![]() I am experiencing the same problems ( multiple definition ofGC_jmp_buf'`) using R 4.1, BioC 3.13, msa 1.24.0 on Linux. Loaded via a namespace (and not attached): stats graphics grDevices utils datasets methods base LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C LC_MESSAGES=en_GB.UTF-8 LC_PAPER=en_GB.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 LC_MONETARY=en_GB.UTF-8 # please also include the results of running the following in an R sessionīLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0 # include your problematic code here with any corresponding output Installation of package ‘msa’ had non-zero exit status Make: *** Error 2ĮRROR: compilation failed for package ‘msa’ Make: Leaving directory '/tmp/RtmpvJZCmu/R.INSTALL115a2557e82aa/msa/src/gc-7.2' libs/allchblk.o:/tmp/RtmpvJZCmu/R.INSTALL115a2557e82aa/msa/src/gc-7.2/./include/private/gc_priv.h:2328: first defined hereĬollect2: error: ld returned 1 exit status libs/mach_dep.o:/tmp/RtmpvJZCmu/R.INSTALL115a2557e82aa/msa/src/gc-7.2/./include/private/gc_priv.h:2328: multiple definition of `GC_jmp_buf'. libs/allchblk.o:/tmp/RtmpvJZCmu/R.INSTALL115a2557e82aa/msa/src/gc-7.2/./include/private/gc_priv.h:2328: first defined here libs/pthread_stop_world.o:/tmp/RtmpvJZCmu/R.INSTALL115a2557e82aa/msa/src/gc-7.2/./include/private/gc_priv.h:2328: multiple definition of `GC_jmp_buf'. Libs/allchblk.o:/tmp/RtmpvJZCmu/R.INSTALL115a2557e82aa/msa/src/gc-7.2/./include/private/gc_priv.h:2328: first defined here usr/include/assert.h:50: note: this is the location of the previous definitionĥ0 | # define assert(expr) (_ASSERT_VOID_CAST (0))Įverything goes well until this point. In file included from /usr/include/c++/10/cassert:44,įrom /home/doctoras/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include/Rcpp/utils/tinyformat/tinyformat.h:137,įrom /home/doctoras/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include/Rcpp/utils/tinyformat.h:40,įrom /home/doctoras/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include/RcppCommon.h:70,įrom /home/doctoras/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include/Rcpp.h:27,įrom. Muscle/muscle.h:54: warning: "assert" redefined fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c R_init_msa.cpp -o R_init_msa.o Any ideas why this happens? BiocManager::install("msa")īioconductor version 3.12 (BiocManager 1.30.10), R 4.0.2 ()Ĭontent type 'application/x-gzip' length 3767128 bytes (3.6 MB) ![]() I had some issues too on windows enviroment but I managed to resolve these. ![]() Libhdf5_hl.so.These last days I'm trying to install the msa package to perform a multiple sequence alignment on my computer. Unable to load shared object '/home/site-library/hdf5r/libs/hdf5r.so': ** testing if installed package can be loadedĮrror: package or namespace load failed for 'hdf5r' in dyn.load(file, DLLpath = DLLpath. ![]() Installing to /home/site-library/hdf5r/libs lhdf5_hl -lhdf5 -lz -lm -L/usr/lib/R/lib -lR `g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o hdf5r.so const_export.o datatype_export.o Wrapper_auto_H5A.o Wrapper_auto_H5.o Wrapper_auto_H5D.o Wrapper_auto_H5DS.o Wrapper_auto_H5E.o Wrapper_auto_H5F.o Wrapper_auto_H5G.o Wrapper_auto_H5I.o Wrapper_auto_H5IM.o Wrapper_auto_H5L.o Wrapper_auto_H5LT.o Wrapper_auto_H5O.o Wrapper_auto_H5P.o Wrapper_auto_H5R.o Wrapper_auto_H5S.o Wrapper_auto_H5TB.o Wrapper_auto_H5T.o Wrapper_auto_H5Z.o Wrapper_auto_H5FDcore.o Wrapper_auto_H5FDfamily.o Wrapper_auto_H5FDlog.o Wrapper_auto_H5FDsec2.o Wrapper_auto_H5FDstdio.o convert.o hdf5r_init.o H5Error.o H5ls.o Wrapper_manual_H5T.o -L/home/jgalkows/anaconda3/lib -L. ![]()
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