> library(BiocManager); BiocManager::install("Rsamtools")
Bioconductor version 3.15 (BiocManager 1.30.17), R 4.2.0 (2022-04-22)
Installing package(s) 'Rsamtools'
trying URL 'https://bioconductor.org/packages/3.15/bioc/src/contrib/Rsamtools_2.12.0.tar.gz'
Content type 'application/x-gzip' length 2870358 bytes (2.7 MB)
==================================================
downloaded 2.7 MB
* installing *source* package ‘Rsamtools’ ...
** using staged installation
** libs
gcc -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto=auto -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto=auto -c COMPAT_bcf_hdr_read.c -o COMPAT_bcf_hdr_read.o
gcc -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto=auto -c IRanges_stubs.c -o IRanges_stubs.o
g++ -std=gnu++14 -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -Wp,-D_GLIBCXX_ASSERTIONS -flto=auto -c PileupBuffer.cpp -o PileupBuffer.o
g++ -std=gnu++14 -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -Wp,-D_GLIBCXX_ASSERTIONS -flto=auto -c PosCacheColl.cpp -o PosCacheColl.o
gcc -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto=auto -c R_init_Rsamtools.c -o R_init_Rsamtools.o
g++ -std=gnu++14 -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -Wp,-D_GLIBCXX_ASSERTIONS -flto=auto -c ResultManager.cpp -o ResultManager.o
gcc -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto=auto -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto=auto -c XVector_stubs.c -o XVector_stubs.o
gcc -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto=auto -c as_bam.c -o as_bam.o
gcc -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto=auto -c bam.c -o bam.o
gcc -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto=auto -c bam_data.c -o bam_data.o
g++ -std=gnu++14 -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -Wp,-D_GLIBCXX_ASSERTIONS -flto=auto -c bam_mate_iter.cpp -o bam_mate_iter.o
In file included from /usr/lib/R/library/Rhtslib/include/sam.h:29,
from Template.h:9,
from BamIterator.h:10,
from BamRangeIterator.h:7,
from bam_mate_iter.cpp:2:
BamRangeIterator.h: In member function ‘virtual void BamRangeIterator::finalize_inprogress(bamFile)’:
/usr/lib/R/library/Rhtslib/include/bam.h:57:41: warning: ignoring return value of ‘int64_t bgzf_seek(BGZF*, int64_t, int)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
57 | #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
| ~~~~~~~~~^~~~~~~~~~~~~~
BamRangeIterator.h:138:16: note: in expansion of macro ‘bam_seek’
138 | (void) bam_seek(bfile, pos, SEEK_SET);
| ^~~~~~~~
BamIterator.h: In constructor ‘BamIterator::BamIterator(bamFile, const bam_index_t*)’:
/usr/lib/R/library/Rhtslib/include/bam.h:57:41: warning: ignoring return value of ‘int64_t bgzf_seek(BGZF*, int64_t, int)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
57 | #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
| ~~~~~~~~~^~~~~~~~~~~~~~
BamIterator.h:87:16: note: in expansion of macro ‘bam_seek’
87 | (void) bam_seek(bfile, 0, 0);
| ^~~~~~~~
gcc -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto=auto -c bam_plbuf.c -o bam_plbuf.o
gcc -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto=auto -c bam_sort.c -o bam_sort.o
gcc -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto=auto -c bambuffer.c -o bambuffer.o
gcc -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto=auto -c bamfile.c -o bamfile.o
bamfile.c: In function ‘bamfile_isincomplete’:
