Dee-chen
commented
1 year ago This problem is relatively easy to locate. This is because you cannot install ggtree correctly in R language. Possible causes include network connection problems, write permissions, package conflicts, etc. You can manually install dependency packages (such as BiocManager:: install ("ggtree")) in the R environment of the server according to Tree2GD_draw.r after confirming that the network connection is normal. In this way, you can receive the returned debugging information. Look at your current errors. They may be caused by 'ggfun' or 'vctrs'. Your packages are too old. It will prompt you whether to update them. For details, please refer to the instructions of the BiocManager installation package.
Rscript /public/home/zhangyingchun/anaconda3/envs/Tree2gd/lib/python3.8/site-packages/tree2gd/software/Tree2GD_draw.R 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details
replacement repositories: CRAN: http://cran.us.r-project.org
Bioconductor version 3.12 (BiocManager 1.30.19), R 4.0.5 (2021-03-31) Installing package(s) 'ggtree' trying URL 'https://bioconductor.org/packages/3.12/bioc/src/contrib/ggtree_2.4.2.tar.gz' Content type 'application/octet-stream' length 338402 bytes (330 KB)
downloaded 330 KB
The downloaded source packages are in ‘/tmp/Rtmp10kakF/downloaded_packages’ Updating HTML index of packages in '.Library' Making 'packages.html' ... done Old packages: 'ggfun', 'vctrs' Warning message: In install.packages(...) : installation of package ‘ggtree’ had non-zero exit status Error in library("ggtree") : there is no package called ‘ggtree’ Execution halted
I also encountered testing problems. I also ran this according to your method. But I don't know how to deal with it later. Could you please tell me how to deal with it here. A novice student