Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Update dependencies #54

Merged
merged 11 commits into from
Nov 10, 2023
Merged

Update dependencies #54

Show file tree
Hide file tree
Changes from 8 commits
Commits
Show all changes
11 commits
Select commit Hold shift + click to select a range
e2d4dfb
update message
nicolerg Nov 9, 2023
556d3b2
add CODEOWNERS
nicolerg Nov 9, 2023
bf6ef90
change RCy3 version
nicolerg Nov 9, 2023
a11554c
add step to check
nicolerg Nov 9, 2023
ec5236c
use bash
nicolerg Nov 9, 2023
5dec0fc
install BiocManager
nicolerg Nov 9, 2023
773dcbe
download RCy3 from remote
nicolerg Nov 9, 2023
9e4bc3f
download plotrix from GitHub to avoid R-CMD-check warning
nicolerg Nov 9, 2023
d6074b7
bump version and update NEWS
nicolerg Nov 9, 2023
1638ef0
move plotrix from imports to suggests
nicolerg Nov 10, 2023
c59598d
increment data package version
nicolerg Nov 10, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions .Rbuildignore
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,3 +11,4 @@ devnotes.md
^workshops$
^\.github$
^reports$
CODEOWNERS
1 change: 1 addition & 0 deletions CODEOWNERS
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
* @nicolerg
7 changes: 5 additions & 2 deletions DESCRIPTION
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -36,6 +36,7 @@ Imports:
magrittr,
metap,
methods,
plotrix,
purrr,
r2r,
RColorBrewer,
Expand Down Expand Up @@ -66,7 +67,7 @@ Suggests:
MotrpacBicQC (>= 0.6.9),
multcomp,
parallel,
RCy3,
RCy3 (>= 2.23.2),
repfdr,
RMariaDB,
rmarkdown,
Expand All @@ -89,7 +90,9 @@ Remotes:
MoTrPAC/MotrpacRatTraining6moData,
MoTrPAC/MotrpacBicQC,
YuLab-SMU/ggtree,
nicolerg/ssGSEA2
nicolerg/ssGSEA2,
cytoscape/RCy3,
Copy link
Collaborator Author

@nicolerg nicolerg Nov 9, 2023 •
edited
Loading

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Download development version of RCy3 to avoid R-CMD check error:

  * deps::.: Can't install dependency RCy3 (>= 2.22.1)
  * RCy3: Can't install dependency uchardet
  * uchardet: Can't find package called uchardet.

Oddly, RCy3 v2.22.1 has already removed uchardet as a dependency, and I don't get an error installing RCy3 locally, so I'm not sure why this isn't working for the GitHub Actions check. This is a temporary fix that should be reverted once the GitHub Actions check can pass.

plotrix/plotrix
Copy link
Collaborator Author

@nicolerg nicolerg Nov 9, 2023 •
edited
Loading

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Download plotrix from GitHub to avoid R-CMD check warning Requires (indirectly) orphaned package: ‘plotrix’. CRAN has marked plotrix as orphaned.

Copy link
Collaborator Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

plotrix is a dependency for mutoss, which is a dependency for metap

Config/testthat/edition: 3
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
Expand Down
2 changes: 1 addition & 1 deletion vignettes/MotrpacRatTraining6mo.Rmd
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -64,7 +64,7 @@ div.yellow {

<div class = "yellow">

This vignette is under construction. If something is unclear or obviously missing,
If you run into problems,
please submit an issue [here](https://github.com/MoTrPAC/MotrpacRatTraining6mo/issues).

</div>
Expand Down
2 changes: 1 addition & 1 deletion vignettes/key_metabolites.Rmd
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ output:
highlight: tango

vignette: >
%\VignetteIndexEntry{Tutorial for MotrpacRatTraining6mo R package}
%\VignetteIndexEntry{Key metabolites}
%\VignetteEngine{knitr::rmarkdown}
%\VignetteEncoding{UTF-8}
%\usepackage[utf8]{inputenc}
Expand Down
Loading