c -o faidx.o faidx.cĪr -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 BiocManager_1.30.4 compiler_3.6.0 tools_3.6.0Ĭan you show more of the compilation, of both Rhtslib and Rsamtools? In particular I see (looking for compilation of faidx.c, and generation of libraries) > BiocManager::install("Rhtslib") Loaded via a namespace (and not attached): stats graphics grDevices utils datasets methods base LC_MEASUREMENT=cs_CZ.UTF-8 LC_IDENTIFICATION=C LC_MONETARY=cs_CZ.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LAPACK: /usr/lib/lapack/liblapack.so.3.6.0 * removing ‘/home/kubovcij/R/x86_64-pc-linux-gnu-library/3.6/Rsamtools’ home/kubovcij/R/x86_64-pc-linux-gnu-library/3.6/00LOCK-Rsamtools/00new/Rsamtools/libs/Rsamtools.so: undefined symbol: faidx_fetch_seq2 Unable to load shared object '/home/kubovcij/R/x86_64-pc-linux-gnu-library/3.6/00LOCK-Rsamtools/00new/Rsamtools/libs/Rsamtools.so': ** testing if installed package can be loaded from temporary locationĮrror: package or namespace load failed for ‘Rsamtools’ in dyn.load(file, DLLpath = DLLpath. ** byte-compile and prepare package for lazy loading installing to /home/kubovcij/R/x86_64-pc-linux-gnu-library/3.6/00LOCK-Rsamtools/00new/Rsamtools/libs * installing *source* package ‘Rsamtools’. Any hint? > BiocManager::install('Rsamtools')īioconductor version 3.9 (BiocManager 1.30.4), R 3.6.0 ()Ĭontent type 'application/x-gzip' length 3032600 bytes (2.9 MB) Already tried this old post and changed RHOME/etc/Makeconf flags, but didn't help. No problem with Rsamtools in previous R version, local instalation of Rsamtools from source package v1.34.1 also worked fine in R 3.6.0. I have troubles installing Rsamtools on R 3.6.0 (Bioc 3.9) on ubuntu via both BiocManager::install() and source package (v1.99.6).
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