TheChymera
commented
4 years ago Dear @salma1601 thank you so much for giving our pipeline package a try!
Of course we recommend using Gentoo, but it's not a prerequisite. It's just what we decided to use on all our servers at the ETH and UZH in Zurich, because it works so well for scientific software. Other labs have reported using the pipelines in Ubuntu.
Regarding your current issue, it is standard policy for Gentoo to prompt you if an installation requires configuration changes to your system. You simply need to accept them.
emerge -v samri --autounmask-continuewould do this automatically.
I notice there is also a license issue. This is a feature of Gentoo allowing you to select what licenses are acceptable for your work. Assuming you are doing academic work, under fair use policy (and barring constraints of your institute), you can do:
echo 'ACCEPT_LICENSE="*"' >> /etc/portage/make.confHowever, since we use a lot of cutting-edge software versions, in order to best get comparability with our work, it might be best to get the very newest versions of packages by also enabling the Chymeric Overlay (these new versions will also be included in Gentoo Science, but that usually takes a few weeks), and enabling all “unstable” versions.
After installing the overlay, do:
echo 'ACCEPT_KEYWORDS="~amd64"' >> /etc/portage/make.confAfter doing this, it might be advisable to first run:
emerge --sync
emerge -vaDNu world #(this updates your system to use unstable versions)and only thereafter run:
emerge -v samri --autounmask-continueLet me know if there are further issues. We're happy to include such helpful tips in the README.
salma1601
Dear SAMRI experts,
I am trying to install SAMRI. I installed gentoo in my home, installed the overlay science in
/home/salma/gentoo/var/db/reposand tried to emerge samri but I am getting the following errorThe following USE changes are necessary to proceed: (see "package.use" in the portage(5) man page for more details)
required by sci-libs/scipy-1.1.0::gentoo
required by dev-python/bottleneck-1.2.1::gentoo
required by dev-python/pandas-0.24.2::gentoo[-minimal]
required by dev-python/seaborn-0.9.0::gentoo
required by sci-biology/samri-0.2::science
required by samri (argument)
=dev-python/numpy-1.16.5 lapack
required by sci-libs/nipype-1.1.1-r1::science[python_targets_python2_7]
required by sci-biology/samri-0.2::science
required by samri (argument)
The following license changes are necessary to proceed: (see "package.license" in the portage(5) man page for more details)
required by sci-biology/samri-0.2::science
required by samri (argument)
Use --autounmask-write to write changes to config files (honoring CONFIG_PROTECT). Carefully examine the list of proposed changes, paying special attention to mask or keyword changes that may expose experimental or unstable packages.
!!! The following updates are masked by LICENSE changes:
For more information, see the MASKED PACKAGES section in the emerge man page or refer to the Gentoo Handbook.
emerge: there are no ebuilds built with USE flags to satisfy "dev-python/numpy[lapack,python_targets_python2_7(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,python_targets_python3_7(-)?,-python_single_target_python2_7(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-),-python_single_target_python3_7(-)]". !!! One of the following packages is required to complete your request: