can not install nichenetr #306
Comments
|
Dear user, Bests, |
|
Dear Daniele,
Thanks for your help. I understood the error messages after I asked on Github, but I found that ggplot2 v3.5.0 and above are not very compatible with my Seurat v4.4.0. FeaturePlot and VlnPlot can't generate plots as usual. If I upgrade ggplot2, I need to upgrade to Seurat V5 first, but I don't want to upgrade to Seurat V5 at the moment. So, I’d like to ask if there is a version of nichenetr that is compatible with ggplot 3.4 or Seurat V4.
Bests,
Yajie Rong
3113522904
***@***.***
…------------------ 原始邮件 ------------------
发件人: "saeyslab/nichenetr" ***@***.***>;
发送时间: 2024年10月17日(星期四) 晚上9:27
***@***.***>;
***@***.******@***.***>;
主题: Re: [saeyslab/nichenetr] can not install nichenetr (Issue #306)
Dear user,
I would suggest trying to update ggplot2 to version 3.5.0 or higher in a new session and reiterate nichenet installation again.
Bests,
Daniele
—
Reply to this email directly, view it on GitHub, or unsubscribe.
You are receiving this because you authored the thread.Message ID: ***@***.***>
|
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
devtools::install_github("saeyslab/nichenetr", ref = "v2.0.0")
Downloading GitHub repo saeyslab/[email protected]
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?
1: All
2: CRAN packages only
3: None
4: colorspace (2.1-0 -> 2.1-1 ) [CRAN]
5: rlang (1.1.2 -> 1.1.4 ) [CRAN]
6: munsell (0.5.0 -> 0.5.1 ) [CRAN]
7: glue (1.6.2 -> 1.8.0 ) [CRAN]
8: farver (2.1.1 -> 2.1.2 ) [CRAN]
9: cli (3.6.1 -> 3.6.3 ) [CRAN]
10: fansi (1.0.5 -> 1.0.6 ) [CRAN]
11: withr (2.5.2 -> 3.0.1 ) [CRAN]
12: vctrs (0.6.4 -> 0.6.5 ) [CRAN]
13: gtable (0.3.4 -> 0.3.5 ) [CRAN]
14: Rcpp (1.0.11 -> 1.0.13 ) [CRAN]
15: cpp11 (0.4.6 -> 0.5.0 ) [CRAN]
16: ggplot2 (3.4.1 -> 3.5.1 ) [CRAN]
17: cowplot (1.1.1 -> 1.1.3 ) [CRAN]
18: stringi (1.7.12 -> 1.8.4 ) [CRAN]
19: SparseM (1.81 -> 1.84-2 ) [CRAN]
20: doBy (4.6.22 -> 4.6.24 ) [CRAN]
21: RcppEigen (0.3.3.9.4 -> 0.3.4.0.2) [CRAN]
22: nloptr (2.0.3 -> 2.1.1 ) [CRAN]
23: minqa (1.2.6 -> 1.2.8 ) [CRAN]
24: lme4 (1.1-35.1 -> 1.1-35.5 ) [CRAN]
25: quantreg (5.97 -> 5.98 ) [CRAN]
26: pbkrtest (0.5.2 -> 0.5.3 ) [CRAN]
27: abind (1.4-5 -> 1.4-8 ) [CRAN]
28: stringr (1.5.0 -> 1.5.1 ) [CRAN]
29: backports (1.4.1 -> 1.5.0 ) [CRAN]
