Install from source fails

[Kotaro Tanaka]

Hi,

I encountered errors upon source installation in Ubuntu 18.04.

The commands are as follows:

# Old anaconda was already cleaned up
./Anaconda3-2019.10-Linux-x86_64.sh

source anaconda3/etc/profile.d/conda.sh

conda init bash

conda config --set auto_activate_base False

conda config --set auto_update_conda False

conda create -n eman2 eman-deps=16.1 cmake=3.14 boost=1.66 -c cryoem -c defaults -c conda-forge
# Error here

The error messages:

Collecting package metadata (current_repodata.json): done
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: |
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed
UnsatisfiableError: The following specifications were found to be incompatible with each other:


Package curl conflicts for:
cmake=3.14 -> curl[version='>=7.61.1,<8.0a0']
Package ncurses conflicts for:
cmake=3.14 -> ncurses[version='>=6.1,<6.2.0a0|>=6.1,<7.0a0']
Package libgcc-ng conflicts for:
cmake=3.14 -> libgcc-ng[version='>=7.3.0']
Package expat conflicts for:
cmake=3.14 -> expat[version='>=2.2.5,<2.3.0a0|>=2.2.6,<3.0a0']
Package bzip2 conflicts for:
cmake=3.14 -> bzip2[version='>=1.0.6,<2.0a0']
Package pyopengl conflicts for:
eman-deps=16.1 -> pyopengl=3.1.0
Package rhash conflicts for:
cmake=3.14 -> rhash[version='>=1.3.8,<2.0a0']
Package pyqt conflicts for:
eman-deps=16.1 -> pyqt=5
Package boost-cpp conflicts for:
boost=1.66 -> boost-cpp==1.66.0
Package zlib conflicts for:
cmake=3.14 -> zlib[version='>=1.2.11,<1.3.0a0']
Package numpy conflicts for:
boost=1.66 -> numpy[version='>=1.8']
Package python_abi conflicts for:
boost=1.66 -> python_abi=[build='*_cp36m|*_cp35m|*_cp27mu']
Package xz conflicts for:
cmake=3.14 -> xz[version='>=5.2.4,<5.3.0a0|>=5.2.4,<6.0a0']
Package eman-deps-cli conflicts for:
eman-deps=16.1 -> eman-deps-cli==16.1=1
Package libcurl conflicts for:
cmake=3.14 -> libcurl[version='>=7.64.0,<8.0a0']
Package python conflicts for:
boost=1.66 -> python[version='2.7.*|3.5.*|3.6.*']
Package libstdcxx-ng conflicts for:
cmake=3.14 -> libstdcxx-ng[version='>=7.3.0']
Package libuv conflicts for:
cmake=3.14 -> libuv

I have no idea what to do...

I will appreciate any suggestion, thanks.

Kotaro

[Steve Ludtke]

Hi Kotaro,

you must use the specific version of anaconda (actually Miniconda) linked from the source building instructions:

https://repo.continuum.io/miniconda/Miniconda3-4.6.14-Linux-x86_64.sh

While Anaconda is terrific in that they provide all of the packages you need as dependencies in a cross-platform compatible way, unfortunately they tend to have stability problems if you use the most up to date version. That is, any time you update all of your Anaconda packages to the most recent version, there are good odds that one or more packages will have some little glitch. They are pretty good about fixing things pretty quickly.

Anyway, we have adopted the strategy of picking one specific version of Anaconda and all dependencies which is known to work with a particular version of EMAN2 (eman-deps=16.1). This is where Anaconda's environment system comes into play. You can have one environment set up using eman-deps=16.1 for EMAN2.31 and another environment set up with eman-deps=21 for the current Python3 based development version, all within the same Anaconda install (using conda activate to switch among them)

--------------------------------------------------------------------------------------
Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine 
Charles C. Bell Jr., Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology                      (www.bcm.edu/biochem)
Academic Director, CryoEM Core                                        (cryoem.bcm.edu)
Co-Director CIBR Center                                    (www.bcm.edu/research/cibr)

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[Kotaro Tanaka]

Hi, 

Thank you for the solution and the information! Now I understand.

