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3.3.0

Released on CRAN 202X-XX-XX

Addressed R CMD check --as-cran GAPIT_3.5.0.tar.gz issues 2025-10

Found the following (possibly) invalid URLs: URL: http://www.r-project.org From: README.md Status: 200 Message: OK R-project URL not in canonical form URL: http://www.rstudio.com (moved to https://posit.co/) From: README.md Status: 200 Message: OK URL: http://zzlab.net/GEMT (moved to https://zzlab.net/GEMT) From: inst/doc/FAQ.html Status: 404 Message: Not Found URL: http://zzlab.net/WorkshopISU (moved to https://zzlab.net/WorkshopISU/) From: inst/doc/FAQ.html Status: 200 Message: OK Canonical www.R-project.org URLs use https.

  • checking package dependencies ... INFO Package in Depends/Imports which should probably only be in LinkingTo: ‘RcppArmadillo’

  • checking R code for possible problems ... [42s/42s] NOTE Possibly missing '()' after 'return' in the following function: ‘GAPIT.Manhattan’

Addressed R CMD check GAPIT_3.5.0.tar.gz issues 2025-10

Note: break used in wrong context: no loop is visible at GAPIT.R:531 Note: possible error in 'GAPIT(Y = Y, CV = CV, ': unused argument (GTindex = GTindex) at GAPIT.Bus.R:24 Note: possible error in 'layout(title = "Interactive.Manhattan.Plot", ': unused arguments (title = "Interactive.Manhattan.Plot", xaxis = list(title = "Chromsome", zeroline = FALSE, showticklabels = FALSE), yaxis = list(title = "-Log10(p)")) at GAPIT.Interactive.Manhattan.R:85 Note: possible error in 'layout(title = "Interactive.Multiple_Synthesis.Manhattan.Plot", ': unused arguments (title = "Interactive.Multiple_Synthesis.Manhattan.Plot", xaxis = list(title = "Chromsome", zeroline = FALSE, showticklabels = FALSE), yaxis = list(title = "-Log10(p)")) at GAPIT.Multiple_Synthesis.R:244 Note: possible error in 'layout(title = "Interactive.Multiple_Synthesis.Manhattan.Plot", ': unused arguments (title = "Interactive.Multiple_Synthesis.Manhattan.Plot", xaxis = list(title = "Chromsome", zeroline = FALSE, showticklabels = FALSE), yaxis = list(title = "-Log10(p)")) at GAPIT.Multiple_Synthesis.R:277 Note: possible error in 'GAPIT(Y = myY, GD = myGD, ': unused arguments (threshold.output = 0.001, iteration.output = TRUE) at GAPIT.Power.compare_plink.R:123 Note: possible error in 'GAPIT(Y = myY, GD = myGD, ': unused arguments (threshold.output = 0.001, iteration.output = TRUE) at GAPIT.Power.compare_plink.R:140 Note: possible error in 'GAPIT(Y = myY, GD = myGD, ': unused arguments (LD = 0.1, threshold.output = 0.001, iteration.output = TRUE) at GAPIT.Power.compare_plink.R:159 Note: possible error in 'GAPIT(Y = myY, GD = myGD, ': unused arguments (threshold.output = 0.001, iteration.output = TRUE) at GAPIT.Power.compare_plink.R:177 Note: possible error in 'GAPIT(Y = myY, G = myG, ': unused arguments (threshold.output = 0.001, iteration.output = TRUE) at GAPIT.Power.compare_plink.R:196

  • checking code files for non-ASCII characters ... WARNING Found the following files with non-ASCII characters: R/GAPIT.3D.PCA.python.R R/GAPIT.Main.R Portable packages must use only ASCII characters in their R code and NAMESPACE directives, except perhaps in comments. Use \uxxxx escapes for other characters. Function ‘tools::showNonASCIIfile’ can help in finding non-ASCII characters in files.

