安装R包-SeuratDisk

探序基因肿瘤研究院

作者下载了一个单细胞数据，是h5ad格式的，想转换成R的Seurat格式。要安装R包SeuratDisk。

install.packages("devtools")

devtools::install_github("mojaveazure/seurat-disk")

于是发现报错：

checking for h5cc... no

checking for h5pcc... no

checking for HDF5 libraries... no

configure: WARNING:

Unable to locate HDF5 compilation helper scripts 'h5cc' or 'h5pcc'.

Please specify --with-hdf5=<LOCATION> as the full path to h5cc or h5pcc.

HDF5 support is being disabled (equivalent to --with-hdf5=no).

configure: error: hdf5 does not seem to be installed on your platform.

  Please install the hdf5 library.

  The required HDF5 library files can be installed as follows:

      - Debian-based (e.g. Debian >= 8.0, Ubuntu >= 15.04): 'sudo apt-get install libhdf5-dev'

        - Old Debian-based (e.g Debian < 8.0, Ubuntu < 15.04): Install from source (see INSTALL)

        - OS X using Homebrew: 'brew install hdf5'

        - RPM-based (e.g Fedora): 'sudo yum install hdf5-devel'

ERROR: configuration failed for package ‘hdf5r’

* removing ‘/home/xxx/R/x86_64-pc-linux-gnu-library/4.3/hdf5r’

下载的程序包在

‘/tmp/Rtmpx5fPWU/downloaded_packages’里

── R CMD build ────────────────────────────────────────────────────────────────────

✔  checking for file ‘/tmp/Rtmpx5fPWU/remotes19221c77e66f35/mojaveazure-seurat-disk-877d4e1/DESCRIPTION’ (580ms)

─  preparing ‘SeuratDisk’:

✔  checking DESCRIPTION meta-information

─  checking for LF line-endings in source and make files and shell scripts

─  checking for empty or unneeded directories

  Omitted ‘LazyData’ from DESCRIPTION

─  building ‘SeuratDisk_0.0.0.9021.tar.gz’

将程序包安装入‘/home/xxx/R/x86_64-pc-linux-gnu-library/4.3’

(因为‘lib’没有被指定)

ERROR: dependency ‘hdf5r’ is not available for package ‘SeuratDisk’

* removing ‘/home/xxx/R/x86_64-pc-linux-gnu-library/4.3/SeuratDisk’

Warning messages:

1: In i.p(...) : 安装程序包‘hdf5r’时退出狀態的值不是0

2: In i.p(...) :

  安装程序包‘/tmp/Rtmpx5fPWU/file19221c3f6d4f37/SeuratDisk_0.0.0.9021.tar.gz’时退出狀態的值不是0

再：yum install hdf5-devel

发现：

错误：

问题: 冲突的请求

  - nothing provides libsz.so.2()(64bit) needed by hdf5-1.10.5-4.el8.x86_64 from epel

(尝试添加 '--skip-broken' 来跳过无法安装的软件包 或 '--nobest' 来不只使用软件包的最佳候选)

或者：

nothing provides libaec-devel(x86-64) needed by hdf5-devel-1.10.5-4.el8.x86_64 from epel