length two c([cost of producing a DH line],[cost of testing a DH in nursery]). The default value is {0,0}. }        | ^
• 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 examples ... [21s/53s] OK
• checking PDF version of manual ... [8s/22s] 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