[英]How to fix 'gcc: error: “/usr/lib64/R/library/Rhdf5lib/lib/libhdf5.a”: No such file or directory' in R
I am trying to install minfi in R:我正在尝试在 R 中安装 minfi:
BiocManager::install("minfi")
but the installation stops during the compiling of HDF5Array with the following errors:但是在编译 HDF5Array 期间安装停止,并出现以下错误:
gcc: error: "/usr/lib64/R/library/Rhdf5lib/lib/libhdf5.a": No such file or
directory
gcc: error: "/usr/lib64/R/library/Rhdf5lib/lib/libsz.a": No such file or
directory
make: *** [HDF5Array.so] Error 1
ERROR: compilation failed for package ‘HDF5Array’
I've already installed rhdf5
and Rhdf5lib
package plus the files R "can't see" actually exist in the exact directory (/usr/lib64/R/library/Rhdf5lib/lib/) where it supposedly "searches" for them.我已经安装了rhdf5
和Rhdf5lib
package 以及文件 R “看不到”实际上存在于它应该“搜索”的确切目录中(/usr/lib64/R/library/Rhdf5lib/lib/)
ls /usr/lib64/R/library/Rhdf5lib/lib/
libhdf5.a libhdf5_cpp.a libsz.a
My R version is 3.6.0, my GCC version is 4.8.5 20150623 (Red Hat 4.8.5-39) and my CentOS distribution is 7.6.1810我的ZE1E1D3D40573127EE9EE0480CAF1283D6Z版本是3.6.0,我的Z32D8B233E3C58A262A0B75872297D8D8D55Z版本是4.8.5 20150623(RED HAT 4.8.5-5-39)
I would appreciate any suggestions.我将不胜感激任何建议。
Thank you.谢谢你。
I met the same problem.我遇到了同样的问题。 http://bioconductor.org/checkResults/release/bioc-LATEST/HDF5Array/ mentions that "HDF5Array(1.12.2)" failed to be installed. http://bioconductor.org/checkResults/release/bioc-LATEST/HDF5Array/提到“HDF5Array(1.12.2)”安装失败。 So wait for improvements.所以等待改进。
There is a way: installing an older version of "HDF5Array".有一种方法:安装旧版本的“HDF5Array”。
url<-"https://bioconductor.org/packages/3.8/bioc/src/contrib/HDF5Array_1.10.1.tar.gz"
install.packages(url,repos=NULL,type="source")
BiocManager::install("minfi")
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