Kotaro

2020年2月27日木曜日 22時01分31秒 UTC+9 Steve Ludtke:

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[Grant Ludlam]

Hi I am getting a similar error, but I am using miniconda3/4.6.14

-bash-4.2$ ml miniconda3/4.6 

-bash-4.2$ echo $PATH

/apps/miniconda3/4.6.14/bin:/apps/patchelf/0.9/gcc-6.4.0/bin:/zhome/pianonan/software/cryosparc/cryosparc2_master/bin:/zhome/pianonan/software/cryosparc/cryosparc2_master/deps/external/mongodb/bin:/zhome/pianonan/software/cryosparc/cryosparc2_master/deps/anaconda/bin:/zhome/pianonan/software/cryosparc/cryosparc2_master/bin:/zhome/pianonan/software/cryosparc/cryosparc2_master/deps/anaconda/bin:/zhome/pianonan/software/cryosparc/cryosparc2_master/bin:/apps/openmpi/3.0.0/gcc-6.4.0/bin:/apps/gdb/8.1/gcc-6.4.0/bin:/apps/gcc/6.4.0/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/opt/ganglia/bin:/opt/ganglia/sbin:/opt/ibutils/bin:/usr/java/latest/bin:/opt/rocks/bin:/opt/rocks/sbin:/opt/dell/srvadmin/bin:~/software/relion/bin

-bash-4.2$ echo $LD_LIBRARY_PATH

-bash-4.2$ echo $PYTHONPATH

-bash-4.2$ source /apps/miniconda3/4.6.14/etc/profile.d/conda.sh 

-bash-4.2$ conda config --set auto_activate_base False

-bash-4.2$ conda config --set auto_update_conda False

-bash-4.2$ conda create -n eman2 eman-deps=16.1 cmake=3.14 boost=1.66 -c cryoem -c defaults -c conda-forge

Collecting package metadata (current_repodata.json): done

Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.

Collecting package metadata (repodata.json): done

Solving environment: | 

Found conflicts! Looking for incompatible packages.

This can take several minutes.  Press CTRL-C to abort.

failed                                                                          

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Package numpy conflicts for:

boost=1.66 -> numpy[version='>=1.8']

Package expat conflicts for:

cmake=3.14 -> expat[version='>=2.2.5,<2.3.0a0|>=2.2.6,<3.0a0']

Package ncurses conflicts for:

cmake=3.14 -> ncurses[version='>=6.1,<6.2.0a0|>=6.1,<7.0a0']

Package bzip2 conflicts for:

cmake=3.14 -> bzip2[version='>=1.0.6,<2.0a0']

Package rhash conflicts for:

cmake=3.14 -> rhash[version='>=1.3.8,<2.0a0']

Package xz conflicts for:

cmake=3.14 -> xz[version='>=5.2.4,<5.3.0a0|>=5.2.4,<6.0a0']

Package python conflicts for:

boost=1.66 -> python[version='2.7.*|3.5.*|3.6.*']

Package python_abi conflicts for:

boost=1.66 -> python_abi=[build='*_cp27mu|*_cp35m|*_cp36m']

Package libcurl conflicts for:

cmake=3.14 -> libcurl[version='>=7.64.0,<8.0a0']

Package boost-cpp conflicts for:

boost=1.66 -> boost-cpp==1.66.0

Package pyopengl conflicts for:

eman-deps=16.1 -> pyopengl=3.1.0

Package curl conflicts for:

cmake=3.14 -> curl[version='>=7.61.1,<8.0a0']

Package libstdcxx-ng conflicts for:

cmake=3.14 -> libstdcxx-ng[version='>=7.3.0']

Package zlib conflicts for:

cmake=3.14 -> zlib[version='>=1.2.11,<1.3.0a0']

Package libgcc-ng conflicts for:

cmake=3.14 -> libgcc-ng[version='>=7.3.0']

Package pyqt conflicts for:

eman-deps=16.1 -> pyqt=5

Package libuv conflicts for:

cmake=3.14 -> libuv

Package eman-deps-cli conflicts for:

eman-deps=16.1 -> eman-deps-cli==16.1=1

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[Steve Ludtke]

Hi Grant,

maybe Tunay can comment. Occasionally we run into brief periods of time where there is an internal version conflict within Anaconda (usually impacting specific combinations). These are generally resolved quickly when someone notices/reports (by Anaconda, not us). 

Personally at this point I would suggest switching to a Python 3 environment. We are getting very close now, I think, to having a Python 3 release. We still occasionally find a small bug in EMAN2/Py3, but all of the major programs/pipelines are working well. Indeed, particularly in the tomography pipeline, you will find some major improvements since the release last fall.  If you are using SPARX/SPHIRE, I can't comment on their current state in Py3.

--------------------------------------------------------------------------------------
Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine 

Charles C. Bell Jr., Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology                      (www.bcm.edu/biochem)

Academic Director, CryoEM Core                                        (cryoem.bcm.edu)
Co-Director CIBR Center                                    (www.bcm.edu/research/cibr)

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[shadow walker]

Grant,

Are you sure your conda version is 4.6.14? Run "conda info" or "conda -V".

To view this discussion on the web visit https://groups.google.com/d/msgid/eman2/C858C431-08E0-4543-A1B5-3F9E6C8753B9%40gmail.com.

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shadow_walker