diff --git a/DESCRIPTION b/DESCRIPTION index 6c2100a..3d6e1a3 100755 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,43 +1,44 @@ -Type: Package -Package: BioGA -Title: Bioinformatics Genetic Algorithm (BioGA) -Version: 0.99.6 -Authors@R: - person("Dany", "Mukesha", , "danymukesha@gmail.com", - role = c("aut", "cre"), - comment = c(ORCID = "0009-0001-9514-751X")) -Description: Genetic algorithm are a class of optimization algorithms - inspired by the process of natural selection and genetics. This - package allows users to analyze and optimize high throughput genomic - data using genetic algorithms. The functions provided are implemented - in C++ for improved speed and efficiency, with an easy-to-use - interface for use within R. -License: MIT + file LICENSE -URL: https://danymukesha.github.io/BioGA/ -BugReports: https://github.com/danymukesha/BioGA/issues -Imports: - ggplot2, - graphics, - Rcpp, - SummarizedExperiment, - animation, - rlang, - biocViews, - sessioninfo, - BiocStyle -Depends: - R (>= 4.4) -Suggests: - knitr, - rmarkdown, - testthat (>= 3.0.0) -LinkingTo: - Rcpp -VignetteBuilder: - knitr -biocViews: ExperimentalDesign, Technology -Encoding: UTF-8 -LazyData: false -Roxygen: list(markdown = TRUE) -RoxygenNote: 7.3.1 -Config/testthat/edition: 3 +Type: Package +Package: BioGA +Title: Bioinformatics Genetic Algorithm (BioGA) +Version: 0.99.6 +Authors@R: + person("Dany", "Mukesha", , "danymukesha@gmail.com", + role = c("aut", "cre"), + comment = c(ORCID = "0009-0001-9514-751X")) +Description: Genetic algorithm are a class of optimization algorithms + inspired by the process of natural selection and genetics. This + package allows users to analyze and optimize high throughput genomic + data using genetic algorithms. The functions provided are implemented + in C++ for improved speed and efficiency, with an easy-to-use + interface for use within R. +License: MIT + file LICENSE +URL: https://danymukesha.github.io/BioGA/, + https://bioconductor.org/packages/BioGA/ +BugReports: https://github.com/danymukesha/BioGA/issues +Imports: + ggplot2, + graphics, + Rcpp, + SummarizedExperiment, + animation, + rlang, + biocViews, + sessioninfo, + BiocStyle +Depends: + R (>= 4.4) +Suggests: + knitr, + rmarkdown, + testthat (>= 3.0.0) +LinkingTo: + Rcpp +VignetteBuilder: + knitr +biocViews: ExperimentalDesign, Technology +Encoding: UTF-8 +LazyData: false +Roxygen: list(markdown = TRUE) +RoxygenNote: 7.3.2 +Config/testthat/edition: 3 diff --git a/README.Rmd b/README.Rmd index 2221ed3..1d53847 100755 --- a/README.Rmd +++ b/README.Rmd @@ -15,6 +15,7 @@ knitr::opts_chunk$set( [![R-CMD-check](https://github.com/danymukesha/BioGA/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/danymukesha/BioGA/actions/workflows/R-CMD-check.yaml) + [![](https://img.shields.io/badge/devel%20version-0.99.6-blue.svg)](https://github.com/danymukesha/BioGA) # BioGA BioGA website @@ -28,7 +29,7 @@ with an easy-to-use interface for use within R. You can install the package directly from GitHub using the `devtools` package: -```{r} +```{r eval=FALSE} devtools::install_github("danymukesha/BioGA") ``` diff --git a/README.html b/README.html new file mode 100755 index 0000000..6376806 --- /dev/null +++ b/README.html @@ -0,0 +1,623 @@ + + + + + + + + + + + + + + + + + + + + + + + +

R-CMD-check

+ + +

BioGA +BioGA website

+

The BioGA package provides a set of functions for +genetic algorithm optimization tailored for analyzing high throughput +genomic data. These functions are implemented in C++ for improved speed +and efficiency, with an easy-to-use interface for use within R.

+

Installation

+

You can install the package directly from GitHub using the +devtools package:

