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
