installing SAMRI #102
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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. would 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: However, 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: After doing this, it might be advisable to first run: and only thereafter run: Let me know if there are further issues. We're happy to include such helpful tips in the README. |
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Dear @TheChymera
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Dear @salma1601 can you please paste the output of |
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Dear @TheChymera here is the output of
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Please uncomment one of the lines in If you encounter further issues, please consult the localization guide. In the end, Having said that, please enable the chymeric overlay as well (as described above). I am noticing now the newest SAMRI version in Gentoo Science is 0.2. That's pretty outdated, and we're running at 0.4 now. |
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Dear @TheChymera
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Dear @salma1601 , the relevant errors are contained within the |
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Dear @TheChymera , here is the log file |
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I see. This looks very much like a Gentoo Prefix system. Now that I re-read your original post, it appears that's what you meant by home. Sorry abut that, I thought you meant on your home computer :) That shouldn't be an issue. We have transitioned all our systems to full Gentoo, but we had prefix until a few months ago, and it worked, and should in any case continue to work. Can you try |
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@salma1601 what script did you use to set up the prefix installation? |
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@TheChymera I used the bootstrp-prefix.sh script https://gitweb.gentoo.org/repo/proj/prefix.git/plain/scripts/bootstrap-prefix.sh |
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@TheChymera I tried the |
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Hmmmmm... ok, so if you look at your error log this is related to a libexpat symbol. The issue seems to have cropped up a number of times (not on Gentoo, but on other distros), e.g. here: sqlmapproject/sqlmap#2194 . I am assuming something from your user config is confusing the prefixed system. Did you perhaps do some exotic edits to your user's Sorry for the inconvenience, and for not having a straight answer as I did to the initial problems, but Prefix is a bit of a special case. At any rate, don't worry, we'll get this up and running! |
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dear @TheChymera , thank you for your support ! You are right, I have changed my |
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@salma1601 good, we're making progress :) No, the dcmtk error is clearly a download issue. Can you reproduce this, or did your network maybe drop? I find it also curious that your system is trying to emerge What command are you using to get this error? |
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You are right! Actually it was a licence issue because I run the command Now the emerge fails at step 10 of 47 with |
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This is strange... nipy is complaining that it cannot find nibabel, but nibabel is listed as one of its dependencies, and should thus be already present. What does Not least of all, |
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@TheChymera licence is OK and this is the output of |
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so you have the newest version of nibabel already installed. Strange that nipy isn't finding it. Can you try importing it in the Python interpreter? |
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Yes I do have nibabel because I already use it with other nipy libraries. Here is the output of
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@salma1601 but I assume this is outside of Prefix? So the way Prefix works, is it creates its own system inside of From the output you pasted, this looks like nibabel from the parent system installation. Prefix can obviously not use this, because otherwise it would lead to significant confusion as to which packages are being used. If you get this output running |
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OK I understand better. Actually I have miniconda3 binaries added to my
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@salma1601 hm.... yes, looks like it's properly accessible now. The error message seems to come from the package's Maybe this is Python-version contingent (though, again, Portage should be handling all of this automatically, and based on your And please post the output of: |
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@TheChymera here are the outputs
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@salma1601 I see, something is quite obviously broken with the Python 2.7 installation of nibabel. It appears there is an extra runtime dependency, specific for python2.7, which I have failed to document. please check with |
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Now it is failing because of my |
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Dear @salma1601 as far as I can tell, this is not because of your own dcmtk, but because prefix detected the package wanted to install outside of the prefix. This is most likely due to the developer not having tested the package for prefix. We try to be careful about this sort of things, but as I said, Prefix is a bit of an edge case, and most developers do not use this functionality on their own machines. A quick search indicates that the guilty developer is.... me :-/ gentoo/gentoo@3494cfe I am working on updating this package, so it should be back in order soon. |
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@salma1601 I believe I have fixed it. Try running |
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@TheChymera I think you did fix it! Now failing for ANTs :) |
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It seems to nit find ITK. can you paste the output of: |
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@TheChymera the output of * dev-python/nuitka
Available versions: 0.6.0.6 0.6.2 0.6.4 0.6.5 {PYTHON_TARGETS="python2_7 python3_5 python3_6 python3_7"}
Homepage: https://www.nuitka.net
Description: Python to native compiler
* dev-tcltk/itk
Available versions: 3.4.1^t 4.0.0 4.0.1 4.1.0^t {test}
