Installation fails about fineradstructure HOT 7 CLOSED

I had the same error as Marissa89 when cloning with git but was able to complete the make by installing from the zip file. Issue solved, but mystery remains. What's the difference?

from fineradstructure.

Hello

I am also having problems but with the config, here is the error

configure: error: could not find required version of GSL

from fineradstructure.

Marisa89, did you download the zip file of the repository or clone it with git?

from fineradstructure.

Hi guys,

as an alternative, you can install fineRADstructure with conda manager from Bioconda channel. It worked for me just fine.

I added the channel to my conda setup (see the link above), but you can also just use something like this:
conda install -c bioconda fineradstructure

Hope it helps ;)

from fineradstructure.

I'm on macosx. I set up the Bioconda channel as suggested but I get an error saying "The following packages are not available from current channels: fineradstructure". Not sure what's up. When I try installing by cloning from git or from the zip file, I get:

tom$ ./configure
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
/Applications/fineRADstructure-master/config/missing: Unknown --is-lightweight' option Try /Applications/fineRADstructure-master/config/missing --help' for more information
configure: WARNING: 'missing' script is too old or missing
checking for a thread-safe mkdir -p... config/install-sh -c -d
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for g++... g++
checking whether the C++ compiler works... no
configure: error: in /Applications/fineRADstructure-master': configure: error: C++ compiler cannot create executables See config.log' for more details

from fineradstructure.

@tommydevitt The setup you linked contains different order (priority) of channels as the current official website that I linked - it could cause e.g. unsupported version of C++ compiler to be installed. Also based on the presence of R channel, which has been dropped from official documentation some time ago I suspect the instructions you used are outdated.

You could for example try creating new environment and pulling packages from channels in the new order by using this command:

conda create --name fineradstr -c conda-forge -c bioconda fineradstructure

Then you activate the new environment with either source activate fineradstr or conda activate fineradstr, depending if you have set up conda init.

EDIT: According to anaconda.org there is actually no build of fineradstructure for macOS. You could try Virtualbox or something else, but I found the MCMC step of finestructure quite memory-intensive.

from fineradstructure.

@janxkoci You're right that there isn't a build for macOS. I also tried on our Linux server and couldn't get it to build using conda. But I was able to install a containerized version.

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