• using R Under development (unstable) (2024-12-18 r87448)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     Debian clang version 19.1.5 (1)     Debian flang-new version 19.1.5 (1)
• running under: Debian GNU/Linux trixie/sid
• using session charset: UTF-8
• 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
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• checking for sufficient/correct file permissions ... OK
• checking whether package ‘selectiongain’ can be installed ... OK See the install log for details.
• 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
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• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... [0s/0s] OK
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• checking R code for possible problems ... [22s/28s] OK
• checking Rd files ... [0s/1s] 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
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• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
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• checking for unstated dependencies in examples ... OK
• checking examples ... [13s/19s] OK Examples with CPU (user + system) or elapsed time > 5s                           user system elapsed multistageoptimum.search 5.723 0.028 8.259
• checking PDF version of manual ... [5s/7s] OK
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• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 NOTE