Problem installing Rhtslib on renv

[clanna]

Hi, I'm trying to install Rhtslib through Bioconductor inside renv but it's not completing. Here is the output from my installation attempt:

` BiocManager::install("Rhtslib") 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories: CRAN: https://cran.rstudio.com

Bioconductor version 3.12 (BiocManager 1.30.16), R 4.0.5 (2021-03-31) Installing package(s) 'Rhtslib' trying URL 'https://bioconductor.org/packages/3.12/bioc/src/contrib/Rhtslib_1.22.0.tar.gz' Content type 'application/x-gzip' length 1472143 bytes (1.4 MB)

downloaded 1.4 MB

• installing source package ‘Rhtslib’ ... using non-staged installation via StagedInstall field libs cd "htslib-1.7" && make -f "/usr/lib/R/etc/Makeconf" -f "Makefile.Rhtslib" make[1]: Entering directory '/tmp/RtmpmYAm14/R.INSTALLfd623cf97f9f/Rhtslib/src/htslib-1.7' Makefile.Rhtslib:128: warning: overriding recipe for target '.c.o' /usr/lib/R/etc/Makeconf:172: warning: ignoring old recipe for target '.c.o' gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o kfunc.o kfunc.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o knetfile.o knetfile.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o kstring.o kstring.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o bcf_sr_sort.o bcf_sr_sort.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o bgzf.o bgzf.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o errmod.o errmod.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o faidx.o faidx.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o hfile.o hfile.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o hfile_net.o hfile_net.c echo '#define HTS_VERSION "1.7"' > version.h gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o hts.o hts.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o hts_os.o hts_os.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o md5.o md5.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o multipart.o multipart.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o probaln.o probaln.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o realn.o realn.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o regidx.o regidx.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o sam.o sam.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o synced_bcf_reader.o synced_bcf_reader.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o vcf_sweep.o vcf_sweep.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o tbx.o tbx.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o textutils.o textutils.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o thread_pool.o thread_pool.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o vcf.o vcf.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o vcfutils.o vcfutils.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_codecs.o cram/cram_codecs.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_decode.o cram/cram_decode.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_encode.o cram/cram_encode.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_external.o cram/cram_external.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_index.o cram/cram_index.c In file included from /usr/include/string.h:495, from cram/cram_index.c:57: In function ‘memcpy’, inlined from ‘kputsn’ at ./htslib/kstring.h:148:2, inlined from ‘kputs’ at ./htslib/kstring.h:156:9, inlined from ‘cram_index_build’ at cram/cram_index.c:571:9: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:10: warning: ‘builtin_memcpy’ specified bound 18446744073709551614 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] 34 | return _builtinmemcpy_chk (dest, src, len, bos0 (dest)); | ^~~~~~~~~~~~~~ gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_io.o cram/cram_io.c cram/cram_io.c: In function ‘cram_populate_ref’: cram/cramio.c:2178:27: warning: ‘.tmp’ directive writing 5 bytes into a region of size between 1 and 4096 [-Wformat-overflow=] 2178 | sprintf(pathtmp, "%s.tmp%d%u%u", path, pid, thrid, t); | ^~~~~ cram/cram_io.c:2178:24: note: using the range [0, 4294967295] for directive argument 2178 | sprintf(pathtmp, "%s.tmp%d%u%u", path, pid, thrid, t); | ^~~~~ cram/cram_io.c:2178:24: note: using the range [0, 4294967295] for directive argument In file included from /usr/include/stdio.h:867, from cram/cram_io.c:49: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘builtin_sprintf_chk’ output between 11 and 4134 bytes into a destination of size 4096 36 | return builtin_sprintf_chk (s, USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~ 37 | bos (s), fmt, va_arg_pack ()); | ~~~~~~~~~ gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_samtools.o cram/cram_samtools.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_stats.o cram/cram_stats.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/files.o cram/files.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/mFILE.o cram/mFILE.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/open_trace_file.o cram/open_trace_file.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/pooled_alloc.o cram/pooled_alloc.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/rANS_static.o cram/rANS_static.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/sam_header.o cram/sam_header.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/string_alloc.o cram/string_alloc.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o hfile_libcurl.o hfile_libcurl.c ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o hfile_libcurl.o ranlib libhts.a gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o kfunc.pico kfunc.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o knetfile.pico knetfile.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o kstring.pico kstring.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o bcf_sr_sort.pico bcf_sr_sort.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o bgzf.pico bgzf.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o errmod.pico errmod.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o faidx.pico faidx.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o hfile.pico hfile.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o hfile_net.pico hfile_net.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o hts.pico hts.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o hts_os.pico hts_os.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o md5.pico md5.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o multipart.pico multipart.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o probaln.pico probaln.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o realn.pico realn.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o regidx.pico regidx.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o sam.pico sam.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o synced_bcf_reader.pico synced_bcf_reader.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o vcf_sweep.pico vcf_sweep.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o tbx.pico tbx.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o textutils.pico textutils.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o thread_pool.pico thread_pool.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o vcf.pico vcf.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o vcfutils.pico vcfutils.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_codecs.pico cram/cram_codecs.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_decode.pico cram/cram_decode.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_encode.pico cram/cram_encode.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_external.pico cram/cram_external.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_index.pico cram/cram_index.c In file included from /usr/include/string.h:495, from cram/cram_index.c:57: In function ‘memcpy’, inlined from ‘kputsn’ at ./htslib/kstring.h:148:2, inlined from ‘kputs’ at ./htslib/kstring.h:156:9, inlined from ‘cram_index_build’ at cram/cram_index.c:571:9: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:10: warning: ‘builtin_memcpy’ specified bound 18446744073709551614 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] 34 | return builtin___memcpy_chk (dest, src, len, bos0 (dest)); | ^~~~~~~~~~~~~~ gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_io.pico cram/cram_io.c cram/cram_io.c: In function ‘cram_populate_ref’: cram/cramio.c:2178:27: warning: ‘.tmp’ directive writing 5 bytes into a region of size between 1 and 4096 [-Wformat-overflow=] 2178 | sprintf(pathtmp, "%s.tmp%d%u%u", path, pid, thrid, t); | ^~~~~ cram/cram_io.c:2178:24: note: using the range [0, 4294967295] for directive argument 2178 | sprintf(pathtmp, "%s.tmp%d%u%u", path, pid, thrid, t); | ^~~~~ cram/cram_io.c:2178:24: note: using the range [0, 4294967295] for directive argument In file included from /usr/include/stdio.h:867, from cram/cram_io.c:49: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘builtin___sprintf_chk’ output between 11 and 4134 bytes into a destination of size 4096 36 | return builtin_sprintf_chk (s, USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~ 37 | bos (s), fmt, __va_arg_pack ()); | ~~~~~~~~~ gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_samtools.pico cram/cram_samtools.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_stats.pico cram/cram_stats.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/files.pico cram/files.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/mFILE.pico cram/mFILE.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/open_trace_file.pico cram/open_trace_file.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/pooled_alloc.pico cram/pooled_alloc.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/rANS_static.pico cram/rANS_static.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/sam_header.pico cram/sam_header.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/string_alloc.pico cram/string_alloc.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o hfile_libcurl.pico hfile_libcurl.c gcc -std=gnu99 -shared -Wl,-soname,libhts.so.2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o libhts.so kfunc.pico knetfile.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico hfile.pico hfile_net.pico hts.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico sam.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico textutils.pico thread_pool.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_external.pico cram/cram_index.pico cram/cram_io.pico cram/cram_samtools.pico cram/cram_stats.pico cram/files.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/rANS_static.pico cram/sam_header.pico cram/string_alloc.pico hfile_libcurl.pico -lz -lm -lbz2 -llzma -lcurl -lpthread ln -sf libhts.so libhts.so.2 make[1]: Leaving directory '/tmp/RtmpmYAm14/R.INSTALLfd623cf97f9f/Rhtslib/src/htslib-1.7' mkdir -p "/media/clanna/Data/Temp/Temp/sgwfc-gene-r/renv/library/R-4.0/x86_64-pc-linux-gnu/Rhtslib/include/htslib" cd "htslib-1.7/htslib" && cp * "/media/clanna/Data/Temp/Temp/sgwfc-gene-r/renv/library/R-4.0/x86_64-pc-linux-gnu/Rhtslib/include/htslib" && cd .. && cp textutils_internal.h hts_internal.h "/media/clanna/Data/Temp/Temp/sgwfc-gene-r/renv/library/R-4.0/x86_64-pc-linux-gnu/Rhtslib/include" gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/media/clanna/Data/Temp/Temp/sgwfc-gene-r/renv/library/R-4.0/x86_64-pc-linux-gnu/Rhtslib/include" -I'/media/clanna/Data/Temp/Temp/sgwfc-gene-r/renv/library/R-4.0/x86_64-pc-linux-gnu/zlibbioc/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c R_init_Rhtslib.c -o R_init_Rhtslib.o mkdir -p "/media/clanna/Data/Temp/Temp/sgwfc-gene-r/renv/library/R-4.0/x86_64-pc-linux-gnu/Rhtslib/usrlib" cd "htslib-1.7" && cp libhts.so libhts.a "/media/clanna/Data/Temp/Temp/sgwfc-gene-r/renv/library/R-4.0/x86_64-pc-linux-gnu/Rhtslib/usrlib" cd "/media/clanna/Data/Temp/Temp/sgwfc-gene-r/renv/library/R-4.0/x86_64-pc-linux-gnu/Rhtslib/usrlib" && ln -s libhts.so libhts.so.2 ln: failed to create symbolic link 'libhts.so.2': Operation not permitted make: *** [Makevars:28: populate-usrlib-dir] Error 1 ERROR: compilation failed for package ‘Rhtslib’
• removing ‘/media/clanna/Data/Temp/Temp/sgwfc-gene-r/renv/library/R-4.0/x86_64-pc-linux-gnu/Rhtslib’

