Error in installation

Question

Error in installation

HLHsieh opened this issue 2 years ago · comments

Hi there,

I am trying to use DeepRepeat, and I tried to install DeepRepeat via conda.

After typing the following code
h5c++ -O3 -std=c++11 -I $DR_conda_base/include -L$DR_conda_base/lib -lhts -o genomic1FE ComFunction.c ComOption.c BamReader.c Fast5Index.c Fast5Reader.c RepeatFeatExtract.c genomic1FE.c $DR_conda_base//lib/libhdf5_hl_cpp.a $DR_conda_base//lib/libhdf5_cpp.a $DR_conda_base//lib/libhdf5_hl.a $DR_conda_base//lib/libhdf5.a -lz -ldl -lpthread

I got the following error:

/home/miniconda3/envs/py36deeprepeat/bin/../lib/gcc/x86_64-conda-linux-gnu/7.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/miniconda3/envs/py36deeprepeat//lib/libstdc++.so: undefined reference to 'memcpy@GLIBC_2.14'
/home/miniconda3/envs/py36deeprepeat/bin/../lib/gcc/x86_64-conda-linux-gnu/7.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/miniconda3/envs/py36deeprepeat//lib/libstdc++.so: undefined reference to 'aligned_alloc@GLIBC_2.16'
/home/miniconda3/envs/py36deeprepeat/bin/../lib/gcc/x86_64-conda-linux-gnu/7.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/miniconda3/envs/py36deeprepeat//lib/libstdc++.so: undefined reference to 'clock_gettime@GLIBC_2.17'
collect2: error: ld returned 1 exit status

I would appreciate it if there is any tips to fix it.
Thank you!

Kai Wang · Answer 1 · Thu Mar 16 2023 22:31:30 GMT+0800 (China Standard Time)

try conda install glibc to see if it works.

…

On Thu, Mar 16, 2023 at 2:35 AM HLHsieh ***@***.***> wrote: Hi there, I am trying to use DeepRepeat, and I tried to install DeepRepeat via conda. After typing the following code h5c++ -O3 -std=c++11 -I $DR_conda_base/include -L$DR_conda_base/lib -lhts -o genomic1FE ComFunction.c ComOption.c BamReader.c Fast5Index.c Fast5Reader.c RepeatFeatExtract.c genomic1FE.c $DR_conda_base//lib/libhdf5_hl_cpp.a $DR_conda_base//lib/libhdf5_cpp.a $DR_conda_base//lib/libhdf5_hl.a $DR_conda_base//lib/libhdf5.a -lz -ldl -lpthread I got the following error: /home/hsinlun/miniconda3/envs/py36deeprepeat/bin/../lib/gcc/x86_64-conda-linux-gnu/7.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/hsinlun/miniconda3/en vs/py36deeprepeat//lib/libstdc++.so: undefined reference to ***@***.***_2.14' /home/hsinlun/miniconda3/envs/py36deeprepeat/bin/../lib/gcc/x86_64-conda-linux-gnu/7.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/hsinlun/miniconda3/en vs/py36deeprepeat//lib/libstdc++.so: undefined reference to ***@***.***_2.16' /home/hsinlun/miniconda3/envs/py36deeprepeat/bin/../lib/gcc/x86_64-conda-linux-gnu/7.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/hsinlun/miniconda3/en vs/py36deeprepeat//lib/libstdc++.so: undefined reference to ***@***.***_2.17' collect2: error: ld returned 1 exit status I would appreciate it if there is any tips to fix it. Thank you! — Reply to this email directly, view it on GitHub <#12>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNG3OGXMDN6JBJYLFB2SCTW4KYBXANCNFSM6AAAAAAV4Y6NBU> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

HLHsieh · Answer 2 · Fri Mar 17 2023 00:02:40 GMT+0800 (China Standard Time)

Hi @kaichop,

Thanks for your timely response. I have tried conda install -c rmg glibc. Unfortunately, it did not work, and I got other error message as follows

/home/miniconda3/envs/py36deeprepeat/bin/h5c++: line 304: 2860677 Segmentation fault (core dumped) /home/miniconda3/envs/py36deeprepeat/bin/x86_64-conda_cos6-linux-gnu-c++ -I/home/miniconda3/envs/py36deeprepeat/include -I/home/miniconda3/envs/py36deeprepeat/include -D_FORTIFY_SOURCE=2 -O2 -fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -c -O3 -std=c++11 -I /home/miniconda3/envs/py36deeprepeat//include -L/home/miniconda3/envs/py36deeprepeat//lib ComFunction.c ComOption.c BamReader.c Fast5Index.c Fast5Reader.c RepeatFeatExtract.c genomic1FE.c

liuqianhn · Answer 3 · Fri Mar 17 2023 01:17:13 GMT+0800 (China Standard Time)

@HLHsieh which glibc version do you use? You can also try to use gxx_linux-64=7.5 rather than gxx_linux-64 during the installation of virtual environment.

HLHsieh · Answer 4 · Fri Mar 17 2023 03:58:16 GMT+0800 (China Standard Time)

Hi @liuqianhn,

Thanks for your prompt response. I have used gxx_linux-64=7.5 during the installation of virtual environment as like you predefined in environment.yml. The glibc version is 2.19.

Best Regards,
Hsin

liuqianhn · Answer 5 · Fri Mar 17 2023 07:35:47 GMT+0800 (China Standard Time)

@HLHsieh It is weird. Could you please share what is your output for the commands below
ldd --version
strings /home/miniconda3/envs/py36deeprepeat//lib/libstdc++.so | grep GLIBC
ldd strings /home/miniconda3/envs/py36deeprepeat//lib/libstdc++.so

By the way, are you able to use docker version? Thanks.

HLHsieh · Answer 6 · Fri Mar 17 2023 08:16:18 GMT+0800 (China Standard Time)

Hi @liuqianhn,

ldd --version
It returned

ldd (GNU libc) 2.19
Copyright (C) 2014 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
Written by Roland McGrath and Ulrich Drepper.

strings /home/miniconda3/envs/py36deeprepeat//lib/libstdc++.so | grep GLIBC
It returned a bunch of stuff, and I attached it here output.txt.

ldd strings /home/miniconda3/envs/py36deeprepeat//lib/libstdc++.so
It returned

strings:
ldd: ./strings: No such file or directory
/home/miniconda3/envs/py36deeprepeat//lib/libstdc++.so:
        not a dynamic executable

I have not tried docker version since I am not familiar with docker. I will try it if necessary.

Thank you,
Hsin

liuqianhn · Answer 7 · Fri Mar 17 2023 14:43:13 GMT+0800 (China Standard Time)

@HLHsieh Thank you for sharing. My apologies: the last command is ldd /home/miniconda3/envs/py36deeprepeat//lib/libstdc++.so

HLHsieh · Answer 8 · Fri Mar 17 2023 22:17:30 GMT+0800 (China Standard Time)

Hi @liuqianhn

ldd /home/miniconda3/envs/py36deeprepeat//lib/libstdc++.so returned

        not a dynamic executable

HLHsieh · Answer 9 · Tue Mar 28 2023 04:02:11 GMT+0800 (China Standard Time)

Hi there,

I still can’t install it, so I used docker instead.