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installing SAMRI

Open salma1601 opened this issue 6 years ago • 46 comments

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/repos and tried to emerge samri but I am getting the following error

Calculating dependencies... done! [ebuild N ] dev-util/gperf-3.1 [ebuild N ] sci-biology/mouse-brain-atlases-0.5.3 USE="-hires" [ebuild N ] x11-misc/xbitmaps-1.1.2-r1 [ebuild N ] dev-util/re2c-1.2.1 USE="-debug" [ebuild N ] dev-libs/libpthread-stubs-0.4-r1 [ebuild N ] sys-devel/llvm-common-9.0.0 [ebuild N ] sys-apps/tcp-wrappers-7.6.28 USE="ipv6 (split-usr) -netgroups -static-libs" [ebuild N ] dev-libs/lzo-2.10 USE="(split-usr) -examples -static-libs" [ebuild N ] dev-lang/fpc-3.0.4 USE="-doc -ide -source" [ebuild N ] dev-util/boost-build-1.71.0 USE="-examples -python -test" PYTHON_TARGETS="python2_7" [ebuild N ] acct-group/input-0 [ebuild N ] acct-group/kvm-0 [ebuild N ] acct-group/render-0 [ebuild N ] media-fonts/liberation-fonts-2.00.5 USE="-X -fontforge" [ebuild N ] dev-util/byacc-20191125 [ebuild N ] dev-util/ninja-1.9.0 USE="-doc -emacs -test -vim-syntax" [ebuild N ] dev-python/backports-1.0 PYTHON_TARGETS="python2_7 python3_6 -pypy -pypy3 -python3_5 -python3_7 -python3_8" [ebuild N ] virtual/ttf-fonts-1-r1 [ebuild N ] sci-biology/bru2nii-1.0.20180303 USE="-gui" [ebuild N ] sci-libs/scikits-0.1-r2 USE="-examples" PYTHON_TARGETS="python2_7 python3_6 -pypy -python3_5 -python3_7" [ebuild N ] dev-python/mpmath-1.1.0 USE="-gmp -matplotlib -test" PYTHON_TARGETS="python2_7 python3_6 -python3_5 -python3_7" [ebuild N ] dev-python/ptyprocess-0.5.2 USE="-test" PYTHON_TARGETS="python2_7 python3_6 -pypy -pypy3 -python3_5 -python3_7 -python3_8" [ebuild N ] dev-python/functools32-3.2.3 PYTHON_TARGETS="python2_7 -pypy" [ebuild N ] dev-python/subprocess32-3.5.4 USE="-test" PYTHON_TARGETS="python2_7" [ebuild N ] sys-libs/e2fsprogs-libs-1.45.4 USE="(split-usr) -static-libs" [ebuild N ] dev-libs/fribidi-1.0.7 USE="-static-libs" [ebuild N ] dev-python/pexpect-4.6.0 USE="-doc -examples -test" PYTHON_TARGETS="python2_7 python3_6 -pypy -pypy3 -python3_5 -python3_7 -python3_8" [ebuild N ] media-fonts/stix-fonts-2.0.0 USE="-X" [ebuild N ] dev-python/sympy-1.3 USE="-doc -examples -gtk -imaging -ipython -latex -mathml -opengl -pdf -png -pyglet -symengine -test (-texmacs) -theano" PYTHON_TARGETS="python2_7 python3_6 -python3_5 -python3_7" [ebuild N ] dev-libs/boost-1.71.0 USE="bzip2 nls threads zlib -context -debug -doc -icu -lzma -mpi -numpy -python -static-libs -tools -zstd" PYTHON_TARGETS="python2_7 python3_6 -python3_5 -python3_7" [ebuild N ] dev-libs/gobject-introspection-common-1.60.2 [ebuild N ] media-libs/freetype-2.10.1 USE="adobe-cff bzip2 cleartype_hinting -X -bindist -debug -doc -fontforge -harfbuzz -infinality -png -static-libs -utils" [ebuild N ] media-libs/libpng-1.6.37 USE="-apng (-neon) -static-libs" CPU_FLAGS_X86="sse" [ebuild N ] media-libs/lcms-2.9 USE="threads -doc -jpeg -static-libs -test -tiff" [ebuild N ] dev-lang/swig-4.0.0 USE="pcre -ccache -doc" [ebuild N ] dev-libs/libbsd-0.10.0 USE="-static-libs" [ebuild N ] app-eselect/eselect-opengl-1.3.1-r4 [ebuild N ] virtual/fortran-0 USE="openmp" [ebuild N ] media-libs/netpbm-10.76.00 USE="zlib -X -doc -jbig -jpeg -png -postscript -rle -static-libs (-svga) -tiff -xml" CPU_FLAGS_X86="sse2" [ebuild N ] app-text/build-docbook-catalog-1.21 [ebuild N ] app-text/docbook-xsl-stylesheets-1.79.1-r2 USE="-ruby" [ebuild N ] sys-libs/binutils-libs-2.33.1 USE="nls -64-bit-bfd -multitarget -static-libs" [ebuild N ] dev-libs/elfutils-0.178 USE="bzip2 nls utils -lzma -static-libs -test (-threads) -valgrind" [ebuild N ] virtual/libelf-3 [ebuild N ] app-crypt/rhash-1.3.8 USE="nls ssl -debug -libressl -static-libs" [ebuild N ] dev-python/six-1.13.0 USE="-doc -test" PYTHON_TARGETS="python2_7 python3_6 -pypy -pypy3 -python3_5 -python3_7 -python3_8" [ebuild N ] dev-python/cython-0.29.14-r1 USE="-doc -emacs -test" PYTHON_TARGETS="python2_7 python3_6 -pypy -pypy3 -python3_5 -python3_7 -python3_8" [ebuild N ] dev-util/meson-0.52.0 USE="-test" PYTHON_TARGETS="python3_6 -python3_5 -python3_7" [ebuild N ] dev-python/pyparsing-2.4.0 USE="-examples" PYTHON_TARGETS="python2_7 python3_6 -pypy -pypy3 -python3_5 -python3_7 -python3_8" [ebuild N ] dev-python/joblib-0.12.2 USE="-doc -test" PYTHON_TARGETS="python2_7 python3_6 -pypy -python3_5 -python3_7" [ebuild N ] dev-python/pytz-2019.3 PYTHON_TARGETS="python2_7 python3_6 -pypy -pypy3 -python3_5 -python3_7 -python3_8" [ebuild N ] dev-python/nose-1.3.7-r4 USE="-coverage -doc -examples -test" PYTHON_TARGETS="python2_7 python3_6 -pypy -pypy3 -python3_5 -python3_7 -python3_8" [ebuild N ] dev-python/grabbit-0.2.6 USE="-test" PYTHON_TARGETS="python2_7 python3_6 -python3_5" [ebuild N ] dev-python/num2words-0.5.6 PYTHON_TARGETS="python2_7 python3_6 -python3_5" [ebuild N ] dev-python/click-7.0-r1 USE="-doc -examples -test" PYTHON_TARGETS="python2_7 python3_6 -pypy -pypy3 -python3_5 -python3_7 -python3_8" [ebuild N ] dev-python/simplejson-3.17.0 PYTHON_TARGETS="python2_7 python3_6 -pypy -pypy3 -python3_5 -python3_7 -python3_8" [ebuild N ] dev-python/future-0.18.2 USE="-doc -test" PYTHON_TARGETS="python2_7 python3_6 -pypy -pypy3 -python3_5 -python3_7 -python3_8" [ebuild N ] dev-python/futures-3.2.0 USE="-doc" PYTHON_TARGETS="python2_7 -pypy" [ebuild N ] dev-python/configparser-3.5.0-r1 PYTHON_TARGETS="python2_7 -pypy" [ebuild N ] dev-python/webencodings-0.5.1-r1 USE="-test" PYTHON_TARGETS="python2_7 python3_6 -pypy -pypy3 -python3_5 -python3_7 -python3_8" [ebuild N ] dev-python/decorator-4.4.1 PYTHON_TARGETS="python2_7 python3_6 -pypy -pypy3 -python3_5 -python3_7 -python3_8" [ebuild N ] dev-python/kiwisolver-1.0.1 PYTHON_TARGETS="python2_7 python3_6 -python3_5 -python3_7" [ebuild N ] dev-python/versioneer-0.18 PYTHON_TARGETS="python2_7 python3_6 -pypy -python3_5 -python3_7" [ebuild N ] dev-python/setuptools_scm-3.3.1 USE="-test" PYTHON_TARGETS="python2_7 