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| RE: nonlinearTseries.so: undefined symbol: _ZTIN4Rcpp7RObjectE prevents install RHRV [ Reply ] By: Michael Youngblood on 2016-02-14 00:45 | [forum:42936] |
| Fixed by loading the Rcpp package first | |
| nonlinearTseries.so: undefined symbol: _ZTIN4Rcpp7RObjectE prevents install RHRV [ Reply ] By: Michael Youngblood on 2016-02-13 22:00 | [forum:42934] |
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Ubuntu 14.04.3 LTS running headless R version 3.2.3 (2015-12-10) -- "Wooden Christmas-Tree" Platform: x86_64-pc-linux-gnu (64-bit) RHRV is not loaded because there is some kind of issue with the nonlinearTseries package that RHRV needs nonlinearTseries will build and create a shared object file, but has some sort of symbol issue Error in dyn.load("/usr/local/lib/R/site-library/nonlinearTseries/libs/nonlinearTseries.so") : unable to load shared object '/usr/local/lib/R/site-library/nonlinearTseries/libs/nonlinearTseries.so': /usr/local/lib/R/site-library/nonlinearTseries/libs/nonlinearTseries.so: undefined symbol: _ZTIN4Rcpp7RObjectE Execution halted root@8783b266b006:/nonlinearTseries/src# R CMD ldd /usr/local/lib/R/site-library/nonlinearTseries/libs/nonlinearTseries.so linux-vdso.so.1 => (0x00007ffd94f15000) libR.so => /usr/lib/R/lib/libR.so (0x00007f2564250000) libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007f2563f4c000) libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f2563c3b000) libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f2563a25000) libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f2563660000) libblas.so.3 => /usr/lib/libblas.so.3 (0x00007f2561e56000) libreadline.so.6 => /lib/x86_64-linux-gnu/libreadline.so.6 (0x00007f2561c10000) libpcre.so.3 => /lib/x86_64-linux-gnu/libpcre.so.3 (0x00007f25619d2000) liblzma.so.5 => /lib/x86_64-linux-gnu/liblzma.so.5 (0x00007f25617af000) libbz2.so.1.0 => /lib/x86_64-linux-gnu/libbz2.so.1.0 (0x00007f256159f000) libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f2561386000) librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f256117d000) libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f2560f79000) libgomp.so.1 => /usr/lib/x86_64-linux-gnu/libgomp.so.1 (0x00007f2560d6a000) libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f2560b4b000) /lib64/ld-linux-x86-64.so.2 (0x000055de87dcf000) libtinfo.so.5 => /lib/x86_64-linux-gnu/libtinfo.so.5 (0x00007f2560922000) Note that from the ldd review that all dependent libraries are available. I verified that all were installed and available on the system. root@8783b266b006:/nonlinearTseries/src# ls /lib64/ld-linux-x86-64.so.2 /lib64/ld-linux-x86-64.so.2 root@8783b266b006:/nonlinearTseries/src# ls /usr/lib/R/lib/libR.so /usr/lib/R/lib/libR.so root@8783b266b006:/nonlinearTseries/src# ls -la /lib64/ld-linux-x86-64.so.2 lrwxrwxrwx 1 root root 32 Feb 25 2015 /lib64/ld-linux-x86-64.so.2 -> /lib/x86_64-linux-gnu/ld-2.19.so root@8783b266b006:/nonlinearTseries/src# ls /usr/lib/x86_64-linux-gnu/libstdc++.so.6 /usr/lib/x86_64-linux-gnu/libstdc++.so.6 root@8783b266b006:/nonlinearTseries/src# ls -la /usr/lib/x86_64-linux-gnu/libstdc++.so.6 lrwxrwxrwx 1 root root 19 Jan 27 06:30 /usr/lib/x86_64-linux-gnu/libstdc++.so.6 -> libstdc++.so.6.0.19 root@8783b266b006:/nonlinearTseries/src# ls -la /lib/x86_64-linux-gnu/libm.so.6 lrwxrwxrwx 1 root root 12 Feb 25 2015 /lib/x86_64-linux-gnu/libm.so.6 -> libm-2.19.so root@8783b266b006:/nonlinearTseries/src# ls -la /lib/x86_64-linux-gnu/libgcc_s.so.1 -rw-r--r-- 1 root root 90160 Nov 25 00:02 /lib/x86_64-linux-gnu/libgcc_s.so.1 root@8783b266b006:/nonlinearTseries/src# ls -la /lib/x86_64-linux-gnu/libc.so.6 lrwxrwxrwx 1 root root 12 Feb 25 2015 /lib/x86_64-linux-gnu/libc.so.6 -> libc-2.19.so root@8783b266b006:/nonlinearTseries/src# ls -la /usr/lib/libblas.so.3 lrwxrwxrwx 1 root root 30 Feb 13 10:58 /usr/lib/libblas.so.3 -> /etc/alternatives/libblas.so.3 root@8783b266b006:/nonlinearTseries/src# ls -la /lib/x86_64-linux-gnu/libreadline.so.6 lrwxrwxrwx 1 root root 18 Mar 28 2014 /lib/x86_64-linux-gnu/libreadline.so.6 -> libreadline.so.6.3 root@8783b266b006:/nonlinearTseries/src# ls -la /lib/x86_64-linux-gnu/libpcre.so.3 lrwxrwxrwx 1 root root 17 Jul 24 2015 /lib/x86_64-linux-gnu/libpcre.so.3 -> libpcre.so.3.13.1 root@8783b266b006:/nonlinearTseries/src# ls -la /lib/x86_64-linux-gnu/liblzma.so.5 lrwxrwxrwx 1 root root 16 Feb 12 2014 /lib/x86_64-linux-gnu/liblzma.so.5 -> liblzma.so.5.0.0 root@8783b266b006:/nonlinearTseries/src# ls -la /lib/x86_64-linux-gnu/libbz2.so.1.0 lrwxrwxrwx 1 root root 15 Oct 21 2013 /lib/x86_64-linux-gnu/libbz2.so.1.0 -> libbz2.so.1.0.4 root@8783b266b006:/nonlinearTseries/src# ls -la /lib/x86_64-linux-gnu/libz.so.1 lrwxrwxrwx 1 root root 13 May 13 2013 /lib/x86_64-linux-gnu/libz.so.1 -> libz.so.1.2.8 root@8783b266b006:/nonlinearTseries/src# ls -la /lib/x86_64-linux-gnu/librt.so.1 lrwxrwxrwx 1 root root 13 Feb 25 2015 /lib/x86_64-linux-gnu/librt.so.1 -> librt-2.19.so root@8783b266b006:/nonlinearTseries/src# ls -la /lib/x86_64-linux-gnu/libdl.so.2 lrwxrwxrwx 1 root root 13 Feb 25 2015 /lib/x86_64-linux-gnu/libdl.so.2 -> libdl-2.19.so root@8783b266b006:/nonlinearTseries/src# ls -la /usr/lib/x86_64-linux-gnu/libgomp.so.1 lrwxrwxrwx 1 root root 16 Jan 27 06:35 /usr/lib/x86_64-linux-gnu/libgomp.so.1 -> libgomp.so.1.0.0 root@8783b266b006:/nonlinearTseries/src# ls -la /lib/x86_64-linux-gnu/libpthread.so.0 lrwxrwxrwx 1 root root 18 Feb 25 2015 /lib/x86_64-linux-gnu/libpthread.so.0 -> libpthread-2.19.so root@8783b266b006:/nonlinearTseries/src# ls -la /lib/x86_64-linux-gnu/libtinfo.so.5 lrwxrwxrwx 1 root root 15 Mar 22 2014 /lib/x86_64-linux-gnu/libtinfo.so.5 -> libtinfo.so.5.9 The linux-vdso.so.1 is a "library" that is injected into every process by the kernel. I cannot tell where the undefined symbol is coming from. Any ideas? I cannot install RHRV without this dependency. Thanks! |
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