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commented
3 years ago Hi @nayaracleite ,
Sorry for the delay. Were you able to solve this? Rhtslilb requires liblzma so make sure you have this library on your system. See SystemRequirements in the DESCRIPTION file of the package for all the requirements. You can also see the requirements on the package landing page here:
https://bioconductor.org/packages/Rhtslib
Thanks
I am trying to install package 'Rhtslib' in R 3.6.3 using R studio, I am getting the following error:
/tmp/RtmpMZkpPD/R.INSTALL2d98e6b76b32a/Rhtslib/src/htslib-1.7' Makefile.Rhtslib:128: warning: overriding recipe for target.c.o' /n/helmod/apps/centos7/Core/R_core/3.6.3-fasrc01/lib64/R/etc/Makeconf:168: warning: ignoring old recipe for target `.c.o' gcc -I/n/helmod/apps/centos7/Core/curl/7.45.0-fasrc01/include -I/n/helmod/apps/centos7/Core/bzip2/1.0.6-fasrc01/include -I/n/helmod/apps/centos7/Core/pcre/8.37-fasrc02/include -I/n/helmod/apps/centos7/Core/readline/6.3-fasrc02/include -L/n/helmod/apps/centos7/Core/bzip2/1.0.6-fasrc01/lib -L/n/helmod/apps/centos7/Core/pcre/8.37-fasrc02/lib -L/n/helmod/apps/centos7/Core/curl/7.45.0-fasrc01/lib -L/n/helmod/apps/centos7/Core/readline/6.3-fasrc02/lib64 -std=gnu99 -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o kfunc.o kfunc.c gcc -I/n/helmod/apps/centos7/Core/curl/7.45.0-fasrc01/include -I/n/helmod/apps/centos7/Core/bzip2/1.0.6-fasrc01/include -I/n/helmod/apps/centos7/Core/pcre/8.37-fasrc02/include -I/n/helmod/apps/centos7/Core/readline/6.3-fasrc02/include -L/n/helmod/apps/centos7/Core/bzip2/1.0.6-fasrc01/lib -L/n/helmod/apps/centos7/Core/pcre/8.37-fasrc02/lib -L/n/helmod/apps/centos7/Core/curl/7.45.0-fasrc01/lib -L/n/helmod/apps/centos7/Core/readline/6.3-fasrc02/lib64 -std=gnu99 -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o knetfile.o knetfile.c gcc -I/n/helmod/apps/centos7/Core/curl/7.45.0-fasrc01/include -I/n/helmod/apps/centos7/Core/bzip2/1.0.6-fasrc01/include -I/n/helmod/apps/centos7/Core/pcre/8.37-fasrc02/include -I/n/helmod/apps/centos7/Core/readline/6.3-fasrc02/include -L/n/helmod/apps/centos7/Core/bzip2/1.0.6-fasrc01/lib -L/n/helmod/apps/centos7/Core/pcre/8.37-fasrc02/lib -L/n/helmod/apps/centos7/Core/curl/7.45.0-fasrc01/lib -L/n/helmod/apps/centos7/Core/readline/6.3-fasrc02/lib64 -std=gnu99 -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o kstring.o kstring.c gcc -I/n/helmod/apps/centos7/Core/curl/7.45.0-fasrc01/include -I/n/helmod/apps/centos7/Core/bzip2/1.0.6-fasrc01/include -I/n/helmod/apps/centos7/Core/pcre/8.37-fasrc02/include -I/n/helmod/apps/centos7/Core/readline/6.3-fasrc02/include -L/n/helmod/apps/centos7/Core/bzip2/1.0.6-fasrc01/lib -L/n/helmod/apps/centos7/Core/pcre/8.37-fasrc02/lib -L/n/helmod/apps/centos7/Core/curl/7.45.0-fasrc01/lib -L/n/helmod/apps/centos7/Core/readline/6.3-fasrc02/lib64 -std=gnu99 -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o bcf_sr_sort.o bcf_sr_sort.c gcc -I/n/helmod/apps/centos7/Core/curl/7.45.0-fasrc01/include -I/n/helmod/apps/centos7/Core/bzip2/1.0.6-fasrc01/include -I/n/helmod/apps/centos7/Core/pcre/8.37-fasrc02/include -I/n/helmod/apps/centos7/Core/readline/6.3-fasrc02/include -L/n/helmod/apps/centos7/Core/bzip2/1.0.6-fasrc01/lib -L/n/helmod/apps/centos7/Core/pcre/8.37-fasrc02/lib -L/n/helmod/apps/centos7/Core/curl/7.45.0-fasrc01/lib -L/n/helmod/apps/centos7/Core/readline/6.3-fasrc02/lib64 -std=gnu99 -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o bgzf.o bgzf.c gcc -I/n/helmod/apps/centos7/Core/curl/7.45.0-fasrc01/include -I/n/helmod/apps/centos7/Core/bzip2/1.0.6-fasrc01/include -I/n/helmod/apps/centos7/Core/pcre/8.37-fasrc02/include -I/n/helmod/apps/centos7/Core/readline/6.3-fasrc02/include -L/n/helmod/apps/centos7/Core/bzip2/1.0.6-fasrc01/lib -L/n/helmod/apps/centos7/Core/pcre/8.37-fasrc02/lib -L/n/helmod/apps/centos7/Core/curl/7.45.0-fasrc01/lib -L/n/helmod/apps/centos7/Core/readline/6.3-fasrc02/lib64 -std=gnu99 -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o errmod.o errmod.c gcc -I/n/helmod/apps/centos7/Core/curl/7.45.0-fasrc01/include -I/n/helmod/apps/centos7/Core/bzip2/1.0.6-fasrc01/include -I/n/helmod/apps/centos7/Core/pcre/8.37-fasrc02/include -I/n/helmod/apps/centos7/Core/readline/6.3-fasrc02/include -L/n/helmod/apps/centos7/Core/bzip2/1.0.6-fasrc01/lib -L/n/helmod/apps/centos7/Core/pcre/8.37-fasrc02/lib -L/n/helmod/apps/centos7/Core/curl/7.45.0-fasrc01/lib -L/n/helmod/apps/centos7/Core/readline/6.3-fasrc02/lib64 -std=gnu99 -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o faidx.o faidx.c gcc -I/n/helmod/apps/centos7/Core/curl/7.45.0-fasrc01/include -I/n/helmod/apps/centos7/Core/bzip2/1.0.6-fasrc01/include -I/n/helmod/apps/centos7/Core/pcre/8.37-fasrc02/include -I/n/helmod/apps/centos7/Core/readline/6.3-fasrc02/include -L/n/helmod/apps/centos7/Core/bzip2/1.0.6-fasrc01/lib -L/n/helmod/apps/centos7/Core/pcre/8.37-fasrc02/lib -L/n/helmod/apps/centos7/Core/curl/7.45.0-fasrc01/lib -L/n/helmod/apps/centos7/Core/readline/6.3-fasrc02/lib64 -std=gnu99 -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hfile.o hfile.c gcc -I/n/helmod/apps/centos7/Core/curl/7.45.0-fasrc01/include -I/n/helmod/apps/centos7/Core/bzip2/1.0.6-fasrc01/include -I/n/helmod/apps/centos7/Core/pcre/8.37-fasrc02/include -I/n/helmod/apps/centos7/Core/readline/6.3-fasrc02/include -L/n/helmod/apps/centos7/Core/bzip2/1.0.6-fasrc01/lib -L/n/helmod/apps/centos7/Core/pcre/8.37-fasrc02/lib -L/n/helmod/apps/centos7/Core/curl/7.45.0-fasrc01/lib -L/n/helmod/apps/centos7/Core/readline/6.3-fasrc02/lib64 -std=gnu99 -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hfile_net.o hfile_net.c echo '#define HTS_VERSION "1.7"' > version.h gcc -I/n/helmod/apps/centos7/Core/curl/7.45.0-fasrc01/include -I/n/helmod/apps/centos7/Core/bzip2/1.0.6-fasrc01/include -I/n/helmod/apps/centos7/Core/pcre/8.37-fasrc02/include -I/n/helmod/apps/centos7/Core/readline/6.3-fasrc02/include -L/n/helmod/apps/centos7/Core/bzip2/1.0.6-fasrc01/lib -L/n/helmod/apps/centos7/Core/pcre/8.37-fasrc02/lib -L/n/helmod/apps/centos7/Core/curl/7.45.0-fasrc01/lib -L/n/helmod/apps/centos7/Core/readline/6.3-fasrc02/lib64 -std=gnu99 -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hts.o hts.c gcc -I/n/helmod/apps/centos7/Core/curl/7.45.0-fasrc01/include -I/n/helmod/apps/centos7/Core/bzip2/1.0.6-fasrc01/include -I/n/helmod/apps/centos7/Core/pcre/8.37-fasrc02/include -I/n/helmod/apps/centos7/Core/readline/6.3-fasrc02/include -L/n/helmod/apps/centos7/Core/bzip2/1.0.6-fasrc01/lib -L/n/helmod/apps/centos7/Core/pcre/8.37-fasrc02/lib -L/n/helmod/apps/centos7/Core/curl/7.45.0-fasrc01/lib -L/n/helmod/apps/centos7/Core/readline/6.3-fasrc02/lib64 -std=gnu99 -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hts_os.o hts_os.c gcc -I/n/helmod/apps/centos7/Core/curl/7.45.0-fasrc01/include -I/n/helmod/apps/centos7/Core/bzip2/1.0.6-fasrc01/include -I/n/helmod/apps/centos7/Core/pcre/8.37-fasrc02/include -I/n/helmod/apps/centos7/Core/readline/6.3-fasrc02/include -L/n/helmod/apps/centos7/Core/bzip2/1.0.6-fasrc01/lib -L/n/helmod/apps/centos7/Core/pcre/8.37-fasrc02/lib -L/n/helmod/apps/centos7/Core/curl/7.45.0-fasrc01/lib -L/n/helmod/apps/centos7/Core/readline/6.3-fasrc02/lib64 -std=gnu99 -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o md5.o md5.c gcc -I/n/helmod/apps/centos7/Core/curl/7.45.0-fasrc01/include -I/n/helmod/apps/centos7/Core/bzip2/1.0.6-fasrc01/include -I/n/helmod/apps/centos7/Core/pcre/8.37-fasrc02/include -I/n/helmod/apps/centos7/Core/readline/6.3-fasrc02/include -L/n/helmod/apps/centos7/Core/bzip2/1.0.6-fasrc01/lib -L/n/helmod/apps/centos7/Core/pcre/8.37-fasrc02/lib -L/n/helmod/apps/centos7/Core/curl/7.45.0-fasrc01/lib -L/n/helmod/apps/centos7/Core/readline/6.3-fasrc02/lib64 -std=gnu99 -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o multipart.o multipart.c gcc -I/n/helmod/apps/centos7/Core/curl/7.45.0-fasrc01/include -I/n/helmod/apps/centos7/Core/bzip2/1.0.6-fasrc01/include -I/n/helmod/apps/centos7/Core/pcre/8.37-fasrc02/include -I/n/helmod/apps/centos7/Core/readline/6.3-fasrc02/include -L/n/helmod/apps/centos7/Core/bzip2/1.0.6-fasrc01/lib -L/n/helmod/apps/centos7/Core/pcre/8.37-fasrc02/lib -L/n/helmod/apps/centos7/Core/curl/7.45.0-fasrc01/lib -L/n/helmod/apps/centos7/Core/readline/6.3-fasrc02/lib64 -std=gnu99 -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o probaln.o probaln.c gcc -I/n/helmod/apps/centos7/Core/curl/7.45.0-fasrc01/include -I/n/helmod/apps/centos7/Core/bzip2/1.0.6-fasrc01/include -I/n/helmod/apps/centos7/Core/pcre/8.37-fasrc02/include -I/n/helmod/apps/centos7/Core/readline/6.3-fasrc02/include -L/n/helmod/apps/centos7/Core/bzip2/1.0.6-fasrc01/lib -L/n/helmod/apps/centos7/Core/pcre/8.37-fasrc02/lib -L/n/helmod/apps/centos7/Core/curl/7.45.0-fasrc01/lib -L/n/helmod/apps/centos7/Core/readline/6.3-fasrc02/lib64 -std=gnu99 -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o realn.o realn.c gcc -I/n/helmod/apps/centos7/Core/curl/7.45.0-fasrc01/include -I/n/helmod/apps/centos7/Core/bzip2/1.0.6-fasrc01/include -I/n/helmod/apps/centos7/Core/pcre/8.37-fasrc02/include -I/n/helmod/apps/centos7/Core/readline/6.3-fasrc02/include -L/n/helmod/apps/centos7/Core/bzip2/1.0.6-fasrc01/lib -L/n/helmod/apps/centos7/Core/pcre/8.37-fasrc02/lib -L/n/helmod/apps/centos7/Core/curl/7.45.0-fasrc01/lib -L/n/helmod/apps/centos7/Core/readline/6.3-fasrc02/lib64 -std=gnu99 -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o regidx.o regidx.c gcc -I/n/helmod/apps/centos7/Core/curl/7.45.0-fasrc01/include -I/n/helmod/apps/centos7/Core/bzip2/1.0.6-fasrc01/include -I/n/helmod/apps/centos7/Core/pcre/8.37-fasrc02/include -I/n/helmod/apps/centos7/Core/readline/6.3-fasrc02/include -L/n/helmod/apps/centos7/Core/bzip2/1.0.6-fasrc01/lib -L/n/helmod/apps/centos7/Core/pcre/8.37-fasrc02/lib -L/n/helmod/apps/centos7/Core/curl/7.45.0-fasrc01/lib -L/n/helmod/apps/centos7/Core/readline/6.3-fasrc02/lib64 -std=gnu99 -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o sam.o sam.c gcc -I/n/helmod/apps/centos7/Core/curl/7.45.0-fasrc01/include -I/n/helmod/apps/centos7/Core/bzip2/1.0.6-fasrc01/include -I/n/helmod/apps/centos7/Core/pcre/8.37-fasrc02/include -I/n/helmod/apps/centos7/Core/readline/6.3-fasrc02/include -L/n/helmod/apps/centos7/Core/bzip2/1.0.6-fasrc01/lib -L/n/helmod/apps/centos7/Core/pcre/8.37-fasrc02/lib -L/n/helmod/apps/centos7/Core/curl/7.45.0-fasrc01/lib -L/n/helmod/apps/centos7/Core/readline/6.3-fasrc02/lib64 -std=gnu99 -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o synced_bcf_reader.o synced_bcf_reader.c gcc -I/n/helmod/apps/centos7/Core/curl/7.45.0-fasrc01/include -I/n/helmod/apps/centos7/Core/bzip2/1.0.6-fasrc01/include -I/n/helmod/apps/centos7/Core/pcre/8.37-fasrc02/include -I/n/helmod/apps/centos7/Core/readline/6.3-fasrc02/include -L/n/helmod/apps/centos7/Core/bzip2/1.0.6-fasrc01/lib -L/n/helmod/apps/centos7/Core/pcre/8.37-fasrc02/lib -L/n/helmod/apps/centos7/Core/curl/7.45.0-fasrc01/lib -L/n/helmod/apps/centos7/Core/readline/6.3-fasrc02/lib64 -std=gnu99 -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o vcf_sweep.o vcf_sweep.c gcc -I/n/helmod/apps/centos7/Core/curl/7.45.0-fasrc01/include -I/n/helmod/apps/centos7/Core/bzip2/1.0.6-fasrc01/include -I/n/helmod/apps/centos7/Core/pcre/8.37-fasrc02/include -I/n/helmod/apps/centos7/Core/readline/6.3-fasrc02/include -L/n/helmod/apps/centos7/Core/bzip2/1.0.6-fasrc01/lib -L/n/helmod/apps/centos7/Core/pcre/8.37-fasrc02/lib -L/n/helmod/apps/centos7/Core/curl/7.45.0-fasrc01/lib -L/n/helmod/apps/centos7/Core/readline/6.3-fasrc02/lib64 -std=gnu99 -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o tbx.o tbx.c gcc -I/n/helmod/apps/centos7/Core/curl/7.45.0-fasrc01/include -I/n/helmod/apps/centos7/Core/bzip2/1.0.6-fasrc01/include -I/n/helmod/apps/centos7/Core/pcre/8.37-fasrc02/include -I/n/helmod/apps/centos7/Core/readline/6.3-fasrc02/include -L/n/helmod/apps/centos7/Core/bzip2/1.0.6-fasrc01/lib -L/n/helmod/apps/centos7/Core/pcre/8.37-fasrc02/lib -L/n/helmod/apps/centos7/Core/curl/7.45.0-fasrc01/lib -L/n/helmod/apps/centos7/Core/readline/6.3-fasrc02/lib64 -std=gnu99 -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o textutils.o textutils.c gcc -I/n/helmod/apps/centos7/Core/curl/7.45.0-fasrc01/include -I/n/helmod/apps/centos7/Core/bzip2/1.0.6-fasrc01/include -I/n/helmod/apps/centos7/Core/pcre/8.37-fasrc02/include -I/n/helmod/apps/centos7/Core/readline/6.3-fasrc02/include -L/n/helmod/apps/centos7/Core/bzip2/1.0.6-fasrc01/lib -L/n/helmod/apps/centos7/Core/pcre/8.37-fasrc02/lib -L/n/helmod/apps/centos7/Core/curl/7.45.0-fasrc01/lib -L/n/helmod/apps/centos7/Core/readline/6.3-fasrc02/lib64 -std=gnu99 -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o thread_pool.o thread_pool.c gcc -I/n/helmod/apps/centos7/Core/curl/7.45.0-fasrc01/include -I/n/helmod/apps/centos7/Core/bzip2/1.0.6-fasrc01/include -I/n/helmod/apps/centos7/Core/pcre/8.37-fasrc02/include -I/n/helmod/apps/centos7/Core/readline/6.3-fasrc02/include -L/n/helmod/apps/centos7/Core/bzip2/1.0.6-fasrc01/lib -L/n/helmod/apps/centos7/Core/pcre/8.37-fasrc02/lib -L/n/helmod/apps/centos7/Core/curl/7.45.0-fasrc01/lib -L/n/helmod/apps/centos7/Core/readline/6.3-fasrc02/lib64 -std=gnu99 -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o vcf.o vcf.c gcc -I/n/helmod/apps/centos7/Core/curl/7.45.0-fasrc01/include -I/n/helmod/apps/centos7/Core/bzip2/1.0.6-fasrc01/include -I/n/helmod/apps/centos7/Core/pcre/8.37-fasrc02/include -I/n/helmod/apps/centos7/Core/readline/6.3-fasrc02/include -L/n/helmod/apps/centos7/Core/bzip2/1.0.6-fasrc01/lib -L/n/helmod/apps/centos7/Core/pcre/8.37-fasrc02/lib -L/n/helmod/apps/centos7/Core/curl/7.45.0-fasrc01/lib -L/n/helmod/apps/centos7/Core/readline/6.3-fasrc02/lib64 -std=gnu99 -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o vcfutils.o vcfutils.c gcc -I/n/helmod/apps/centos7/Core/curl/7.45.0-fasrc01/include -I/n/helmod/apps/centos7/Core/bzip2/1.0.6-fasrc01/include -I/n/helmod/apps/centos7/Core/pcre/8.37-fasrc02/include -I/n/helmod/apps/centos7/Core/readline/6.3-fasrc02/include -L/n/helmod/apps/centos7/Core/bzip2/1.0.6-fasrc01/lib -L/n/helmod/apps/centos7/Core/pcre/8.37-fasrc02/lib -L/n/helmod/apps/centos7/Core/curl/7.45.0-fasrc01/lib -L/n/helmod/apps/centos7/Core/readline/6.3-fasrc02/lib64 -std=gnu99 -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_codecs.o cram/cram_codecs.c gcc -I/n/helmod/apps/centos7/Core/curl/7.45.0-fasrc01/include -I/n/helmod/apps/centos7/Core/bzip2/1.0.6-fasrc01/include -I/n/helmod/apps/centos7/Core/pcre/8.37-fasrc02/include -I/n/helmod/apps/centos7/Core/readline/6.3-fasrc02/include -L/n/helmod/apps/centos7/Core/bzip2/1.0.6-fasrc01/lib -L/n/helmod/apps/centos7/Core/pcre/8.37-fasrc02/lib -L/n/helmod/apps/centos7/Core/curl/7.45.0-fasrc01/lib -L/n/helmod/apps/centos7/Core/readline/6.3-fasrc02/lib64 -std=gnu99 -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_decode.o cram/cram_decode.c gcc -I/n/helmod/apps/centos7/Core/curl/7.45.0-fasrc01/include -I/n/helmod/apps/centos7/Core/bzip2/1.0.6-fasrc01/include -I/n/helmod/apps/centos7/Core/pcre/8.37-fasrc02/include -I/n/helmod/apps/centos7/Core/readline/6.3-fasrc02/include -L/n/helmod/apps/centos7/Core/bzip2/1.0.6-fasrc01/lib -L/n/helmod/apps/centos7/Core/pcre/8.37-fasrc02/lib -L/n/helmod/apps/centos7/Core/curl/7.45.0-fasrc01/lib -L/n/helmod/apps/centos7/Core/readline/6.3-fasrc02/lib64 -std=gnu99 -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_encode.o cram/cram_encode.c gcc -I/n/helmod/apps/centos7/Core/curl/7.45.0-fasrc01/include -I/n/helmod/apps/centos7/Core/bzip2/1.0.6-fasrc01/include -I/n/helmod/apps/centos7/Core/pcre/8.37-fasrc02/include -I/n/helmod/apps/centos7/Core/readline/6.3-fasrc02/include -L/n/helmod/apps/centos7/Core/bzip2/1.0.6-fasrc01/lib -L/n/helmod/apps/centos7/Core/pcre/8.37-fasrc02/lib -L/n/helmod/apps/centos7/Core/curl/7.45.0-fasrc01/lib -L/n/helmod/apps/centos7/Core/readline/6.3-fasrc02/lib64 -std=gnu99 -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_external.o cram/cram_external.c gcc -I/n/helmod/apps/centos7/Core/curl/7.45.0-fasrc01/include -I/n/helmod/apps/centos7/Core/bzip2/1.0.6-fasrc01/include -I/n/helmod/apps/centos7/Core/pcre/8.37-fasrc02/include -I/n/helmod/apps/centos7/Core/readline/6.3-fasrc02/include -L/n/helmod/apps/centos7/Core/bzip2/1.0.6-fasrc01/lib -L/n/helmod/apps/centos7/Core/pcre/8.37-fasrc02/lib -L/n/helmod/apps/centos7/Core/curl/7.45.0-fasrc01/lib -L/n/helmod/apps/centos7/Core/readline/6.3-fasrc02/lib64 -std=gnu99 -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_index.o cram/cram_index.c gcc -I/n/helmod/apps/centos7/Core/curl/7.45.0-fasrc01/include -I/n/helmod/apps/centos7/Core/bzip2/1.0.6-fasrc01/include -I/n/helmod/apps/centos7/Core/pcre/8.37-fasrc02/include -I/n/helmod/apps/centos7/Core/readline/6.3-fasrc02/include -L/n/helmod/apps/centos7/Core/bzip2/1.0.6-fasrc01/lib -L/n/helmod/apps/centos7/Core/pcre/8.37-fasrc02/lib -L/n/helmod/apps/centos7/Core/curl/7.45.0-fasrc01/lib -L/n/helmod/apps/centos7/Core/readline/6.3-fasrc02/lib64 -std=gnu99 -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_io.o cram/cram_io.c cram/cram_io.c:61:18: fatal error: lzma.h: No such file or directoryinclude
compilation terminated. make[1]: Leaving directory `/tmp/RtmpMZkpPD/R.INSTALL2d98e6b76b32a/Rhtslib/src/htslib-1.7' make[1]: [cram/cram_io.o] Error 1 make: [htslib] Error 2 ERROR: compilation failed for package ‘Rhtslib’
The downloaded source packages are in ‘/tmp/RtmpHhKHkY/downloaded_packages’ Installation path not writeable, unable to update packages: DT, MCMCpack, RCurl, Rcpp, RcppArmadillo, SnowballC, StanHeaders, akima, ape, arm, backports, bit64, broom, callr, car, carData, cubature, data.table, devtools, dplyr, ellipsis, expm, foreach, forecast, fs, gamm4, ggplot2, git2r, glmnet, glue, gplots, grplasso, gss, gtools, haven, htmlTable, htmltools, httpuv, httr, intervals, isoband, jsonlite, knitr, later, lhs, lme4, loo, maptools, mclust, meta, multcomp, mvtnorm, nloptr, openssl, openxlsx, pillar, pkgbuild, pkgload, plotrix, processx, promises, ps, psych, purrr, quantmod, quantreg, raster, remotes, reshape2, rex, rgl, rlang, rootSolve, roxygen2, rversions, scales, sem, shiny, sp, survey, svmpath, sys, texreg, tibble, tidyr, tidyselect, usethis, vcd, vctrs, withr, xfun, xml2, zoo, KernSmooth, MASS, boot, class, lattice, nlme, nnet, spatial, survival
Warning message: In install.packages(...) : installation of package ‘Rhtslib’ had non-zero exit status