vertesy / codeandroll2 Goto Github PK

it should handle tibble or raise an error

any.duplicated() is not found, even if part of the package.
Found in NAMESPACE, and in man. Mistery.

Based on
R you sure you’re using this package?

we recommend:
NCmisc (version 1.1.6) list.functions.in.file: Show all functions used in an R script file, by package

Buggy Behavior

• If you do not subset to unique, it does not find the difference

> symdiff(unique(obj.CHOOSE.full$celltype_ctrl_transfer_coarse), unique(obj.CHOOSE.full$celltype_ctrl_transfer))
$`Only in unique(obj.CHOOSE.full$celltype_ctrl_transfer_coarse)`
character(0)

$`Only in unique(obj.CHOOSE.full$celltype_ctrl_transfer)`
[1] "OPC"

> f$symdiff
[1] "CodeAndRoll2"
> symdiff(obj.CHOOSE.full$celltype_ctrl_transfer_coarse, obj.CHOOSE.full$celltype_ctrl_transfer)
$`Only in obj.CHOOSE.full$celltype_ctrl_transfer_coarse`
character(0)

$`Only in obj.CHOOSE.full$celltype_ctrl_transfer`
character(0)

In

> obj.CHOOSE.full
An object of class Seurat 
38411 features across 49754 samples within 6 assays 
Active assay: RNA (33850 features, 2000 variable features)
 3 layers present: counts, data, scale.data
 5 other assays present: integrated, guide_assignments, guide_assignments_ctrl, modules_pos, modules_neg
 12 dimensional reductions calculated: pca, umap, harmony2, humap2, css2, cssumap2, harmony, humap, css, cssumap, seurat, sumap

hi Vertesy,

The CodeAndRoll2 PKG
sounds great.
But following your instructions exactly,
it does not install ,
( "had non-zero exit status" ).

My PC:

• UBUNTU LINUX 20.04
• Rstudio v 2023.06.0 Build 421
• R 4.3.1

Can you please help?...
Looking forward to using your PKG!.
( install output below my SIG ).

SFd99
San Francisco
============

devtools::install_github(repo = "vertesy/CodeAndRoll2")
Downloading GitHub repo vertesy/CodeAndRoll2@HEAD
Skipping 1 packages not available: Stringendo
── R CMD build ───────────────────────────────────────────
✔ checking for file ‘/tmp/RtmpOtWwOo/remotes30ef43b8d794/vertesy-CodeAndRoll2-9635b15/DESCRIPTION’ ...
─ preparing ‘CodeAndRoll2’:
✔ checking DESCRIPTION meta-information ...
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ building ‘CodeAndRoll2_2.4.6.tar.gz’

Installing package into ‘/home/ray/R/x86_64-pc-linux-gnu-library/4.3’
(as ‘lib’ is unspecified)
ERROR: dependency ‘Stringendo’ is not available for package ‘CodeAndRoll2’

• removing ‘/home/ray/R/x86_64-pc-linux-gnu-library/4.3/CodeAndRoll2’
  Warning message:
  In i.p(...) :
  installation of package ‘/tmp/RtmpOtWwOo/file30ef47d098a/CodeAndRoll2_2.4.6.tar.gz’ had non-zero exit status

• https://r-pkgs.org/whole-game.html
• https://www.rstudio.com/resources/videos/you-can-make-a-package-in-20-minutes/
• https://support.rstudio.com/hc/en-us/articles/200486488-Developing-Packages-with-RStudio

I tried installing CodeAndRoll2 with

require("devtools")
devtools::install_github(repo = "vertesy/CodeAndRoll2")

but got the following error:
Error: Failed to install 'unknown package' from GitHub:
HTTP error 404.
No commit found for the ref master

Did you spell the repo owner (vertesy) and repo name (CodeAndRoll2) correctly?

• If spelling is correct, check that you have the required permissions to access the repo.

This only worked once I installed it from the main branch and not the master. Might be useful in the future for others:
devtools::install_github(repo = "vertesy/CodeAndRoll2", ref = 'main')

As of 2021 it is a major task to format this library into a proper package

Core functionality

• Data object operations

Move to StringsAndPaths

• StringsAndPath operations
• helpers for Markdownreports and ggExpress

Move to FileWriter or IO

• Input Output
• write.simple functions

Move to Rocinante

• Anything not core and StringsAndPaths
• No

To Do

• My package dependency should be a tree, not a network. → See draw.io.
• Packages should import specific fun, not depend (=and load) an entire package
  • Define what load-dependencies are essential for each package
  • Then rest of fun's get ::.
• Add ::-s
• Check dependencies in each package
  • Get a package that fixes dependencies.
  • Maria tools::package_dependencies.

Description
as.named.vector() on a DF column gives back a vector much longer than the original dimensions

Expected Behavior

• complain if not uni dimensional?

Buggy Behavior

> l(as.named.vector(obj@meta.data[ , assignments]))
[1] 35860
> dim((obj@meta.data[ , assignments]))
[1] 7172    5

Fun

 as.named.vector <- function (df_col, WhichDimNames = 1) 
{
    namez = dimnames(df_col)[[WhichDimNames]]
    if (is.list(df_col) & !is.data.frame(df_col)) {
        namez = names(df_col)
    }
    vecc = as.vector(unlist(df_col))
    names(vecc) = namez
    return(vecc)
}
<bytecode: 0x7fd41b108ba8>
<environment: namespace:CodeAndRoll2>