  • checking dependencies in R code ... WARNING 'library' or 'require' calls not declared from: ‘lme4’ ‘plotly’ ‘rgl’ ‘rglwidget’ 'library' or 'require' calls in package code: ‘lme4’ ‘plotly’ ‘rgl’ ‘rglwidget’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Namespaces in Imports field not imported from: ‘grid’ ‘lattice’ ‘rgl’ All declared Imports should be used.

  • checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘grid’ ‘lattice’ ‘rgl’ All declared Imports should be used.

  • checking R code for possible problems ... NOTE GAPIT.Bread: warning in GAPIT(Y = Y, CV = CV, Z = Z, KI = KI, GD = GD, GM = GM, model = ("GLM"), QC = FALSE, CV.Extragenetic = CV.Extragenetic, file.output = file.output): partial argument match of 'QC' to 'QC.Y' (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Bread.R:24-36) GAPIT.Bread: warning in GAPIT(Y = Y, CV = CV, Z = Z, KI = KI, GD = GD, GM = GM, model = "MLM", QC = FALSE, CV.Extragenetic = CV.Extragenetic, file.output = file.output): partial argument match of 'QC' to 'QC.Y' (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Bread.R:49-61) GAPIT.Bread: warning in GAPIT(Y = Y, CV = CV, Z = Z, KI = KI, GD = GD, GM = GM, model = "CMLM", QC = FALSE, CV.Extragenetic = CV.Extragenetic, file.output = file.output): partial argument match of 'QC' to 'QC.Y' (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Bread.R:73-85)

Added library_name:: prefix to function names.