The downloaded source packages are in ‘/tmp/RtmpZ8pLxk/downloaded_packages’ Warning message: In .inet_warning(msg) : installation of package ‘Rhtslib’ had non-zero exit status`

I thought it was a permission issue or something related to the htslib installation, but neither running R as sudo or installing htslib solved the problem.

[hpages]

Hi,

Looks like packages get installed under /media/clanna/ on your system. On many Linux distributions (e.g. Ubuntu), /media is where external storage devices get mounted. Are you installing packages on an external device? If so, what kind of file system is on the device? It should be a Posix-compliant file system so symlinks can be created. Note that many external storage devices are pre-formatted with a file system that is not Posix-compliant (e.g. FAT16). Trying to create a symlink on such device will always fail, even as sudo.

H.

[clanna]

It's being installed in an external drive formatted as exFAT. I'm using it with renv on multiple computers using this disk and restoring the library worked before on Windows and macOS. I'll try cloning the project to a local directory and see if it works.

[hpages]

This sounds like a recipe for problems. AFAIK there is no guarantee that the packages installed in the R library folder are relocatable. Maybe most of them will, but maybe some of them won't. So it's like playing lottery.

[clanna]

Yes, I agree. Even though it was creating OS-specific libraries, it wasn't a good idea. Installing it locally did the trick. Thanks!