issue to use cget install -f requirements.txt #33
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You will need to install a more recent version of CMake (>= v3.2). Also, can you provide the output of |
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Also, were there more messages printed before the link error?
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Thanks a lot for quickly reply. My cget is 0.1.9 and cmake is 3.17.0. Will this be problematic? (raremetal) bash-4.2$ cget --version |
-- Build files have been written to: /hpc/hers_en/blin/program/raremetal/cget/cget/build/tmp-b229da5ccdc54d68a5061e4e967e3722/build -- Build files have been written to: /hpc/hers_en/blin/program/raremetal/cget/cget/build/tmp-a9f7201f83484bc6a5f2f225dc32176d/build An interface source of target "shrinkwrap" has a relative path. -- Configuring done -- Build files have been written to: /hpc/hers_en/blin/program/raremetal/cget/cget/build/tmp-884910bb46ab41d484c1f68859ef9332/build -- Build files have been written to: /hpc/hers_en/blin/program/raremetal/cget/cget/build/tmp-e96bd472ec46421b9bcb59929875cd52/build [100%] Built target hts -- Build files have been written to: /hpc/hers_en/blin/program/raremetal/cget/cget/build/tmp-740a7c191d914bcea41fbd94b354a442/build |
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Ok, can you try running |
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Still the same error: PackageNotInstalledError: Package is not installed in prefix. (raremetal) bash-4.2$ conda update cmake PackageNotInstalledError: Package is not installed in prefix. (raremetal) bash-4.2$ CMake suite maintained and supported by Kitware (kitware.com/cmake). Downloading https://github.com/statgen/savvy/archive/019a1ddaa9ec588f807f234f68787862f94ea057.tar.gz -- Build files have been written to: /hpc/hers_en/blin/program/raremetal/cget/cget/build/tmp-bf7e7b7a9340431a9b12cfedd42d373f/build |
I checked glibc version is 2.17 |
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I'm guessing the conda environment might be using an older c compiler. With the "raremetal" conda environment activated, please run: |
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Thanks a lot! (raremetal) bash-4.2$ /usr/bin/gcc --version (raremetal) bash-4.2$ cat /etc/os-release CENTOS_MANTISBT_PROJECT="CentOS-7" |
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Ok, I'm going to try to reproduce this on my end. I'll try to get back to you by tomorrow. |
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Thank you a lot for your time and effort!
I thought it beacuse glibc is not in conda list, so I installed it, and end with error again.
(raremetal) bash-4.2$ conda install -c fridh glibc
Collecting package metadata (current_repodata.json): done
Solving environment: done
## Package Plan ##
environment location: /hpc/hers_en/blin/program/miniconda3/envs/raremetal
added / updated specs:
- glibc
The following packages will be downloaded:
package | build
…---------------------------|-----------------
glibc-2.17 | 0 1.4 MB fridh
------------------------------------------------------------
Total: 1.4 MB
The following NEW packages will be INSTALLED:
glibc fridh/linux-64::glibc-2.17-0
The following packages will be UPDATED:
ca-certificates conda-forge::ca-certificates-2021.5.3~ --> pkgs/main::ca-certificates-2021.7.5-h06a4308_1
certifi conda-forge/linux-64::certifi-2019.11~ --> pkgs/main/noarch::certifi-2020.6.20-pyhd3eb1b0_3
openssl conda-forge::openssl-1.1.1k-h7f98852_0 --> pkgs/main::openssl-1.1.1l-h7f8727e_0
Proceed ([y]/n)? y
Downloading and Extracting Packages
glibc-2.17 | 1.4 MB | ############################################################################################## | 100%
Preparing transaction: done
Verifying transaction: done
(raremetal) bash-4.2$ cget install -DCMAKE_C_STANDARD=11 -f requirements.txt
/hpc/hers_en/blin/program/miniconda3/envs/raremetal/bin/python2.7: relocation error: /lib64/libm.so.6: symbol __strtold_nan, version GLIBC_PRIVATE not defined in file libc.so.6 with link time reference
From: Jonathon LeFaive ***@***.***>
Reply to: statgen/raremetal ***@***.***>
Date: Monday, 13 September 2021 at 18:12
To: statgen/raremetal ***@***.***>
Cc: "Lin-2, B. (Bochao)" ***@***.***>, Author ***@***.***>
Subject: Re: [statgen/raremetal] issue to use cget install -f requirements.txt (#33)
Ok, I'm going to try to reproduce this on my end. I'll try to get back to you by tomorrow.