  • checking R code for possible problems ... NOTE GAPIT.Bus: no visible binding for global variable ‘FDR.Rate’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Bus.R:124) GAPIT.Bus: no visible binding for global variable ‘FDR.Rate’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Bus.R:435) GAPIT.Cor.matrix: no visible global function definition for ‘cor’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Cor.matrix.R:6) GAPIT.EMMAxP3D: no visible global function definition for ‘var’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.EMMAxP3D.R:838-843) GAPIT.Genotype.View: no visible global function definition for ‘median’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Genotype.View.R:109) GAPIT.Genotype.View: no visible global function definition for ‘par’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Genotype.View.R:121) GAPIT.Genotype.View: no visible global function definition for ‘axis’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Genotype.View.R:124) GAPIT.Genotype.View: no visible global function definition for ‘axis’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Genotype.View.R:125) GAPIT.Genotype.View: no visible global function definition for ‘axis’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Genotype.View.R:126) GAPIT.Genotype.View: no visible global function definition for ‘head’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Genotype.View.R:130) GAPIT.Genotype.View: no visible global function definition for ‘axis’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Genotype.View.R:133) GAPIT.Genotype.View: no visible global function definition for ‘axis’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Genotype.View.R:134) GAPIT.Genotype.View: no visible global function definition for ‘axis’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Genotype.View.R:135) GAPIT.Genotype.View: no visible global function definition for ‘hist’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Genotype.View.R:138) GAPIT.Genotype.View: no visible global function definition for ‘abline’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Genotype.View.R:159) GAPIT.Genotype.View: no visible global function definition for ‘lines’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Genotype.View.R:204) GAPIT.Genotype.View: no visible global function definition for ‘write.csv’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Genotype.View.R:209) GAPIT.Genotype.View: no visible global function definition for ‘layout’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Genotype.View.R:235-237) GAPIT.Genotype.View: no visible global function definition for ‘par’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Genotype.View.R:238) GAPIT.Genotype.View: no visible global function definition for ‘axis’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Genotype.View.R:243) GAPIT.Genotype.View: no visible global function definition for ‘par’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Genotype.View.R:244) GAPIT.Genotype.View: no visible global function definition for ‘write.csv’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Genotype.View.R:249) GAPIT.Genotype.View: no visible global function definition for ‘axis’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Genotype.View.R:252) GAPIT.Genotype.View: no visible global function definition for ‘par’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Genotype.View.R:253) GAPIT.Genotype.View: no visible global function definition for ‘axis’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Genotype.View.R:256) GAPIT.Genotype.View: no visible global function definition for ‘axis’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Genotype.View.R:257) GAPIT.Genotype.View: no visible global function definition for ‘axis’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Genotype.View.R:258) GAPIT.IC: no visible global function definition for ‘rnorm’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.IC.R:115) GAPIT.LD.decay: no visible binding for global variable ‘myGM’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.LD.decay.R:43) GAPIT.LD.decay: no visible global function definition for ‘par’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.LD.decay.R:80) GAPIT.LD.decay: no visible global function definition for ‘par’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.LD.decay.R:86) GAPIT.LD.decay: no visible global function definition for ‘abline’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.LD.decay.R:88) GAPIT.LD.decay: no visible global function definition for ‘axis’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.LD.decay.R:89) GAPIT.LD.decay: no visible global function definition for ‘axis’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.LD.decay.R:90) GAPIT.LD.decay: no visible global function definition for ‘title’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.LD.decay.R:93) GAPIT.LD.decay: no visible global function definition for ‘par’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.LD.decay.R:104) GAPIT.LD.decay: no visible global function definition for ‘axis’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.LD.decay.R:109) GAPIT.LD.decay: no visible global function definition for ‘axis’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.LD.decay.R:110) GAPIT.LD.decay: no visible global function definition for ‘title’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.LD.decay.R:113) GAPIT.LD.decay: no visible global function definition for ‘lines’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.LD.decay.R:132) GAPIT.LD.decay: no visible global function definition for ‘hist’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.LD.decay.R:135) GAPIT.LD.decay: no visible global function definition for ‘hist’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.LD.decay.R:140) GAPIT.LD.decay: no visible global function definition for ‘par’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.LD.decay.R:147) GAPIT.LD.decay: no visible global function definition for ‘axis’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.LD.decay.R:150) GAPIT.LD.decay: no visible global function definition for ‘axis’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.LD.decay.R:151) GAPIT.LD.decay: no visible global function definition for ‘mtext’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.LD.decay.R:153) GAPIT.LD.decay: no visible global function definition for ‘legend’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.LD.decay.R:156-158) GAPIT.LD.decay: no visible global function definition for ‘par’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.LD.decay.R:156-158) GAPIT.Manhattan: no visible global function definition for ‘pdf’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Manhattan.R:97) GAPIT.Manhattan: no visible global function definition for ‘layout’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Manhattan.R:99) GAPIT.Manhattan: no visible global function definition for ‘cor’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Manhattan.R:137) GAPIT.Manhattan: no visible global function definition for ‘colorRampPalette’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Manhattan.R:160) GAPIT.Manhattan: no visible global function definition for ‘par’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Manhattan.R:175) GAPIT.Manhattan: no visible global function definition for ‘par’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Manhattan.R:176) GAPIT.Manhattan: no visible global function definition for ‘abline’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Manhattan.R:183) GAPIT.Manhattan: no visible global function definition for ‘abline’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Manhattan.R:184) GAPIT.Manhattan: no visible global function definition for ‘par’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Manhattan.R:185) GAPIT.Manhattan: no visible global function definition for ‘barplot’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Manhattan.R:187) GAPIT.Manhattan: no visible global function definition for ‘axis’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Manhattan.R:189) GAPIT.Manhattan: no visible global function definition for ‘dev.off’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Manhattan.R:192) GAPIT.Manhattan: no visible global function definition for ‘rainbow’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Manhattan.R:218) GAPIT.Manhattan: no visible global function definition for ‘pdf’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Manhattan.R:294) GAPIT.Manhattan: no visible global function definition for ‘pdf’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Manhattan.R:296) GAPIT.Manhattan: no visible global function definition for ‘par’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Manhattan.R:298) GAPIT.Manhattan: no visible global function definition for ‘abline’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Manhattan.R:304) GAPIT.Manhattan: no visible global function definition for ‘points’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Manhattan.R:305) GAPIT.Manhattan: no visible global function definition for ‘points’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Manhattan.R:306) GAPIT.Manhattan: no visible global function definition for ‘abline’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Manhattan.R:309) GAPIT.Manhattan: no visible global function definition for ‘points’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Manhattan.R:310) GAPIT.Manhattan: no visible global function definition for ‘points’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Manhattan.R:311) GAPIT.Manhattan: no visible global function definition for ‘abline’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Manhattan.R:316) GAPIT.Manhattan: no visible global function definition for ‘abline’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Manhattan.R:318) GAPIT.Manhattan: no visible global function definition for ‘axis’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Manhattan.R:326) GAPIT.Manhattan: no visible global function definition for ‘axis’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Manhattan.R:327) GAPIT.Manhattan: no visible global function definition for ‘axis’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Manhattan.R:328) GAPIT.Manhattan: no visible global function definition for ‘box’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Manhattan.R:330) GAPIT.Manhattan: no visible global function definition for ‘palette’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Manhattan.R:331) GAPIT.Manhattan: no visible global function definition for ‘dev.off’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Manhattan.R:332) GAPIT.Multiple.Manhattan: no visible global function definition for ‘read.csv’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:45) GAPIT.Multiple.Manhattan: no visible global function definition for ‘write.csv’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:80) GAPIT.Multiple.Manhattan: no visible global function definition for ‘rainbow’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:164) GAPIT.Multiple.Manhattan: no visible global function definition for ‘pdf’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:187) GAPIT.Multiple.Manhattan: no visible global function definition for ‘par’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:188) GAPIT.Multiple.Manhattan: no visible global function definition for ‘par’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:194) GAPIT.Multiple.Manhattan: no visible global function definition for ‘par’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:199) GAPIT.Multiple.Manhattan: no visible global function definition for ‘read.csv’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:201) GAPIT.Multiple.Manhattan: no visible global function definition for ‘runif’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:271) GAPIT.Multiple.Manhattan: no visible global function definition for ‘mtext’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:291) GAPIT.Multiple.Manhattan: no visible global function definition for ‘abline’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:294) GAPIT.Multiple.Manhattan: no visible global function definition for ‘points’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:295) GAPIT.Multiple.Manhattan: no visible global function definition for ‘points’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:296) GAPIT.Multiple.Manhattan: no visible global function definition for ‘abline’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:302) GAPIT.Multiple.Manhattan: no visible global function definition for ‘abline’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:304) GAPIT.Multiple.Manhattan: no visible global function definition for ‘abline’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:309) GAPIT.Multiple.Manhattan: no visible global function definition for ‘axis’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:310) GAPIT.Multiple.Manhattan: no visible global function definition for ‘axis’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:311) GAPIT.Multiple.Manhattan: no visible global function definition for ‘axis’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:312) GAPIT.Multiple.Manhattan: no visible global function definition for ‘mtext’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:313) GAPIT.Multiple.Manhattan: no visible global function definition for ‘dev.off’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:315) GAPIT.Multiple.Manhattan: no visible global function definition for ‘pdf’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:320) GAPIT.Multiple.Manhattan: no visible global function definition for ‘par’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:321) GAPIT.Multiple.Manhattan: no visible global function definition for ‘par’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:330) GAPIT.Multiple.Manhattan: no visible global function definition for ‘par’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:335) GAPIT.Multiple.Manhattan: no visible global function definition for ‘read.csv’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:339) GAPIT.Multiple.Manhattan: no visible global function definition for ‘runif’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:416) GAPIT.Multiple.Manhattan: no visible global function definition for ‘mtext’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:444) GAPIT.Multiple.Manhattan: no visible global function definition for ‘abline’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:447) GAPIT.Multiple.Manhattan: no visible global function definition for ‘abline’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:448) GAPIT.Multiple.Manhattan: no visible global function definition for ‘abline’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:451) GAPIT.Multiple.Manhattan: no visible global function definition for ‘points’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:453) GAPIT.Multiple.Manhattan: no visible global function definition for ‘points’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:454) GAPIT.Multiple.Manhattan: no visible global function definition for ‘abline’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:457) GAPIT.Multiple.Manhattan: no visible global function definition for ‘axis’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:458) GAPIT.Multiple.Manhattan: no visible global function definition for ‘axis’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:459) GAPIT.Multiple.Manhattan: no visible global function definition for ‘mtext’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:461) GAPIT.Multiple.Manhattan: no visible global function definition for ‘box’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:463) GAPIT.Multiple.Manhattan: no visible global function definition for ‘dev.off’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:465) GAPIT.Multiple.Manhattan: no visible global function definition for ‘pdf’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:490) GAPIT.Multiple.Manhattan: no visible global function definition for ‘par’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:491) GAPIT.Multiple.Manhattan: no visible global function definition for ‘par’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:492) GAPIT.Multiple.Manhattan: no visible global function definition for ‘axis’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:500) GAPIT.Multiple.Manhattan: no visible global function definition for ‘axis’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:501) GAPIT.Multiple.Manhattan: no visible global function definition for ‘abline’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:502) GAPIT.Multiple.Manhattan: no visible global function definition for ‘abline’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:507) GAPIT.Multiple.Manhattan: no visible global function definition for ‘abline’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:509) GAPIT.Multiple.Manhattan: no visible global function definition for ‘mtext’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:512) GAPIT.Multiple.Manhattan: no visible global function definition for ‘read.csv’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:522) GAPIT.Multiple.Manhattan: no visible global function definition for ‘runif’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:605) GAPIT.Multiple.Manhattan: no visible global function definition for ‘par’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:628) GAPIT.Multiple.Manhattan: no visible global function definition for ‘points’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:634) GAPIT.Multiple.Manhattan: no visible global function definition for ‘abline’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:638) GAPIT.Multiple.Manhattan: no visible global function definition for ‘points’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:640) GAPIT.Multiple.Manhattan: no visible global function definition for ‘axis’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:642) GAPIT.Multiple.Manhattan: no visible global function definition for ‘dev.off’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:645) GAPIT.Multiple.Manhattan: no visible global function definition for ‘write.csv’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:692) GAPIT.Multiple.Manhattan: no visible global function definition for ‘pdf’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:693) GAPIT.Multiple.Manhattan: no visible global function definition for ‘par’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:694) GAPIT.Multiple.Manhattan: no visible global function definition for ‘par’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:695) GAPIT.Multiple.Manhattan: no visible global function definition for ‘par’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:702) GAPIT.Multiple.Manhattan: no visible global function definition for ‘points’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:714-716) GAPIT.Multiple.Manhattan: no visible global function definition for ‘text’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:717) GAPIT.Multiple.Manhattan: no visible global function definition for ‘points’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:726-728) GAPIT.Multiple.Manhattan: no visible global function definition for ‘text’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:729) GAPIT.Multiple.Manhattan: no visible global function definition for ‘points’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:739-741) GAPIT.Multiple.Manhattan: no visible global function definition for ‘text’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:742) GAPIT.Multiple.Manhattan: no visible global function definition for ‘points’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:748-750) GAPIT.Multiple.Manhattan: no visible global function definition for ‘text’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:751) GAPIT.Multiple.Manhattan: no visible global function definition for ‘dev.off’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.Manhattan.R:757) GAPIT.Multiple.QQ: no visible global function definition for ‘runif’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.QQ.R:19) GAPIT.Multiple.QQ: no visible global function definition for ‘pdf’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.QQ.R:40) GAPIT.Multiple.QQ: no visible global function definition for ‘par’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.QQ.R:41) GAPIT.Multiple.QQ: no visible global function definition for ‘par’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.QQ.R:42) GAPIT.Multiple.QQ: no visible global function definition for ‘par’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.QQ.R:43) GAPIT.Multiple.QQ: no visible global function definition for ‘par’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple.QQ.R:96) GAPIT.Multiple_Synthesis: no visible global function definition for ‘read.csv’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple_Synthesis.R:34) GAPIT.Multiple_Synthesis: no visible global function definition for ‘read.csv’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple_Synthesis.R:122) GAPIT.Multiple_Synthesis: no visible global function definition for ‘runif’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple_Synthesis.R:206) GAPIT.Multiple_Synthesis: no visible global function definition for ‘add_markers’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple_Synthesis.R:244-270) GAPIT.Multiple_Synthesis: no visible global function definition for ‘add_markers’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Multiple_Synthesis.R:277-303) GAPIT.PCA: no visible global function definition for ‘legend’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.PCA.R:50-51) GAPIT.PCA: no visible global function definition for ‘par’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.PCA.R:50-51) GAPIT.PCA: no visible global function definition for ‘write.csv’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.PCA.R:62) GAPIT.PCA: no visible global function definition for ‘legend’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.PCA.R:84-85) GAPIT.PCA: no visible global function definition for ‘par’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.PCA.R:84-85) GAPIT.PagainstP: no visible global function definition for ‘par’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.PagainstP.R:117) GAPIT.PagainstP: no visible global function definition for ‘par’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.PagainstP.R:118) GAPIT.PagainstP: no visible global function definition for ‘abline’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.PagainstP.R:126) GAPIT.PagainstP: no visible global function definition for ‘abline’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.PagainstP.R:127) GAPIT.PagainstP: no visible global function definition for ‘par’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.PagainstP.R:131) GAPIT.PagainstP: no visible global function definition for ‘cor’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.PagainstP.R:139) GAPIT.PagainstP: no visible global function definition for ‘axis’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.PagainstP.R:143) GAPIT.PagainstP: no visible global function definition for ‘axis’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.PagainstP.R:144) GAPIT.PagainstP: no visible global function definition for ‘mtext’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.PagainstP.R:145) GAPIT.PagainstP: no visible global function definition for ‘mtext’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.PagainstP.R:146) GAPIT.PagainstP: no visible global function definition for ‘legend’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.PagainstP.R:148-150) GAPIT.Phenotype.View: no visible global function definition for ‘layout’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Phenotype.View.R:27-29) GAPIT.Phenotype.View: no visible global function definition for ‘par’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Phenotype.View.R:32) GAPIT.Phenotype.View: no visible global function definition for ‘par’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Phenotype.View.R:34) GAPIT.Phenotype.View: no visible global function definition for ‘hist’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Phenotype.View.R:35) GAPIT.Phenotype.View: no visible global function definition for ‘par’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Phenotype.View.R:36) GAPIT.Phenotype.View: no visible global function definition for ‘density’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Phenotype.View.R:37) GAPIT.Phenotype.View: no visible global function definition for ‘na.omit’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Phenotype.View.R:37) GAPIT.Phenotype.View: no visible global function definition for ‘par’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Phenotype.View.R:38) GAPIT.Phenotype.View: no visible global function definition for ‘boxplot’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Phenotype.View.R:39) GAPIT.Phenotype.View: no visible global function definition for ‘par’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Phenotype.View.R:40) GAPIT.Phenotype.View: no visible global function definition for ‘ecdf’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Phenotype.View.R:41) GAPIT.Phenotype.afterGWAS: no visible global function definition for ‘par’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Phenotype.afterGWAS.R:53) GAPIT.Phenotype.afterGWAS: no visible global function definition for ‘boxplot’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Phenotype.afterGWAS.R:85-87) GAPIT.Phenotype.afterGWAS: no visible global function definition for ‘points’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Phenotype.afterGWAS.R:91) GAPIT.Phenotype.afterGWAS: no visible global function definition for ‘runif’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Phenotype.afterGWAS.R:91) GAPIT.Phenotype.afterGWAS: no visible global function definition for ‘axis’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Phenotype.afterGWAS.R:94) GAPIT.Phenotype.afterGWAS: no visible global function definition for ‘axis’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Phenotype.afterGWAS.R:95) GAPIT.Phenotype.afterGWAS: no visible global function definition for ‘mtext’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Phenotype.afterGWAS.R:98) GAPIT.Phenotype.afterGWAS: no visible global function definition for ‘mtext’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Phenotype.afterGWAS.R:99) GAPIT.Power.compare: no visible binding for global variable ‘myGM’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Power.compare.R:50) GAPIT.Power.compare: no visible global function definition for ‘rainbow’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Power.compare.R:81) GAPIT.RandomModel: no visible global function definition for ‘var’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.RandomModel.R:36) GAPIT.RandomModel: no visible global function definition for ‘layout’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.RandomModel.R:200-202) GAPIT.RandomModel: no visible global function definition for ‘par’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.RandomModel.R:203) GAPIT.Remove.outliers: no visible global function definition for ‘quantile’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Remove.outliers.R:18) GAPIT.Remove.outliers: no visible global function definition for ‘IQR’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Remove.outliers.R:20) GAPIT.SS: no visible global function definition for ‘quantile’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.SS.R:213) GAPIT.Validation: no visible global function definition for ‘cor’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Validation.R:45) GAPIT.Validation: no visible global function definition for ‘cor’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Validation.R:46) GAPIT.Validation: no visible global function definition for ‘cor’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Validation.R:61) GAPIT.Validation: no visible global function definition for ‘cor’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.Validation.R:80)

GAPIT.cross_validation.compare: no visible binding for global variable ‘myGD’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.cross_validation.compare.R:23) GAPIT.cross_validation.compare: no visible binding for global variable ‘rel’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.cross_validation.compare.R:126) GAPIT.cross_validation.compare: no visible binding for global variable ‘rel’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.cross_validation.compare.R:132) GAPIT.cross_validation.compare: no visible binding for global variable ‘rel’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.cross_validation.compare.R:150) GAPIT.cross_validation.compare: no visible binding for global variable ‘rel’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.cross_validation.compare.R:151) GAPIT.cross_validation.compare: no visible binding for global variable ‘rel’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.cross_validation.compare.R:157) GAPIT.cross_validation.compare: no visible binding for global variable ‘rel’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.cross_validation.compare.R:158) GAPIT.get.LL: no visible binding for global variable ‘var’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.get.LL.R:23-28) emmreml: no visible global function definition for ‘ginv’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.emmreml.R:14) emmreml: no visible global function definition for ‘optimize’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.emmreml.R:32-33) emmreml: no visible global function definition for ‘ginv’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.emmreml.R:39) emmreml: no visible global function definition for ‘ginv’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.emmreml.R:47) emmreml: no visible global function definition for ‘ginv’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.emmreml.R:70-71) emmreml: no visible global function definition for ‘ginv’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.emmreml.R:83-84) emmreml: no visible global function definition for ‘ginv’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.emmreml.R:94) emmreml: no visible global function definition for ‘pchisq’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.emmreml.R:99) emmreml: no visible binding for global variable ‘p.adjust.methods’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.emmreml.R:100) emmreml : : no visible global function definition for ‘p.adjust’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.emmreml.R:101-102) emmreml: no visible global function definition for ‘pchisq’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.emmreml.R:104-105) emmreml : : no visible global function definition for ‘p.adjust’ (/home/knausb/gits/GAPIT.Rcheck/00_pkg_src/GAPIT/R/GAPIT.emmreml.R:106-107)

Addressed testthat::test_check() 2025-10

  • Moved 3d.PDC.py from R/ to inst/

  • Added escape (%) for percentage signs in GAPIT.R

  • Added if( exists("eig.R"") ){ rm(eig.R) } to GAPIT.EMMAxP3D

  • Added if(SNP.P3D == TRUE & exists("eig.L"") ){ rm(eig.L) } to GAPIT.EMMAxP3D

  • Added Lambdas[ Lambdas <= 0 ] <- 1e-9 to GAPIT.emma.REMLE

  • Changed Depends: R (<= 4.4.1) to Depends: R (>= 4.4.1)

  • updated GAPIT.Rproj

  • Added roxygen to GAPIT.

  • Omitted install.packages() calls.

  • Replaced library() and require() calls with package::function().

  • Added tests for models MLM, GLM, CMLM, MMLM, SUPER, FarmCPU, gBLUP, and cBLUP.

  • Created manual page for GAPIT3::GAPIT().

  • Created manual page for GAPIT3::GAPIT.Compression.Visualization(), added parameter file.output.

  • Created manual page for GAPIT3::GAPIT.ID(), file.output is respected for testing, returns an invisible NULL to facilitate testing.

  • Omitted uncalled function BlinkR.SUB().

  • Documented example data sets.