Package Details: r-rsamtools 2.12.0-2

Git Clone URL: https://aur.archlinux.org/r-rsamtools.git (read-only, click to copy)
Package Base: r-rsamtools
Description: Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
Upstream URL: https://bioconductor.org/packages/release/bioc/html/Rsamtools.html
Licenses: Artistic-2.0
Submitter: greyltc
Maintainer: greyltc (peippo)
Last Packager: peippo
Votes: 0
Popularity: 0.000000
First Submitted: 2019-02-09 14:35 (UTC)
Last Updated: 2022-05-01 15:11 (UTC)

Latest Comments

peippo commented on 2022-05-08 12:58 (UTC)

This now builds fine with r>=4.2.0-2 from the community repo

peippo commented on 2022-05-01 14:26 (UTC)

It seems to be connected to R being built with LTO. For the time being, please build your own R using options=(!lto), then rebuild r-rhtslib and r-rsamtools.

I filed a bug report with the r package in the community repo, hope it’s picked up quickly: https://bugs.archlinux.org/task/74609

malacology commented on 2022-04-29 23:45 (UTC)

You can see similar issue here

https://github.com/BioArchLinux/Packages/issues/40

peippo commented on 2022-04-29 14:48 (UTC)

Waiting for upstream to suggest ways to install the new version; see https://github.com/Bioconductor/Rsamtools/issues/36

dviktor commented on 2022-01-17 20:13 (UTC)

I'm leaving maintenance and support for this package in favor of new repository. You can install pre-built packages from my repo

malacology commented on 2021-12-24 23:02 (UTC)

Ranges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -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' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -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' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -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 -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
/usr/bin/ld: can not find /usr/lib/R/library/Rhtslib/usrlib/libhts.a: no such file dor dir 
collect2: error:ld return 1
make: *** [/usr/share/R//make/shlib.mk:10:Rsamtools.so] error 1