30: car (3.1-2 -> 3.1-3 ) [CRAN]
31: tidyselect (1.2.0 -> 1.2.1 ) [CRAN]
32: corrplot (0.92 -> 0.95 ) [CRAN]
33: dplyr (1.1.3 -> 1.1.4 ) [CRAN]
34: broom (1.0.5 -> 1.0.7 ) [CRAN]
35: tidyr (1.3.0 -> 1.3.1 ) [CRAN]
36: BH (1.81.0-1 -> 1.84.0-0 ) [CRAN]
37: dqrng (0.3.1 -> 0.4.1 ) [CRAN]
38: RSpectra (0.16-1 -> 0.16-2 ) [CRAN]
39: RcppAnnoy (0.0.21 -> 0.0.22 ) [CRAN]
40: FNN (1.1.3.2 -> 1.1.4.1 ) [CRAN]
41: polyclip (1.10-6 -> 1.10-7 ) [CRAN]
42: deldir (1.0-9 -> 2.0-4 ) [CRAN]
43: spatstat.... (3.0-4 -> 3.1-0 ) [CRAN]
44: spatstat.... (3.0-0 -> 3.0-1 ) [CRAN]
45: spatstat.... (3.0-3 -> 3.1-2 ) [CRAN]
46: spatstat.... (3.0-3 -> 3.1-0 ) [CRAN]
47: spatstat.... (3.2-1 -> 3.3-2 ) [CRAN]
48: spatstat.... (3.2-7 -> 3.3-3 ) [CRAN]
49: fs (1.6.3 -> 1.6.4 ) [CRAN]
50: digest (0.6.33 -> 0.6.37 ) [CRAN]
51: sass (0.4.7 -> 0.4.9 ) [CRAN]
52: cachem (1.0.8 -> 1.1.0 ) [CRAN]
53: bslib (0.5.1 -> 0.8.0 ) [CRAN]
54: commonmark (1.9.0 -> 1.9.2 ) [CRAN]
55: fastmap (1.1.1 -> 1.2.0 ) [CRAN]
56: crayon (1.5.2 -> 1.5.3 ) [CRAN]
57: promises (1.2.1 -> 1.3.0 ) [CRAN]
58: later (1.3.1 -> 1.3.2 ) [CRAN]
59: htmltools (0.5.7 -> 0.5.8.1 ) [CRAN]
60: jsonlite (1.8.7 -> 1.8.9 ) [CRAN]
61: httpuv (1.6.12 -> 1.6.15 ) [CRAN]
62: parallelly (1.36.0 -> 1.38.0 ) [CRAN]
63: listenv (0.9.0 -> 0.9.1 ) [CRAN]
64: globals (0.16.2 -> 0.16.3 ) [CRAN]
65: RcppArmad... (0.12.6.6.0 -> 14.0.2-1 ) [CRAN]
66: matrixStats (1.1.0 -> 1.4.1 ) [CRAN]
67: future (1.33.0 -> 1.34.0 ) [CRAN]
68: future.apply (1.11.0 -> 1.11.2 ) [CRAN]
69: bitops (1.0-7 -> 1.0-9 ) [CRAN]
70: caTools (1.18.2 -> 1.18.3 ) [CRAN]
71: gtools (3.9.4 -> 3.9.5 ) [CRAN]
72: gplots (3.1.3 -> 3.2.0 ) [CRAN]
73: sys (3.4.2 -> 3.4.3 ) [CRAN]
74: tinytex (0.48 -> 0.53 ) [CRAN]
75: askpass (1.2.0 -> 1.2.1 ) [CRAN]
76: xfun (0.41 -> 0.48 ) [CRAN]
77: highr (0.10 -> 0.11 ) [CRAN]
78: evaluate (0.23 -> 1.0.1 ) [CRAN]
79: openssl (2.1.1 -> 2.2.2 ) [CRAN]
80: curl (5.1.0 -> 5.2.3 ) [CRAN]
81: yaml (2.3.7 -> 2.3.10 ) [CRAN]
82: rmarkdown (2.25 -> 2.28 ) [CRAN]
83: knitr (1.45 -> 1.48 ) [CRAN]
84: data.table (1.14.8 -> 1.16.2 ) [CRAN]
85: crosstalk (1.2.0 -> 1.2.1 ) [CRAN]
86: htmlwidgets (1.6.2 -> 1.6.4 ) [CRAN]
87: shiny (1.7.5.1 -> 1.9.1 ) [CRAN]
88: igraph (1.5.1 -> 2.0.3 ) [CRAN]
89: reticulate (1.34.0 -> 1.39.0 ) [CRAN]
90: dotCall64 (1.1-0 -> 1.2 ) [CRAN]
