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Update dependencies #54

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merged 11 commits into from
Nov 10, 2023
Merged

Update dependencies #54

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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
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1 change: 1 addition & 0 deletions .Rbuildignore
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Expand Up @@ -11,3 +11,4 @@ devnotes.md
^workshops$
^\.github$
^reports$
CODEOWNERS
1 change: 1 addition & 0 deletions CODEOWNERS
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Validating CODEOWNERS rules …
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@@ -0,0 +1 @@
* @nicolerg
11 changes: 7 additions & 4 deletions DESCRIPTION
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Expand Up @@ -2,7 +2,7 @@ Type: Package
Package: MotrpacRatTraining6mo
Title: Analysis of the MoTrPAC endurance exercise training data in
6-month-old rats
Version: 1.6.4
Version: 1.6.5
Authors@R: c(
person("Nicole", "Gay", , "nicole.r.gay@gmail.com", role = c("cre", "aut")),
person("David", "Amar", , "ddam.am@gmail.com", role = "aut"),
Expand Down Expand Up @@ -66,7 +66,8 @@ Suggests:
MotrpacBicQC (>= 0.6.9),
multcomp,
parallel,
RCy3,
plotrix,
RCy3 (>= 2.23.2),
repfdr,
RMariaDB,
rmarkdown,
Expand All @@ -89,12 +90,14 @@ Remotes:
MoTrPAC/MotrpacRatTraining6moData,
MoTrPAC/MotrpacBicQC,
YuLab-SMU/ggtree,
nicolerg/ssGSEA2
nicolerg/ssGSEA2,
cytoscape/RCy3,
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@nicolerg nicolerg Nov 9, 2023 •
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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
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@nicolerg nicolerg Nov 9, 2023 •
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Download plotrix from GitHub to avoid R-CMD check warning Requires (indirectly) orphaned package: ‘plotrix’. CRAN has marked plotrix as orphaned.

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

Config/testthat/edition: 3
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
Depends:
MotrpacRatTraining6moData (>= 1.8.0),
MotrpacRatTraining6moData (>= 2.0.0),
R (>= 2.10)
LazyData: true
7 changes: 7 additions & 0 deletions NEWS.md
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@@ -1,3 +1,10 @@
# MotrpacRatTraining6mo 1.6.5 (2023-11-08)

* Point to development version of `RCy3` from GitHub to avoid `R-CMD check` error `RCy3: Can't install dependency uchardet`.
* Install `plotrix` from GitHub instead of CRAN to avoid `R-CMD check` warning `Requires (indirectly) orphaned package: ‘plotrix’`.
CRAN has marked `plotrix` as orphaned. `plotrix` is a dependency for `mutoss`, which is a dependency for `metap`.
* Increment required `MotrpacRatTraining6moData` version.

# MotrpacRatTraining6mo 1.6.4 (2023-06-02)

* Bug fix in `transcript_timewise_da()` to run with limited contrasts when `tissue="VENACV"`.
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2 changes: 1 addition & 1 deletion vignettes/MotrpacRatTraining6mo.Rmd
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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>
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2 changes: 1 addition & 1 deletion vignettes/key_metabolites.Rmd
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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}
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