bamfile.c:168:20: warning: ignoring return value of ‘bgzf_seek’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
168 | (void) bgzf_seek(bfile->file->x.bam, offset, SEEK_SET);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto=auto -c bcffile.c -o bcffile.o
gcc -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto=auto -c encode.c -o encode.o
gcc -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto=auto -c fafile.c -o fafile.o
gcc -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto=auto -c idxstats.c -o idxstats.o
In file included from /usr/lib/R/library/Rhtslib/include/sam.h:29,
from bamfile.h:5,
from idxstats.c:1:
idxstats.c: In function ‘idxstats_bamfile’:
/usr/lib/R/library/Rhtslib/include/bam.h:57:32: warning: ignoring return value of ‘bgzf_seek’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
57 | #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
| ^~~~~~~~~~~~~~~~~~~~~~~
idxstats.c:20:12: note: in expansion of macro ‘bam_seek’
20 | (void) bam_seek(fp, 0, 0);
| ^~~~~~~~
gcc -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto=auto -c io_sam.c -o io_sam.o
In file included from /usr/lib/R/library/Rhtslib/include/sam.h:29,
from io_sam.c:2:
io_sam.c: In function ‘_scan_bam_all’:
/usr/lib/R/library/Rhtslib/include/bam.h:57:32: warning: ignoring return value of ‘bgzf_seek’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
57 | #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
| ^~~~~~~~~~~~~~~~~~~~~~~
io_sam.c:304:12: note: in expansion of macro ‘bam_seek’
304 | (void) bam_seek(bfile->file->x.bam, bfile->pos0, SEEK_SET);
| ^~~~~~~~
g++ -std=gnu++14 -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -Wp,-D_GLIBCXX_ASSERTIONS -flto=auto -c pbuffer_wrapper.cpp -o pbuffer_wrapper.o
g++ -std=gnu++14 -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -Wp,-D_GLIBCXX_ASSERTIONS -flto=auto -c pileup.cpp -o pileup.o
gcc -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto=auto -c pileupbam.c -o pileupbam.o
gcc -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto=auto -c sam.c -o sam.o
gcc -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto=auto -c sam_opts.c -o sam_opts.o
gcc -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto=auto -c sam_utils.c -o sam_utils.o
gcc -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto=auto -c samtools_patch.c -o samtools_patch.o
gcc -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto=auto -c scan_bam_data.c -o scan_bam_data.o
gcc -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto=auto -c tabixfile.c -o tabixfile.o
tabixfile.c: In function ‘index_tabix’:
tabixfile.c:190:5: warning: ‘bgzf_is_bgzf’ is deprecated: Use bgzf_compression() or hts_detect_format() instead [-Wdeprecated-declarations]
190 | if (bgzf_is_bgzf(fn) != 1)
| ^~
In file included from tabixfile.c:3:
/usr/lib/R/library/Rhtslib/include/htslib/bgzf.h:243:9: note: declared here
243 | int bgzf_is_bgzf(const char *fn) HTS_DEPRECATED("Use bgzf_compression() or hts_detect_format() instead");
| ^~~~~~~~~~~~
gcc -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto=auto -c tagfilter.c -o tagfilter.o
gcc -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto=auto -c utilities.c -o utilities.o
gcc -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto=auto -c zip_compression.c -o zip_compression.o
