我正在编写一个Snakemake管道，其中包含一个将运行R脚本的规则。这个规则有自己的环境，看起来是这样的：
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，它可以安装biocmanager:
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。然而，过了一段时间，我得到了以下错误：
...
** 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
错误似乎源于以下部分：
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
只有当我在Windows上从Ubuntu应用程序运行Snakemake时，我才会出现这个错误。如果我在服务器上运行它，它就会工作：
** 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)
服务器和本地的版本相同，即xml2的版本为1.3.3。我看到了与这个锁问题有关的其他问题(这里和这里(，其中大多数都建议这样做：
install.packages("Rcpp", dependencies = TRUE, INSTALL_opts = '--no-lock')
但这对我来说不起作用，因为该软件包没有安装install.packages()。在安装之前添加options("install.lock"=FALSE)也不起作用。此外，当我检查环境位置中的Rlibrary文件夹时，我看不到00LOCK目录。
有什么建议吗？还是这只是一个不容易修复的Windows问题？在Rstudio中运行分期付款代码确实有效，但我需要将包安装在conda环境中，而不是我的标准Rstudios库中。
显示的YAML不合格(通道顺序不正确(。但更重要的是，在Conda管理的R环境中安装Conda软件包以外的任何软件包通常都无法正常工作。幸运的是，所有Bioconductor包都在biocda通道上(通常带有bioconductor-前缀，全部小写(，因此，只要使用，一切都会很好
channels:
- conda-forge
- bioconda
- defaults
dependencies:
- r-base=4.1.1
- r-ggplot2=3.3.5
- bioconductor-ggbio