91: spam (2.10-0 -> 2.11-0 ) [CRAN]
92: sp (2.1-1 -> 2.1-4 ) [CRAN]
93: checkmate (2.3.0 -> 2.3.2 ) [CRAN]
94: XML (3.99-0.15 -> 3.99-0.17) [CRAN]
95: bit (4.0.5 -> 4.5.0 ) [CRAN]
96: progress (1.2.2 -> 1.2.3 ) [CRAN]
97: bit64 (4.0.5 -> 4.5.2 ) [CRAN]
98: vroom (1.6.4 -> 1.6.5 ) [CRAN]
99: shape (1.4.6 -> 1.4.6.1 ) [CRAN]
100: timechange (0.2.0 -> 0.3.0 ) [CRAN]
101: timeDate (4032.109 -> 4041.110 ) [CRAN]
102: rstudioapi (0.15.0 -> 0.16.0 ) [CRAN]
103: systemfonts (1.0.5 -> 1.1.0 ) [CRAN]
104: tweenr (2.0.2 -> 2.0.3 ) [CRAN]
105: ggsci (3.0.0 -> 3.2.0 ) [CRAN]
106: ggrepel (0.9.4 -> 0.9.6 ) [CRAN]
107: uwot (0.1.16 -> 0.2.2 ) [CRAN]
108: spatstat.... (3.2-5 -> 3.3-2 ) [CRAN]
109: Rtsne (0.16 -> 0.17 ) [CRAN]
110: RcppHNSW (0.5.0 -> 0.6.0 ) [CRAN]
111: RANN (2.6.1 -> 2.6.2 ) [CRAN]
112: plotly (4.10.3 -> 4.10.4 ) [CRAN]
113: patchwork (1.1.3 -> 1.3.0 ) [CRAN]
114: leiden (0.4.3 -> 0.4.3.1 ) [CRAN]
115: ggridges (0.5.4 -> 0.5.6 ) [CRAN]
116: fitdistrplus (1.1-11 -> 1.2-1 ) [CRAN]
117: fastDummies (1.7.3 -> 1.7.4 ) [CRAN]
118: SeuratObject (4.1.4 -> 5.0.2 ) [CRAN]
119: readr (2.1.4 -> 2.1.5 ) [CRAN]
120: e1071 (1.7-13 -> 1.7-16 ) [CRAN]
121: viridis (0.6.4 -> 0.6.5 ) [CRAN]
122: circlize (0.4.15 -> 0.4.16 ) [CRAN]
123: Seurat (4.4.0 -> 5.1.0 ) [CRAN]
124: randomForest (4.7-1.1 -> 4.7-1.2 ) [CRAN]
Enter one or more numbers, or an empty line to skip updates: 3
── R CMD build ──────────────────────────────────────────────────────────────────────────────────────
✔ checking for file 'C:\Users\24216\AppData\Local\Temp\Rtmpug1RtH\remotes89d45c2f13bf\saeyslab-nichenetr-8897e1d/DESCRIPTION' ...
─ preparing 'nichenetr': (1.9s)
✔ checking DESCRIPTION meta-information ...
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ building 'nichenetr_2.0.0.tar.gz'
将程序包安装入‘C:/Users/24216/AppData/Local/R/win-library/4.3’
(因为‘lib’没有被指定)
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
namespace 'ggplot2' 3.4.1 is already loaded, but >= 3.5.0 is required
Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace
Execution halted
ERROR: lazy loading failed for package 'nichenetr'
Warning message:
In i.p(...) :
安装程序包‘C:/Users/24216/AppData/Local/Temp/Rtmpug1RtH/file89d434a63e5c/nichenetr_2.0.0.tar.gz’时退出狀態的值不是0
The text was updated successfully, but these errors were encountered: