installation error #146
Description
When I try to install this package like this, an error occures:
BiocManager::install("rhdf5")
g++ -std=gnu++11 -shared -L/opt/R/4.3.2/lib64/R/lib -L/usr/local/lib64 -o rhdf5.so H5.o H5A.o H5D.o H5E.o H5F.o H5G.o H5I.o H5L.o H5O.o H5P.o H5R.o H5S.o H5S_extras.o H5T.o H5T_extras.o H5Z.o H5constants.o HandleList.o HandleListWrap.o bit64conversion.o external_filters.o h5dump.o h5ls.o h5testLock.o h5writeDataFrame.o printdatatype.o utils.o wrap.o WARNING: ignoring environment value of R_HOME /picb/jinlab/wangjl/R/x86_64-pc-linux-gnu-library/4.3/Rhdf5lib/lib/libhdf5.a -L/picb/jinlab/wangjl/R/x86_64-pc-linux-gnu-library/4.3/Rhdf5lib/lib -lcrypto -lcurl -lsz -laec -lz -ldl -lm -L/opt/R/4.3.2/lib64/R/lib -lR
/bin/ld: cannot find WARNING:: No such file or directory
/bin/ld: cannot find ignoring: No such file or directory
/bin/ld: cannot find environment: No such file or directory
/bin/ld: cannot find value: No such file or directory
/bin/ld: cannot find of: No such file or directory
/bin/ld: cannot find R_HOME: No such file or directory
collect2: error: ld returned 1 exit status
make: *** [rhdf5.so] Error 1
ERROR: compilation failed for package ‘rhdf5’
* removing ‘/picb/jinlab/wangjl/R/x86_64-pc-linux-gnu-library/4.3/rhdf5’
My environment is CentOS7.9, R 4.3.2, Rsudio.
> packageVersion("Seurat")
[1] ‘4.4.0’
> packageVersion("Rhdf5lib")
[1] ‘1.24.1’
> system("which h5cc")
/home/wangjl/.local/bin/h5cc
> system("gcc --version")
gcc (GCC) 12.3.0
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