cran-comments.md

In niaid/HDStIM: High Dimensional Stimulation Immune Mapping ('HDStIM')

Resubmission on

Response to the email from Gregor Seyer

Gregor Seyer [e-mail] 21 June 2022 at 04:38 To: Rohit Farmer [e-mail], CRAN [e-mail]

Dear Gregor,

Thank you for your suggestions. I am resubmitting the package with the corrections.

If there are references describing the methods in your package, please add these in the description field of your DESCRIPTION file in the form authors (year) authors (year) authors (year, ISBN:...) or if those are not available: with no space after 'doi:', 'arXiv:', 'https:' and angle brackets for auto-linking. (If you want to add a title as well please put it in quotes: "Title")

We are still working on the manuscript. I will update the description as soon as I have the relevant information.

Please always write package names, software names and API (application programming interface) names in single quotes in title and description. e.g: --> 'HDStIM'

Done.

\dontrun{} should only be used if the example really cannot be executed (e.g. because of missing additional software, missing API keys, ...) by the user. That's why wrapping examples in \dontrun{} adds the comment ("# Not run:") as a warning for the user. Does not seem necessary. Please unwrap the examples if they are executable in < 5 sec, or replace \dontrun{} with \donttest{}.

I unwraped the examples from most of the functions except marker_ranking_boruta() and plot_umap() where I replaced \dontrun{} with \donttest{}.

Please ensure that you do not use more than 2 cores in your examples, vignettes, etc.

There is only one function, "marker_ranking_boruta()" that calls the Boruta (https://cran.r-project.org/package=Boruta) package, which might be using multiple cores. However, Boruta doesn't provide a way to control the number of cores used. Please let me know if I have misunderstood this comment.

Regards, Rohit

Checks

devtools::check(args = c('--as-cran'))

── R CMD check results ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── HDStIM 0.1.0 ──── Duration: 3m 49.7s

0 errors ✔ | 0 warnings ✔ | 0 notes ✔

Win builder log

• using log directory 'd:/RCompile/CRANguest/R-release/HDStIM.Rcheck'
• using R version 4.2.0 (2022-04-22 ucrt)
• using platform: x86_64-w64-mingw32 (64-bit)
• using session charset: UTF-8
• checking for file 'HDStIM/DESCRIPTION' ... OK
• checking extension type ... Package
• this is package 'HDStIM' version '0.1.0'
• package encoding: UTF-8
• checking CRAN incoming feasibility ... NOTE Maintainer: 'Rohit Farmer [e-mail]'

New submission

Possibly misspelled words in DESCRIPTION: cytometry (21:93, 21:292) intracellular (21:322, 21:608) unstimulated (21:477) vitro (21:246) checking package namespace information ... OK checking package dependencies ... OK checking if this is a source package ... OK checking if there is a namespace ... OK checking for hidden files and directories ... OK checking for portable file names ... OK checking whether package 'HDStIM' can be installed ... OK checking installed package size ... OK checking package directory ... OK checking for future file timestamps ... OK checking 'build' directory ... 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 checking R files for non-ASCII characters ... OK checking R files for syntax errors ... OK checking whether the package can be loaded ... OK checking whether the package can be loaded with stated dependencies ... OK checking whether the package can be unloaded cleanly ... OK checking whether the namespace can be loaded with stated dependencies ... OK checking whether the namespace can be unloaded cleanly ... OK checking loading without being on the library search path ... OK checking use of S3 registration ... OK checking dependencies in R code ... OK checking S3 generic/method consistency ... OK checking replacement functions ... OK checking foreign function calls ... OK checking R code for possible problems ... [18s] OK checking Rd files ... [1s] OK checking Rd metadata ... OK checking Rd line widths ... OK checking Rd cross-references ... OK checking for missing documentation entries ... OK checking for code/documentation mismatches ... OK checking Rd \usage sections ... OK checking Rd contents ... OK checking for unstated dependencies in examples ... OK checking contents of 'data' directory ... OK checking data for non-ASCII characters ... OK checking LazyData ... OK checking data for ASCII and uncompressed saves ... OK checking installed files from 'inst/doc' ... OK checking files in 'vignettes' ... OK checking examples ... [10s] OK checking for unstated dependencies in 'tests' ... OK checking tests ... [44s] OK Running 'testthat.R' [44s] checking for unstated dependencies in vignettes ... OK checking package vignettes in 'inst/doc' ... OK checking re-building of vignette outputs ... [72s] OK checking PDF version of manual ... OK checking for detritus in the temp directory ... OK DONE Status: 1 NOTE

niaid/HDStIM documentation built on Oct. 15, 2023, 4:43 p.m.