jinworks / CellChat

R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics
GNU General Public License v3.0
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Suggests to update the installation command #143

Open ShixiangWang opened 1 month ago

ShixiangWang commented 1 month ago

It's recommended to update the devtools::install_github("jinworks/CellChat") to the following:

# install.packages("BiocManager")
BiocManager::install("jinworks/CellChat")

It's more easy to handle the Bioc depends.

> devtools::install_github("jinworks/CellChat")
Downloading GitHub repo jinworks/CellChat@HEAD
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: fs         (1.6.3    -> 1.6.4   ) [CRAN]
 5: openssl    (2.1.1    -> 2.1.2   ) [CRAN]
 6: gtable     (0.3.4    -> 0.3.5   ) [CRAN]
 7: ggplot2    (3.5.0    -> 3.5.1   ) [CRAN]
 8: brio       (1.1.4    -> 1.1.5   ) [CRAN]
 9: testthat   (3.2.1    -> 3.2.1.1 ) [CRAN]
10: lme4       (1.1-35.2 -> 1.1-35.3) [CRAN]
11: reticulate (1.35.0   -> 1.36.1  ) [CRAN]

Enter one or more numbers, or an empty line to skip updates: 3
Installing 4 packages: network, statnet.common, sna, ggnetwork
Installing packages into ‘/Volumes/EPan/Rlib’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/bin/macosx/big-sur-arm64/contrib/4.3/network_1.18.2.tgz'
Content type 'application/x-gzip' length 853527 bytes (833 KB)
==================================================
downloaded 833 KB

trying URL 'https://cloud.r-project.org/bin/macosx/big-sur-arm64/contrib/4.3/statnet.common_4.9.0.tgz'
Content type 'application/x-gzip' length 276247 bytes (269 KB)
==================================================
downloaded 269 KB

trying URL 'https://cloud.r-project.org/bin/macosx/big-sur-arm64/contrib/4.3/sna_2.7-2.tgz'
Content type 'application/x-gzip' length 1332181 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

trying URL 'https://cloud.r-project.org/bin/macosx/big-sur-arm64/contrib/4.3/ggnetwork_0.5.13.tgz'
Content type 'application/x-gzip' length 2343859 bytes (2.2 MB)
==================================================
downloaded 2.2 MB

The downloaded binary packages are in
    /var/folders/gm/lw6z28md2594gcnws_38_9f40000gn/T//Rtmpf4UI1Y/downloaded_packages
── R CMD build ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
✔  checking for file ‘/private/var/folders/gm/lw6z28md2594gcnws_38_9f40000gn/T/Rtmpf4UI1Y/remotes10026eb748b9/jinworks-CellChat-862ab34/DESCRIPTION’ ...
─  preparing ‘CellChat’:
✔  checking DESCRIPTION meta-information ...
─  cleaning src
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘CellChat_2.1.2.tar.gz’

Installing package into ‘/Volumes/EPan/Rlib’
(as ‘lib’ is unspecified)
ERROR: dependencies ‘ComplexHeatmap’, ‘BiocNeighbors’ are not available for package ‘CellChat’
* removing ‘/Volumes/EPan/Rlib/CellChat’
Warning message:
In i.p(...) :
  installation of package ‘/var/folders/gm/lw6z28md2594gcnws_38_9f40000gn/T//Rtmpf4UI1Y/file100263e8bc8ba/CellChat_2.1.2.tar.gz’ had non-zero exit status