compilation terminated when R package installation in linux without superuser permission
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4 months ago
whaiyu06 ▴ 70

Hello,

I met a problem when I installed R package "spp" in linux without superuser permission. The error was "bed2vector.cpp:15:10 fatal error: bzliv.h: No such file or directory

#include <bzlib.h>

^~~~~~~~~~~~
compilation terminated.
make : *** [/public/home/yyusy/software/anaconda3/envs/lib/R/etc/Makeconf:176: bed2vector.o] Error 1
ERROR : compilation failed for package 'spp'  "


How can I install the libarary of "libbz2” manually without the permission of sudo ?

r spp bzlib • 542 views
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which command line did you use?

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Since you are already using conda as it seems you can either install the package (spp) itself via conda, or install the dependencies with it, e.g. https://anaconda.org/anaconda/bzip2 and then try to compile the R package again.

The old fashioned way would be to compile bzip2 from source https://www.sourceware.org/bzip2/downloads.html

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Thanks a lot. There was another wrong messeage of a new dependent library when I installed libbz2 and I installed the new library file according to the err hint but another new issue occured. There are so many interdependent header files , it seems too verbose to settle these errors.