not able to install on hpc cluster

[wbf520qcp]

I have a file with >50,000 cells, running SCENIC on my laptop seems taking forever. I tried to move to HPC but cannot install packages with the error as follows:

config.status: creating src/Makevars * libs cp 1_10_3/.c 1_10_3/*.h . gcc -I"/risapps/rhel7/R/4.1.0/lib64/R/include" -DNDEBUG -I/risapps/rhel7/hdf5/1.10.5/include -I/usr/local/include -D__USE_MINGW_ANSI_STDIO -fpic -g -O2 -c const_export.c -o const_export.o In file included from const_export.h:22:0, from const_export.c:23: global.h:24:10: fatal error: hdf5_hl.h: No such file or directory

include

      ^~~~~~~~~~~

compilation terminated. make: *** [const_export.o] Error 1 ERROR: compilation failed for package ‘hdf5r’

• removing ‘/rsrch4/home/genomic_med/bwang8/R/x86_64-pc-linux-gnu-library/4.1/hdf5r’

and gmake: * [all] Error 2 ** Error building Arrow C++.
------------------------- NOTE --------------------------- There was an issue preparing the Arrow C++ libraries. See https://arrow.apache.org/docs/r/articles/install.html

ERROR: configuration failed for package ‘arrow’

Any suggestions would be appreciated, Thanks, Bofei

[ryao-mdanderson]

@wbf520qcp I happen to see your post, does 'module load scenic-arrow/1.1' help?

[wbf520qcp]

Thanks for comments. Yes, realized it had been installed on cluster

[wbf520qcp]

@ryao-mdanderson Hi, I wonder if you have run scenic successfully run it on cluster. I got into problem at AUC step as below. Any thoughts on this? Thanks much! y