cran-comments.md

In neyhartj/qgsim: Simulations of Plant Breeding Experiments

Test environment

• local Windows install, R 3.5.1
• ubuntu 14.04.5 (on travis-ci), R 3.5.__
• win-builder (devel and release)

R CMD Check comments

R CMD check results Status: 1 ERROR, 3 WARNINGs, 5 NOTEs

See 'C:/Users/jln54/Documents/Programming/Repositories/pbsim.Rcheck/00check.log' for details.

checking examples ... ERROR Running examples in 'pbsim-Ex.R' failed The error most likely occurred in:

base::assign(".ptime", proc.time(), pos = "CheckExEnv")

Name: find_proxmarkers

Title: Find the position of markers near a locus

Aliases: find_proxmarkers

** Examples

Simulate the genome

n.mar <- c(505, 505, 505) len <- c(120, 130, 140)

genome <- sim_genome(len, n.mar)

Sample marker names to lookup

sample_markers <- sample(markernames(genome), size = 3) Error in qtlnames(genome) : No genetic model has been declared for the genome Calls: sample -> markernames -> qtlnames Execution halted

checking S3 generic/method consistency ... WARNING print: function(x, ...) print.genome: function(x)

summary: function(object, ...) summary.genome: function(x)

See section 'Generic functions and methods' in the 'Writing R Extensions' manual.

Found the following apparent S3 methods exported but not registered: summary.genome See section 'Registering S3 methods' in the 'Writing R Extensions' manual.

checking Rd cross-references ... WARNING Missing link or links in documentation object 'calc_exp_genvar.Rd': 'sim_crossing.block'

Missing link or links in documentation object 'sim_family.Rd': 'subset.pop'

Missing link or links in documentation object 'sim_family_cb.Rd': 'sim_crossing.block'

See section 'Cross-references' in the 'Writing R Extensions' manual.

checking Rd \usage sections ... WARNING Undocumented arguments in documentation object 'qtlnames' 'chr'

Undocumented arguments in documentation object 'sim_family' '...'

Undocumented arguments in documentation object 'sim_founders' 'ignore.gen.model'

Undocumented arguments in documentation object 'sim_multi_gen_model' '...'

Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter 'Writing R documentation files' in the 'Writing R Extensions' manual. S3 methods shown with full name in documentation object 'summary.genome': 'summary.genome'

The \usage entries for S3 methods should use the \method markup and not their full name. See chapter 'Writing R documentation files' in the 'Writing R Extensions' manual.

checking top-level files ... NOTE Non-standard files/directories found at top level: 'README.Rmd' 'cran-comments.md' 'sandbox.R'

checking dependencies in R code ... NOTE ':::' call which should be '::': 'qtl:::mf.h' See the note in ?::: about the use of this operator. There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: 'recombine_hypred'

checking R code for possible problems ... NOTE calc_exp_genvar : : : no visible global function definition for 'dist' calc_genoval: no visible binding for global variable 'ind' find_proxmarkers: no visible binding for global variable '.' find_proxmarkers: no visible binding for global variable 'chr_len' find_proxmarkers: no visible binding for global variable 'chr' find_proxmarkers: no visible binding for global variable 'pos' induce_dh: no visible binding for global variable 'gen' map_to_popvar: no visible binding for global variable '.' ... 53 lines ... subset_pop: no visible binding for global variable 'ind' summary.genome: no visible binding for global variable 'add_eff' summary.genome: no visible binding for global variable 'dom_eff' Undefined global functions or variables: . add_eff check_pop chr chr_len dist dom_eff effect env gen head ind key marker na.omit obs parent1 parent2 pheno_mean phenomean phenoval pos qtl_name rnorm runif tail trait var Consider adding importFrom("stats", "dist", "na.omit", "rnorm", "runif", "var") importFrom("utils", "head", "tail") to your NAMESPACE file.

checking Rd files ... NOTE prepare_Rd: sim_pedigree.Rd:33-35: Dropping empty section \details

checking Rd line widths ... NOTE Rd file 'select_pop.Rd': \examples lines wider than 100 characters: map <- lapply(split(R CMD check results 1 error | 3 warnings | 5 notes s2_snp_info, s2_snp_info$chrom), function(chr) structure(chr$cM_pos, names = chr$rs) )

Rd file 'sim_family_cb.Rd': \examples lines wider than 100 characters: fam_cb <- sim_family_cb(genome = genome, pedigree = ped, founder.pop = founder.pop, crossing.block = cb) fam_cb <- sim_family_cb(genome = genome, pedigree = ped, founder.pop = founder.pop, crossing.block = cb)

Rd file 'sim_genome.Rd': \examples lines wider than 100 characters: map <- lapply(split(s2_snp_info, s2_snp_info$chrom), function(chr) structure(chr$cM_pos, names = chr$rs) )

Rd file 'sim_phenoval.Rd': \examples lines wider than 100 characters: map <- lapply(split(s2_snp_info, s2_snp_info$chrom), function(chr) structure(chr$cM_pos, names = chr$rs) )

Rd file 'subset_pop.Rd': \examples lines wider than 100 characters: map <- lapply(split(s2_snp_info, s2_snp_info$chrom), function(chr) structure(chr$cM_pos, names = chr$rs) )

These lines will be truncated in the PDF manual.

Downstream dependencies

There are currently no downstream dependencies for this package.

neyhartj/qgsim documentation built on Nov. 11, 2023, 4:08 p.m.