Homepage: http://incrtcl.sourceforge.net/
Description: Object Oriented Enhancements for Tcl/Tk
[I] sci-libs/itk [1]
Available versions: 5.0.1^p {debug doc examples fftw python review test vtkglue PYTHON_SINGLE_TARGET="python2_7 python3_5 python3_6 python3_7" PYTHON_TARGETS="python2_7 python3_5 python3_6 python3_7"}
Installed versions: 5.0.1^p(07:02:12 AM 12/08/2019)(-debug -doc -examples -fftw -python -review -test -vtkglue PYTHON_SINGLE_TARGET="python3_6 -python2_7 -python3_5 -python3_7" PYTHON_TARGETS="python2_7 python3_6 -python3_5 -python3_7")
Homepage: http://www.itk.org
Description: NLM Insight Segmentation and Registration Toolkit
* www-apache/mpm_itk
Available versions: 2.4.7_p4-r1 {KERNEL="linux"}
Homepage: http://mpm-itk.sesse.net/
Description: Run virtual hosts under separate users/groups
[1] "science" /home/salma/gentoo/var/db/repos/science
Found 4 matchesand the output of |
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Ok, I submitted a fix, you can try again :) |
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@TheChymera still failing :( |
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@salma1601 apologies, you need to get the fix first (via |
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it is still failing for ANTs, but apparently for another reason |
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@TheChymera any progress on this ? |
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@salma1601 sorry, I missed your previous reply. Hmmm.... what does say? |
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@TheChymera The folder salma@salma-Latitude-E7450 ~/gentoo $ ls /home/salma/gentoo/var/tmp/portage/sci-biology/ants-2.3.1_p20191013/image/usr
ls: cannot access '/home/salma/gentoo/var/tmp/portage/sci-biology/ants-2.3.1_p20191013/image/usr': No such file or directoryIt is located in salma@salma-Latitude-E7450 ~/gentoo $ ls /home/salma/gentoo/var/tmp/portage/sci-biology/ants-2.3.1_p20191013/image/home/salma/gentoo/usr/lib64/
ants
salma@salma-Latitude-E7450 ~/gentoo $ ls /home/salma/gentoo/var/tmp/portage/sci-biology/ants-2.3.1_p20191013/image/home/salma/gentoo/usr/
bin lib lib64 share
salma@salma-Latitude-E7450 ~/gentoo $ ls /home/salma/gentoo/var/tmp/portage/sci-biology/ants-2.3.1_p20191013/image/home/salma/gentoo/
usr |
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Hm... ok, this is a bit of stabbing in the dark on my part since I don't have a prefix, but I think I might have figured it out. Try: |
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failed :( |
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Oh, this is strange. The error you got previously was because the install command was confused about the directories. The error you get now seems to indicate a dependency is missing. Did you change anything else? Does |
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I restarted my laptop meanwhile, so I restarted the prefix and executed |
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* ERROR: sci-biology/ants-2.3.1_p20191013::science failed (configure phase):
* cmake failed
*
* Call stack:
* ebuild.sh, line 125: Called src_configure
* environment, line 2652: Called cmake-utils_src_configure
* environment, line 1123: Called die
* The specific snippet of code:
* "${CMAKE_BINARY}" "${cmakeargs[@]}" "${CMAKE_USE_DIR}" || die "cmake failed";
*
* If you need support, post the output of `emerge --info '=sci-biology/ants-2.3.1_p20191013::science'`,
* the complete build log and the output of `emerge -pqv '=sci-biology/ants-2.3.1_p20191013::science'`.
* The complete build log is located at '/home/salma/gentoo/var/tmp/portage/sci-biology/ants-2.3.1_p20191013/temp/build.log'.
* The ebuild environment file is located at '/home/salma/gentoo/var/tmp/portage/sci-biology/ants-2.3.1_p20191013/temp/environment'.
* Working directory: '/home/salma/gentoo/var/tmp/portage/sci-biology/ants-2.3.1_p20191013/work/ants-2.3.1_p20191013_build'
* S: '/home/salma/gentoo/var/tmp/portage/sci-biology/ants-2.3.1_p20191013/work/ants-2.3.1_p20191013'
>>> Failed to emerge sci-biology/ants-2.3.1_p20191013, Log file:
>>> '/home/salma/gentoo/var/tmp/portage/sci-biology/ants-2.3.1_p20191013/temp/build.log'
* Messages for package sci-biology/ants-2.3.1_p20191013:
* ERROR: sci-biology/ants-2.3.1_p20191013::science failed (configure phase):
* cmake failed
*
* Call stack:
* ebuild.sh, line 125: Called src_configure
* environment, line 2652: Called cmake-utils_src_configure
* environment, line 1123: Called die
* The specific snippet of code:
* "${CMAKE_BINARY}" "${cmakeargs[@]}" "${CMAKE_USE_DIR}" || die "cmake failed";
*
* If you need support, post the output of `emerge --info '=sci-biology/ants-2.3.1_p20191013::science'`,
* the complete build log and the output of `emerge -pqv '=sci-biology/ants-2.3.1_p20191013::science'`.
* The complete build log is located at '/home/salma/gentoo/var/tmp/portage/sci-biology/ants-2.3.1_p20191013/temp/build.log'.
* The ebuild environment file is located at '/home/salma/gentoo/var/tmp/portage/sci-biology/ants-2.3.1_p20191013/temp/environment'.
* Working directory: '/home/salma/gentoo/var/tmp/portage/sci-biology/ants-2.3.1_p20191013/work/ants-2.3.1_p20191013_build'
* S: '/home/salma/gentoo/var/tmp/portage/sci-biology/ants-2.3.1_p20191013/work/ants-2.3.1_p20191013' |
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@salma1601 as usual, could you please paste the actual build log (path is listed on the fourth line from the bottom in the output you just pasted: |
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@TheChymera sorry, here it is |
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Ok, so it seems it's looking for GCC on your parent system: In addition, where did you find the instructions to run |
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)
required by sci-libs/nipype-1.1.1-r1::science[python_targets_python3_6]
required by sci-biology/samri-0.2::science
required by samri (argument)
required by media-gfx/graphviz-2.42.3::gentoo
required by sci-biology/fsl-5.0.11::science
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)
required by sci-biology/samri-0.2::science[atlases]
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:
A copy of the 'OFFIS' license is located at '/home/salma/gentoo/var/db/repos/gentoo/licenses/OFFIS'.
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:
(dependency required by "sci-libs/scikits_learn-0.19.0-r1::gentoo" [ebuild])
(dependency required by "sci-biology/nilearn-0.5.2::science" [ebuild])
(dependency required by "sci-biology/samri-0.2::science" [ebuild])
(dependency required by "samri" [argument])_
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