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millanek / Dsuite

Fast calculation of Patterson's D (ABBA-BABA) and the f4-ratio statistics across many populations/species
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Urgent help: Installing problem #18

Closed foala closed 4 years ago

foala commented 4 years ago

Hello, Thank you for this promising tool. I am excited to get all the D-statistics with vcf file alone.

I have been trying to compile it on a conda environment for two weeks now, but this kept failing. I installed gcc 4.9 (https://anaconda.org/serge-sans-paille/gcc_49) on a new condo environment, but I keep getting this error ./Build/Dsuite: /usr/lib64/libstdc++.so.6: versionGLIBCXX_3.4.21' not found (required by /Build/Dsuite). I tried installing newer gcc versions (5.5, 6, 7.2) all via conda, but I keep getting the same error. When I checked strings /usr/lib64/libstdc++.so.6 | grep GLIBCXX` I got

GLIBCXX_3.4
GLIBCXX_3.4.1
GLIBCXX_3.4.2
GLIBCXX_3.4.3
GLIBCXX_3.4.4
GLIBCXX_3.4.5
GLIBCXX_3.4.6
GLIBCXX_3.4.7
GLIBCXX_3.4.8
GLIBCXX_3.4.9
GLIBCXX_3.4.10
GLIBCXX_3.4.11
GLIBCXX_3.4.12
GLIBCXX_3.4.13
GLIBCXX_3.4.14
GLIBCXX_3.4.15
GLIBCXX_3.4.16
GLIBCXX_3.4.17
GLIBCXX_3.4.18
GLIBCXX_3.4.19
GLIBCXX_DEBUG_MESSAGE_LENGTH

Can you please assist. Your urgent response is highly appreciated. Thanks,

wheatwill commented 4 years ago

I got the same problem after I install GCC (version 10.1.0 ), My systerm GCC version is 4.8.0 )

[ligw@node100 gcc-10.1.0]$ strings /home/ligw/software/gcc-10.1.0/lib64/libstdc++.so.6 | grep GLIBC GLIBCXX_3.4 GLIBCXX_3.4.1 GLIBCXX_3.4.2 GLIBCXX_3.4.3 GLIBCXX_3.4.4 GLIBCXX_3.4.5 GLIBCXX_3.4.6 GLIBCXX_3.4.7 GLIBCXX_3.4.8 GLIBCXX_3.4.9 GLIBCXX_3.4.10 GLIBCXX_3.4.11 GLIBCXX_3.4.12 GLIBCXX_3.4.13 GLIBCXX_3.4.14 GLIBCXX_3.4.15 GLIBCXX_3.4.16 GLIBCXX_3.4.17 GLIBCXX_3.4.18 GLIBCXX_3.4.19 GLIBCXX_3.4.20 GLIBCXX_3.4.21 GLIBCXX_3.4.22 GLIBCXX_3.4.23 GLIBCXX_3.4.24 GLIBCXX_3.4.25 GLIBCXX_3.4.26 GLIBCXX_3.4.27 GLIBCXX_3.4.28 GLIBC_2.2.5 GLIBC_2.3 GLIBC_2.14 GLIBC_2.6 GLIBC_2.4 GLIBC_2.16 GLIBC_2.17 GLIBC_2.3.2

[ligw@node100 gcc-10.1.0]$ strings /lib64/libstdc++.so.6 | grep GLIBC GLIBCXX_3.4 GLIBCXX_3.4.1 GLIBCXX_3.4.2 GLIBCXX_3.4.3 GLIBCXX_3.4.4 GLIBCXX_3.4.5 GLIBCXX_3.4.6 GLIBCXX_3.4.7 GLIBCXX_3.4.8 GLIBCXX_3.4.9 GLIBCXX_3.4.10 GLIBCXX_3.4.11 GLIBCXX_3.4.12 GLIBCXX_3.4.13 GLIBCXX_3.4.14 GLIBCXX_3.4.15 GLIBCXX_3.4.16 GLIBCXX_3.4.17 GLIBCXX_3.4.18 GLIBCXX_3.4.19 GLIBC_2.3 GLIBC_2.2.5 GLIBC_2.14 GLIBC_2.4 GLIBC_2.3.2 GLIBCXX_DEBUG_MESSAGE_LENGTH

wheatwill commented 4 years ago

I had fixed this issue. I add the new version gcc library into the LD_LIBRARY_PATH in the upset of the systerm gcc library. The fellow is my setting.

LD_LIBRARY_PATH=/home/ligw/software/gcc-10.1.0/lib64:/home/ligw/software/gcc-10.1.0:/home/ligw/software/mpc-1.0.2/lib:/home/ligw/software/gmp-5.0.1/lib:/home/ligw/software/mpfr-3.1.2/lib:/home/ligw/lib/isl/lib:/home/ligw/lib/isl:$LD_LIBRARY_PATH:/public/home/ligw/lib:/public/home/ligw/lib64 export LD_LIBRARY_PATH