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Seems like it's trying to link against two different versions of libc, maybe due to mixing conda channels? Not sure. Some of those things aren't necessary either I think in order to compile raremetal. edit: try Jonathon's commands below insteadconda create -n raremetal
conda activate raremetal
conda install -c conda-forge zlib cget fortran-compiler
cget install -f requirements.txt |
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Yes, the conda toolchains don't seem to be configured properly. I have successfully built raremetal on CentOS 7 using the system compilers (including /usr/bin/gfortran). You must first purge your existing "raremetal" conda environment to get rid of conda compilers. |
Thanks a lot!!! After I remove most of pcakges in the existing "raremetal" conda environment, I got following error message,a nd fixed it by install cxx-complier. Then the commend "cget install -f requirements.txt" works ok with many warning messages. Now i am stucked in command "cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_TOOLCHAIN_FILE=/hpc/hers_en/blin/program/raremetal/cget/cget/cget.cmake -DBUILD_TESTS=1 .. " with error message below: (raremetal) bash-4.2$ cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_TOOLCHAIN_FILE=/hpc/hers_en/blin/program/raremetal/cget/cget/cget.cmake -DBUILD_TESTS=1 .. -- Generating done (raremetal) bash-4.2$ cget install -f requirements.txt /usr/local/bin/g++. Call Stack (most recent call first): CMake Error: CMAKE_CXX_COMPILER not set, after EnableLanguage (raremetal) bash-4.2$$ conda install -c conda-forge cxx-compiler /hpc/hers_en/blin/program/miniconda3/envs/raremetal/bin/x86_64-conda_cos6-linux-gnu-cc. CMake Error: CMAKE_C_COMPILER not set, after EnableLanguage The "cget install -f requirements.txt" command works through with warning messgae, I copy paste below: CMake Warning: Successfully installed statgen/savvy -- Build files have been written to: /hpc/hers_en/blin/program/raremetal/cget/cget/build/tmp-8add768f44f84c4793d74f90c8488a8d/build In file included from SamRecord.h:24, -- Build files have been written to: /hpc/hers_en/blin/program/raremetal/cget/cget/build/tmp-0967359a7e0848988d2c9c35b1fc8f16/build |
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I'm having trouble following what you did and in what order you did it. Did you start off by running Alternatively, you could install a newer version of CMake from source and avoid conda entirely. If you see the line |
Thanks I followed the commends you provide one-by-one, and i could not install cget using pip3 . (raremetal) bash-4.2$ conda deactivate Remove all packages in environment /hpc/hers_en/blin/program/miniconda3/envs/raremetal: (base) bash-4.2$ conda create -n raremetal cmake # CMake is the only tool you'll need from conda Package Planenvironment location: /hpc/hers_en/blin/program/miniconda3/envs/raremetal added / updated specs: The following NEW packages will be INSTALLED: _libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge Proceed ([y]/n)? y Preparing transaction: done To activate this environment, use$ conda activate raremetalTo deactivate an active environment, use$ conda deactivate(base) bash-4.2$ conda list -n raremetal packages in environment at /hpc/hers_en/blin/program/miniconda3/envs/raremetal:Name Version Build Channel_libgcc_mutex 0.1 conda_forge conda-forge |
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Please try the attached raremetal executables. They should run on centos7 as long as the system developer tools are installed. |
Thanks, the executive program works well without any issue now! Thanks a lot again for all your effort to help me out!!! |
Dear sir or Madam,
i am new to this program, and i am not able to install rareworker sucessfully. It is so appreciated if you can help me went throughout with this.
$conda create -n raremetal r-base=3.6.1 r-essentials python=2.7
$conda activate raremetal
download & install depdence packages
$conda install -c hcc r-mathlib
$conda install -c conda-forge zlib
$conda install -c conda-forge cget
conda install -c conda-forge fortran-compiler
$cget install -f requirements.txt ## can not be sucessfully conducted
hpc/hers_en/blin/program/miniconda3/envs/raremetal/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: final link failed: nonrepresentable section on output
collect2: error: ld returned 1 exit status
gmake[2]: *** [sav] Error 1
gmake[1]: *** [CMakeFiles/sav.dir/all] Error 2
gmake: *** [all] Error 2
Command failed: ['/hpc/hers_en/blin/program/miniconda3/envs/raremetal/bin/cmake', '--build', '/hpc/hers_en/blin/program/raremetal/cget/cget/build/tmp-5814a2afe7274a3682f99f5bd0fb0530/build', '--config', 'Release', '--', '-j', '64']
Failed to build package statgen/savvy
alternative try to install requirements.txt using pip
$pip3 install -r requirements.txt
Invalid requirement: 'statgen/savvy@019a1ddaa9ec588f807f234f68787862f94ea057'
It looks like a path. Does it exist ?
alternative try to install statgen/savvy using conda or cget
$conda install -c conda-forge -c bioconda savvy
$cget install --prefix /hpc/hers_en/blin/program/raremetal statgen/savvy
$mkdir build && cd build
$cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_TOOLCHAIN_FILE=../cget/cget/cget.cmake -DBUILD_TESTS=1 ..
CMake Error at CMakeLists.txt:1 (cmake_minimum_required):
CMake 3.2 or higher is required. You are running version 2.8.12.2
-- Configuring incomplete, errors occurred!
(raremetal) bash-4.2$ make
make: *** No targets specified and no makefile found. Stop.
(raremetal) bash-4.
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