从 Saezlab 安装 LIANA R 软件包时遇到问题

Question

我正在努力安装藤本植物。我最初按照 saezlab GitHub 上的安装说明进行操作，但收到此错误：

 remotes::install_github('saezlab/liana')
Error: Failed to install 'unknown package' from GitHub:
  Line starting 'Config/testthat/edit ...' is malformed!

然而，这似乎更有希望：

git clone https://github.com/saezlab/liana.git

我下载了它，但在尝试使用 install.packages(".", repos = NULL, type = "source") 从 liana 目录内部安装它时，我收到了此错误：

removing '/gpfs3/well/ludwig/users/ikb229/R/4.1/skylake/liana'
Warning message:
In install.packages(".", repos = NULL, type = "source") :
installation of package '.' had non-zero exit status"

于是我成功安装了basilisk.utils，basilisk。和 OmnipathR：

> find.package("OmnipathR")
[1] "/gpfs3/well/ludwig/users/ikb229/R/4.2/skylake/OmnipathR"
> find.package("basilisk")
[1] "/gpfs3/apps/eb/2020b/skylake/software/R-bundle-Bioconductor/3.15-foss-2022a-R-4.2.1/basilisk"
> find.package("basilisk.utils")
[1] "/gpfs3/apps/eb/2020b/skylake/software/R-bundle-Bioconductor/3.15-foss-2022a-R-4.2.1/basilisk.utils"

然而，当我再次尝试安装 liana 时，我收到了以下消息：

> install.packages(".", repos = NULL, type = "source")
Installing package into '/gpfs3/well/ludwig/users/ikb229/R/4.2/skylake'
(as 'lib' is unspecified)
* installing *source* package 'liana' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error: object 'homologene_download' is not exported by 'namespace:OmnipathR'
Execution halted
ERROR: lazy loading failed for package 'liana'
* removing '/gpfs3/well/ludwig/users/ikb229/R/4.2/skylake/liana'
Warning message:
In install.packages(".", repos = NULL, type = "source") :
  installation of package '.' had non-zero exit status

所以在 R 中我尝试过：

> library(OmnipathR)
?homologene_download
No documentation for 'homologene_download' in specified packages and libraries:
you could try '??homologene_download'
> ??homologene_download
No vignettes or demos or help files found with alias or concept or
title matching 'homologene_download' using regular expression matching.

这些是我在 HPC 集群上使用的模块：

[ikb229@rescomp1 liana]$ module load R/4.2.1-foss-2022a 
[ikb229@rescomp1 liana]$ module load R-bundle-Bioconductor/3.15-foss-2022a-R-4.2.1

会议信息：

> sessionInfo()
R version 4.2.1 (2022-06-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /gpfs3/apps/eb/2020b/skylake/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib64/libflexiblas.so.3.2

locale:
[1] C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] compiler_4.2.1 tools_4.2.1    curl_4.3.2     remotes_2.4.2

有人知道我该如何解决这个问题吗？

Answer 1

请参阅 github.com/saezlab/liana/issues/144 了解解决方案。