Snakemake在rule环境下安装R包报错cannot move 00LOCK permission denied

Question

我正在编写一个带有规则的 Snakemake 管道，该规则将运行一个 R 脚本。此规则有自己的环境，如下所示：

channels:
 - conda-forge
 - r
 - bioconda
dependencies:
 - r-base = 4.1.1
 - r-ggplot2 = 3.3.5
 - r-biocmanager = 1.30.16

除了上面的包，我还需要ggbio，可以用biocmanager安装：

if(!require(ggbio, quietly=TRUE)){  # if the package is not there, install it
  BiocManager::install("ggbio")
}

当通过 Snakemake 执行此规则时，最初一切正常，并且安装了 ggbio 包的大多数依赖项。但是，一段时间后，我收到以下错误：

...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
mv: cannot move '/mnt/c/Users/nicks/Documents/variantcallingpipeline/.snakemake/conda/b98e3353bb11024e3652b19a833d9dc8/lib/R/library/00LOCK-xml2/00new/xml2' to '/mnt/c/Users/nicks/Documents/variantcallingpipeline/.snakemake/conda/b98e3353bb11024e3652b19a833d9dc8/lib/R/library/xml2': Permission denied
ERROR:   moving to final location failed
ERROR: dependency ‘xml2’ is not available for package ‘biomaRt’
* removing ‘/mnt/c/Users/nicks/Documents/variantcallingpipeline/.snakemake/conda/b98e3353bb11024e3652b19a833d9dc8/lib/R/library/biomaRt’
ERROR: dependency ‘biomaRt’ is not available for package ‘GenomicFeatures’
* removing ‘/mnt/c/Users/nicks/Documents/variantcallingpipeline/.snakemake/conda/b98e3353bb11024e3652b19a833d9dc8/lib/R/library/GenomicFeatures’
ERROR: dependency ‘GenomicFeatures’ is not available for package ‘VariantAnnotation’
* removing ‘/mnt/c/Users/nicks/Documents/variantcallingpipeline/.snakemake/conda/b98e3353bb11024e3652b19a833d9dc8/lib/R/library/VariantAnnotation’
ERROR: dependency ‘GenomicFeatures’ is not available for package ‘OrganismDbi’
* removing ‘/mnt/c/Users/nicks/Documents/variantcallingpipeline/.snakemake/conda/b98e3353bb11024e3652b19a833d9dc8/lib/R/library/OrganismDbi’
ERROR: dependency ‘GenomicFeatures’ is not available for package ‘ensembldb’
* removing ‘/mnt/c/Users/nicks/Documents/variantcallingpipeline/.snakemake/conda/b98e3353bb11024e3652b19a833d9dc8/lib/R/library/ensembldb’
ERROR: dependencies ‘GenomicFeatures’, ‘VariantAnnotation’, ‘ensembldb’ are not available for package ‘biovizBase’
* removing ‘/mnt/c/Users/nicks/Documents/variantcallingpipeline/.snakemake/conda/b98e3353bb11024e3652b19a833d9dc8/lib/R/library/biovizBase’
ERROR: dependencies ‘biovizBase’, ‘VariantAnnotation’, ‘GenomicFeatures’, ‘OrganismDbi’, ‘ensembldb’ are not available for package ‘ggbio’
* removing ‘/mnt/c/Users/nicks/Documents/variantcallingpipeline/.snakemake/conda/b98e3353bb11024e3652b19a833d9dc8/lib/R/library/ggbio’

The downloaded source packages are in
        ‘/tmp/RtmpiQdboR/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Old packages: 'fansi'
Warning messages:
1: In .inet_warning(msg) :
  installation of package ‘xml2’ had non-zero exit status
2: In .inet_warning(msg) :
  installation of package ‘biomaRt’ had non-zero exit status
3: In .inet_warning(msg) :
  installation of package ‘GenomicFeatures’ had non-zero exit status
4: In .inet_warning(msg) :
  installation of package ‘VariantAnnotation’ had non-zero exit status
5: In .inet_warning(msg) :
  installation of package ‘OrganismDbi’ had non-zero exit status
6: In .inet_warning(msg) :
  installation of package ‘ensembldb’ had non-zero exit status
7: In .inet_warning(msg) :
  installation of package ‘biovizBase’ had non-zero exit status
8: In .inet_warning(msg) :
  installation of package ‘ggbio’ had non-zero exit status
Error in library(ggbio) : there is no package called ‘ggbio’
Execution halted

错误似乎源自这部分：

mv: cannot move '/mnt/c/Users/nicks/Documents/variantcallingpipeline/.snakemake/conda/b98e3353bb11024e3652b19a833d9dc8/lib/R/library/00LOCK-xml2/00new/xml2' to '/mnt/c/Users/nicks/Documents/variantcallingpipeline/.snakemake/conda/b98e3353bb11024e3652b19a833d9dc8/lib/R/library/xml2': Permission denied

仅当我从 Windows 上的 Ubuntu 应用程序运行 Snakemake 时才收到此错误。如果我运行它在服务器上，它工作：

** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (xml2)
... (and then it continues to the other packages)

服务器端和本地版本相同，xml2为1.3.3。我已经看到与此锁定问题相关的其他问题 (here and here)，其中大多数建议这样做：

install.packages("Rcpp", dependencies = TRUE, INSTALL_opts = '--no-lock')

但这对我不起作用，因为 install.packages() 没有安装软件包。在安装前添加 options("install.lock"=FALSE) 也不起作用。另外，当我检查环境位置中的 R library 文件夹时，我没有看到 00LOCK 目录。

有什么建议吗？或者这只是一个不容易修复的 Windows 问题？运行 Rstudio 中的安装代码确实有效，但我需要在 conda 环境中安装包，而不是我的标准 Rstudio 库。

Answer 1

显示的 YAML 不合标准 (incorrect channel order)。但更重要的是，在 Conda 管理的 R 环境中安装除 Conda 包以外的任何东西通常效果不佳。幸运的是，所有 Bioconductor 包都在 bioconda 频道（通常带有 bioconductor- 前缀且全部小写），因此，一切都应该可以完美地工作：

channels:
 - conda-forge
 - bioconda
 - defaults
dependencies:
 - r-base=4.1.1
 - r-ggplot2=3.3.5
 - bioconductor-ggbio

Snakemake在rule环境下安装R包报错cannot move 00LOCK permission denied

Snakemake installing R package in rule environment: error cannot move 00LOCK permission denied

locking

r

conda

snakemake