g++ -std=gnu++14 -shared -L/usr/lib64/R/lib -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -flto=auto -o Rsamtools.so Biostrings_stubs.o COMPAT_bcf_hdr_read.o IRanges_stubs.o PileupBuffer.o PosCacheColl.o R_init_Rsamtools.o ResultManager.o S4Vectors_stubs.o XVector_stubs.o as_bam.o bam.o bam_data.o bam_mate_iter.o bam_plbuf.o bam_sort.o bambuffer.o bamfile.o bcffile.o encode.o fafile.o idxstats.o io_sam.o pbuffer_wrapper.o pileup.o pileupbam.o sam.o sam_opts.o sam_utils.o samtools_patch.o scan_bam_data.o tabixfile.o tagfilter.o utilities.o zip_compression.o /usr/lib/R/library/Rhtslib/usrlib/libhts.a -lcurl -L/usr/lib64/R/lib -lR
installing to /home/christoph/R/x86_64-pc-linux-gnu-library/4.2/00LOCK-Rsamtools/00new/Rsamtools/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘Rsamtools’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/home/christoph/R/x86_64-pc-linux-gnu-library/4.2/00LOCK-Rsamtools/00new/Rsamtools/libs/Rsamtools.so':
/home/christoph/R/x86_64-pc-linux-gnu-library/4.2/00LOCK-Rsamtools/00new/Rsamtools/libs/Rsamtools.so: undefined symbol: hts_open_format
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/christoph/R/x86_64-pc-linux-gnu-library/4.2/Rsamtools’
The downloaded source packages are in
‘/tmp/RtmpmeoPUu/downloaded_packages’
Installation paths not writeable, unable to update packages
path: /usr/lib/R/library
packages:
checkmate, GenomeInfoDbData, hwriter, IRanges, MASS
Warning message:
In install.packages(...) :
installation of package ‘Rsamtools’ had non-zero exit status
>
> ldd Rsamtools.so
linux-vdso.so.1 (0x00007ffdd95a2000)
libR.so => /usr/lib/R/lib/libR.so (0x00007f29e5abf000)
libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0x00007f29e5899000)
libgcc_s.so.1 => /usr/lib/libgcc_s.so.1 (0x00007f29e587e000)
libc.so.6 => /usr/lib/libc.so.6 (0x00007f29e5674000)
libblas.so.3 => /usr/lib/libblas.so.3 (0x00007f29e561d000)
libm.so.6 => /usr/lib/libm.so.6 (0x00007f29e5535000)
libreadline.so.8 => /usr/lib/libreadline.so.8 (0x00007f29e54dd000)
libpcre2-8.so.0 => /usr/lib/libpcre2-8.so.0 (0x00007f29e5444000)
liblzma.so.5 => /usr/lib/liblzma.so.5 (0x00007f29e541a000)
libbz2.so.1.0 => /usr/lib/libbz2.so.1.0 (0x00007f29e5407000)
libz.so.1 => /usr/lib/libz.so.1 (0x00007f29e53ed000)
libtirpc.so.3 => /usr/lib/libtirpc.so.3 (0x00007f29e53be000)
libicuuc.so.71 => /usr/lib/libicuuc.so.71 (0x00007f29e51bd000)
libicui18n.so.71 => /usr/lib/libicui18n.so.71 (0x00007f29e4e8b000)
libgomp.so.1 => /usr/lib/libgomp.so.1 (0x00007f29e4e46000)
/usr/lib64/ld-linux-x86-64.so.2 (0x00007f29e6007000)
libgfortran.so.5 => /usr/lib/libgfortran.so.5 (0x00007f29e4b8b000)
libncursesw.so.6 => /usr/lib/libncursesw.so.6 (0x00007f29e4b17000)
libpthread.so.0 => /usr/lib/libpthread.so.0 (0x00007f29e4b10000)
libgssapi_krb5.so.2 => /usr/lib/libgssapi_krb5.so.2 (0x00007f29e4abb000)
libicudata.so.71 => /usr/lib/libicudata.so.71 (0x00007f29e2db6000)
libquadmath.so.0 => /usr/lib/../lib/libquadmath.so.0 (0x00007f29e2d6b000)
libkrb5.so.3 => /usr/lib/libkrb5.so.3 (0x00007f29e2c92000)
libk5crypto.so.3 => /usr/lib/libk5crypto.so.3 (0x00007f29e2c60000)
libcom_err.so.2 => /usr/lib/libcom_err.so.2 (0x00007f29e2c5a000)
libkrb5support.so.0 => /usr/lib/libkrb5support.so.0 (0x00007f29e2c4b000)
libkeyutils.so.1 => /usr/lib/libkeyutils.so.1 (0x00007f29e2c44000)
libresolv.so.2 => /usr/lib/libresolv.so.2 (0x00007f29e2c30000)
I’m also on Arch Linux, with R 4.2.0, Rhtslib 1.28.0, and htslib 1.15.1.