+
devtools::install_github("danymukesha/BioGA")
+ + + diff --git a/README.md b/README.md index 851e0e6..3bf6dcb 100644 --- a/README.md +++ b/README.md @@ -3,6 +3,7 @@ [![R-CMD-check](https://github.com/danymukesha/BioGA/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/danymukesha/BioGA/actions/workflows/R-CMD-check.yaml) +[![](https://img.shields.io/badge/devel%20version-0.99.6-blue.svg)](https://github.com/danymukesha/BioGA) # BioGA BioGA website @@ -19,63 +20,4 @@ package: ``` r devtools::install_github("danymukesha/BioGA") -#> Downloading GitHub repo danymukesha/BioGA@HEAD -#> fs (1.6.3 -> 1.6.4 ) [CRAN] -#> fastmap (1.1.1 -> 1.2.0 ) [CRAN] -#> cachem (1.0.8 -> 1.1.0 ) [CRAN] -#> xfun (0.42 -> 0.44 ) [CRAN] -#> tinytex (0.50 -> 0.51 ) [CRAN] -#> knitr (1.45 -> 1.46 ) [CRAN] -#> htmltools (0.5.7 -> 0.5.8.1) [CRAN] -#> bslib (0.6.1 -> 0.7.0 ) [CRAN] -#> rmarkdown (2.26 -> 2.27 ) [CRAN] -#> matrixStats (1.2.0 -> 1.3.0 ) [CRAN] -#> munsell (0.5.0 -> 0.5.1 ) [CRAN] -#> farver (2.1.1 -> 2.1.2 ) [CRAN] -#> BiocManager (1.30.22 -> 1.30.23) [CRAN] -#> bookdown (0.38 -> 0.39 ) [CRAN] -#> gtable (0.3.4 -> 0.3.5 ) [CRAN] -#> ggplot2 (3.5.0 -> 3.5.1 ) [CRAN] -#> Skipping 17 packages ahead of CRAN: BiocGenerics, graph, S4Arrays, IRanges, S4Vectors, MatrixGenerics, GenomeInfoDbData, zlibbioc, XVector, GenomeInfoDb, RBGL, Biobase, DelayedArray, GenomicRanges, BiocStyle, biocViews, SummarizedExperiment -#> Installing 16 packages: fs, fastmap, cachem, xfun, tinytex, knitr, htmltools, bslib, rmarkdown, matrixStats, munsell, farver, BiocManager, bookdown, gtable, ggplot2 -#> Installing packages into 'C:/Users/dany.mukesha/AppData/Local/Temp/Rtmp63bptc/temp_libpath848868d23488' -#> (as 'lib' is unspecified) -#> Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/annotation/bin/windows/contrib/4.3: -#> cannot open URL 'https://bioconductor.org/packages/3.17/data/annotation/bin/windows/contrib/4.3/PACKAGES' -#> Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/experiment/bin/windows/contrib/4.3: -#> cannot open URL 'https://bioconductor.org/packages/3.17/data/experiment/bin/windows/contrib/4.3/PACKAGES' -#> Warning: unable to access index for repository https://bioconductor.org/packages/3.17/workflows/bin/windows/contrib/4.3: -#> cannot open URL 'https://bioconductor.org/packages/3.17/workflows/bin/windows/contrib/4.3/PACKAGES' -#> package 'fs' successfully unpacked and MD5 sums checked -#> package 'fastmap' successfully unpacked and MD5 sums checked -#> package 'cachem' successfully unpacked and MD5 sums checked -#> package 'xfun' successfully unpacked and MD5 sums checked -#> package 'tinytex' successfully unpacked and MD5 sums checked -#> package 'knitr' successfully unpacked and MD5 sums checked -#> package 'htmltools' successfully unpacked and MD5 sums checked -#> package 'bslib' successfully unpacked and MD5 sums checked -#> package 'rmarkdown' successfully unpacked and MD5 sums checked -#> package 'matrixStats' successfully unpacked and MD5 sums checked -#> package 'munsell' successfully unpacked and MD5 sums checked -#> package 'farver' successfully unpacked and MD5 sums checked -#> package 'BiocManager' successfully unpacked and MD5 sums checked -#> package 'bookdown' successfully unpacked and MD5 sums checked -#> package 'gtable' successfully unpacked and MD5 sums checked -#> package 'ggplot2' successfully unpacked and MD5 sums checked -#> -#> The downloaded binary packages are in -#> C:\Users\dany.mukesha\AppData\Local\Temp\RtmpArcJMj\downloaded_packages -#> ── R CMD build ───────────────────────────────────────────────────────────────── -#> checking for file 'C:\Users\dany.mukesha\AppData\Local\Temp\RtmpArcJMj\remotes15e82c92423\danymukesha-BioGA-23ecb91/DESCRIPTION' ... ✔ checking for file 'C:\Users\dany.mukesha\AppData\Local\Temp\RtmpArcJMj\remotes15e82c92423\danymukesha-BioGA-23ecb91/DESCRIPTION' (343ms) -#> ─ preparing 'BioGA': -#> checking DESCRIPTION meta-information ... checking DESCRIPTION meta-information ... ✔ checking DESCRIPTION meta-information -#> ─ cleaning src -#> ─ checking for LF line-endings in source and make files and shell scripts -#> ─ checking for empty or unneeded directories -#> Omitted 'LazyData' from DESCRIPTION -#> ─ building 'BioGA_0.99.5.tar.gz' -#> -#> -#> Installing package into 'C:/Users/dany.mukesha/AppData/Local/Temp/Rtmp63bptc/temp_libpath848868d23488' -#> (as 'lib' is unspecified) ```