checklist for bioC submission - Githubissues

Nanostring-Biostats / InSituType

An R package for performing cell typing in SMI and other single cell data

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checklist for bioC submission #170

Closed patrickjdanaher closed 6 months ago

patrickjdanaher commented 1 year ago

[x] Add MIT license
[ ] look at dependency licenses down to the 2nd order (see note below for a list of 2nd order dependencies)
[x] confirm there's a test for every exported function
[x] issue 161 - subclustering correction
[x] Check roxygen documentation - plenty of incomplete / outdated docs right now
[x] clean up the code detritus in rescaleProfiles.R
[x] speed up geosketch

patrickjdanaher commented 1 year ago

1st order dependencies: Matrix, Rcpp, irlba, lsa, mclust, scales, umap, stats, utils

2nd order: Matix: methods, graphics, grid, stats, utils, lattice

Rcpp: methods, utils

irlba: stats, methods

lsa (gpl3): SnowballC

Mclust: stats, utils, graphics, grDevices

scales: (if needed, can write our own version of the one function we get from this) farver (≥ 2.0.3), labeling, lifecycle, munsell (≥ 0.5), R6, RColorBrewer, rlang (≥ 1.0.0), viridisLite

umap: (if needed, could use a different package like uwot) Matrix, methods, openssl, reticulate, Rcpp (≥ 0.12.6), RSpectra, stats

davidpross commented 1 year ago

First-order and recursive dependencies with license information

package | license -- | -- utf8 | Apache License (== 2.0) \| file LICENSE RColorBrewer | Apache License 2.0 reticulate | Apache License 2.0 MatrixGenerics | Artistic-2.0 matrixStats | Artistic-2.0 colorspace | BSD_3_clause + file LICENSE SnowballC | BSD_3_clause + file LICENSE yaml | BSD_3_clause + file LICENSE highr | GPL knitr | GPL lattice | GPL (>= 2) Rcpp | GPL (>= 2) RcppTOML | GPL (>= 2) digest | GPL (>= 2) mgcv | GPL (>= 2) nlme | GPL (>= 2) lsa | GPL (>= 2) mclust | GPL (>= 2) RcppArmadillo | GPL (>= 2) Matrix | GPL (>= 2) \| file LICENCE RcppEigen | GPL (>= 2) \| file LICENSE png | GPL-2 \| GPL-3 MASS | GPL-2 \| GPL-3 fansi | GPL-2 \| GPL-3 stringr | GPL-2 \| file LICENSE irlba | GPL-3 farver | MIT + file LICENSE lifecycle | MIT + file LICENSE munsell | MIT + file LICENSE R6 | MIT + file LICENSE rlang | MIT + file LICENSE viridisLite | MIT + file LICENSE glue | MIT + file LICENSE openssl | MIT + file LICENSE askpass | MIT + file LICENSE here | MIT + file LICENSE jsonlite | MIT + file LICENSE rappdirs | MIT + file LICENSE withr | MIT + file LICENSE sys | MIT + file LICENSE rprojroot | MIT + file LICENSE gtable | MIT + file LICENSE isoband | MIT + file LICENSE scales | MIT + file LICENSE tibble | MIT + file LICENSE magrittr | MIT + file LICENSE pillar | MIT + file LICENSE pkgconfig | MIT + file LICENSE vctrs | MIT + file LICENSE cli | MIT + file LICENSE evaluate | MIT + file LICENSE xfun | MIT + file LICENSE umap | MIT + file LICENSE ggplot2 | MIT + file LICENSE sparseMatrixStats | MIT + file LICENSE labeling | MIT + file LICENSE \| Unlimited RSpectra | MPL (>= 2) methods | Unknown graphics | Unknown grid | Unknown stats | Unknown utils | Unknown grDevices | Unknown splines | Unknown tools | Unknown R | Unknown stringi | file LICENSE