python3_6 -pypy -pypy3 -python3_5 -python3_7 -python3_8" [ebuild N ] dev-python/markupsafe-1.1.1 USE="-test" PYTHON_TARGETS="python2_7 python3_6 -pypy -pypy3 -python3_5 -python3_7 -python3_8" [ebuild N ] x11-base/xorg-proto-2019.2 [ebuild N ] dev-python/python-dateutil-2.8.1 USE="-test" PYTHON_TARGETS="python2_7 python3_6 -pypy -pypy3 -python3_5 -python3_7 -python3_8" [ebuild N ] dev-python/pydotplus-2.0.2 PYTHON_TARGETS="python2_7 python3_6 -python3_5" [ebuild N ] dev-python/isodate-0.6.0 USE="-test" PYTHON_TARGETS="python2_7 python3_6 -pypy -pypy3 -python3_5 -python3_7" [ebuild N ] dev-python/html5lib-1.0.1-r1 USE="-test" PYTHON_TARGETS="python2_7 python3_6 -pypy -pypy3 -python3_5 -python3_7 -python3_8" [ebuild N ] x11-libs/pixman-0.38.4 USE="(-altivec) (-loongson2f) (-neon)" CPU_FLAGS_X86="mmxext sse2 -ssse3" [ebuild N ] dev-python/cycler-0.10.0 USE="-test" PYTHON_TARGETS="python2_7 python3_6 -python3_5 -python3_7" [ebuild N ] dev-python/backports-functools-lru-cache-1.6.1 USE="-doc -test" PYTHON_TARGETS="python2_7 -pypy" [ebuild N ] dev-python/mako-1.0.7 USE="-doc -test" PYTHON_TARGETS="python2_7 python3_6 -pypy -pypy3 -python3_5 -python3_7" [ebuild N ] virtual/perl-Parse-CPAN-Meta-2.150.10-r2 [ebuild N ] virtual/perl-CPAN-Meta-YAML-0.18.0-r4 [ebuild N ] dev-perl/XML-Parser-2.440.0 [ebuild N ] sys-apps/texinfo-6.7 USE="nls standalone -static" [ebuild N ] dev-perl/TimeDate-2.300.0 [ebuild N ] dev-lang/nasm-2.14.02 USE="-doc" [ebuild N ] virtual/perl-version-0.992.400 [ebuild N ] virtual/perl-podlators-4.110.0 [ebuild N ] virtual/perl-Text-ParseWords-3.300.0-r5 [ebuild N ] virtual/perl-Perl-OSType-1.10.0-r2 [ebuild N ] virtual/perl-Module-Metadata-1.0.36 [ebuild N ] virtual/perl-Getopt-Long-2.500.0-r1 [ebuild N ] virtual/perl-File-Spec-3.780.0 [ebuild N ] virtual/perl-ExtUtils-ParseXS-3.400.0 [ebuild N ] virtual/perl-ExtUtils-Manifest-1.720.0 [ebuild N ] virtual/perl-ExtUtils-Install-2.140.0-r1 [ebuild N ] virtual/perl-ExtUtils-CBuilder-0.280.231 [ebuild N ] virtual/perl-JSON-PP-4.20.0 [ebuild N ] virtual/perl-Scalar-List-Utils-1.500.0-r1 [ebuild N ] virtual/perl-libnet-3.110.0-r1 [ebuild N ] virtual/perl-IO-1.400.0 [ebuild N ] virtual/perl-Digest-SHA-6.20.0 [ebuild N ] virtual/perl-Digest-MD5-2.550.0-r1 [ebuild N ] dev-util/intltool-0.51.0-r2 [ebuild N ] sys-fs/e2fsprogs-1.45.4 USE="nls (split-usr) -cron -fuse -static-libs" [ebuild N ] dev-perl/MailTools-2.190.0 USE="-examples -test" [ebuild N ] dev-perl/Digest-HMAC-1.30.0-r1 [ebuild N ] virtual/perl-CPAN-Meta-2.150.10-r2 [ebuild N ] app-arch/libarchive-3.4.0 USE="acl bzip2 e2fsprogs iconv lzma threads zlib -blake2 -expat -libressl -lz4 -lzo -nettle -static-libs -xattr -zstd" [ebuild N ] dev-perl/Authen-SASL-2.160.0-r1 USE="-kerberos" [ebuild N ] dev-perl/Module-Build-0.422.400 USE="-test" [ebuild N ] dev-perl/Error-0.170.250 USE="-test" [ebuild N ] dev-vcs/git-2.24.0 USE="blksha1 curl gpg iconv nls pcre pcre-jit perl threads webdav -cgi -cvs -doc -emacs -gnome-keyring -highlight -libressl -mediawiki -mediawiki-experimental -perforce (-ppcsha1) -subversion -test -tk -xinetd" PYTHON_SINGLE_TARGET="python3_6 -python2_7 -python3_5 -python3_7" PYTHON_TARGETS="python2_7 python3_6 -python3_5 -python3_7" [ebuild N ] dev-libs/libxslt-1.1.33-r1 USE="crypt -debug -examples -python -static-libs" PYTHON_TARGETS="python2_7" [ebuild N ] x11-libs/xtrans-1.4.0 USE="-doc" [ebuild N ] media-libs/tiff-4.1.0 USE="cxx zlib -jbig -jpeg -lzma -static-libs -test -webp -zstd" [ebuild N ] dev-db/sqlite-3.29.0 USE="readline -debug -doc -icu -secure-delete -static-libs -tcl -test -tools" [ebuild N ] dev-lang/tcl-8.6.9 USE="threads -debug" [ebuild N ] sci-libs/gsl-2.5-r1 USE="deprecated -cblas-external -static-libs" [ebuild N ] app-shells/tcsh-6.21.00 USE="nls -doc" [ebuild N ] x11-libs/libXau-1.0.9 USE="-static-libs" [ebuild N ] x11-libs/libXdmcp-1.1.3 USE="-doc -static-libs" [ebuild N ] dev-libs/libuv-1.33.1 USE="-static-libs" [ebuild N ] sci-libs/hdf5-1.10.5 USE="cxx fortran hl zlib -debug -examples -mpi -szip -threads" [ebuild N ] sci-libs/nlopt-2.4.2-r1 USE="cxx -guile -octave -python -static-libs" PYTHON_TARGETS="python2_7" [ebuild NS ] sys-libs/db-5.3.28-r4 [6.0.35-r2] [ebuild N ] x11-libs/libxshmfence-1.3-r1 USE="-static-libs" [ebuild R ] dev-lang/python-2.7.17 USE="sqlite*" [ebuild R ] dev-lang/python-3.6.9 USE="sqlite*" [ebuild N ] x11-libs/libICE-1.0.10 USE="ipv6 -static-libs" [ebuild N ] dev-python/bsddb3-6.2.4 PYTHON_TARGETS="python2_7 python3_6 -python3_5 -python3_7" [ebuild N ] dev-util/glib-utils-2.60.7 PYTHON_SINGLE_TARGET="python3_6 -python3_5 -python3_7" PYTHON_TARGETS="python3_6 -python3_5 -python3_7" [ebuild N ] dev-python/argh-0.26.2-r2 USE="-test" PYTHON_TARGETS="python2_7 python3_6 -pypy -python3_5 -python3_7" [ebuild N ] x11-libs/libSM-1.2.3 USE="ipv6 uuid -doc -static-libs" [ebuild N ] dev-python/olefile-0.46 USE="-doc" PYTHON_TARGETS="python2_7 python3_6 -pypy -pypy3 -python3_5 -python3_7 -python3_8" [ebuild N ] dev-python/packaging-19.2 USE="-test" PYTHON_TARGETS="python2_7 python3_6 -pypy -pypy3 -python3_5 -python3_7 -python3_8" [ebuild N ] dev-python/lxml-4.4.2 USE="threads -doc -examples -test" PYTHON_TARGETS="python2_7 python3_6 -pypy -pypy3 -python3_5 -python3_7 -python3_8" [ebuild N ] dev-python/rdflib-4.2.2-r1 USE="berkdb -doc -examples -mysql -redland -sqlite -test" PYTHON_TARGETS="python2_7 python3_6 -python3_5 -python3_7" [ebuild N ] dev-python/funcsigs-1.0.2-r1 USE="-test" PYTHON_TARGETS="python2_7 python3_6 -pypy -pypy3 -python3_5 -python3_7" [ebuild N ] x11-base/xcb-proto-1.13 PYTHON_TARGETS="python2_7 python3_6 -python3_5 -python3_7" [ebuild N ] x11-libs/libxcb-1.13.1 USE="-doc (-selinux) -static-libs -test -xkb" [ebuild N ] virtual/python-funcsigs-2-r1 PYTHON_TARGETS="python2_7 python3_6 -pypy -pypy3 -python3_5 -python3_7 -python3_8" [ebuild N ] dev-python/pillow-6.2.1 USE="zlib -doc -examples -imagequant -jpeg -jpeg2k -lcms -test -tiff -tk -truetype -webp" PYTHON_TARGETS="python2_7 python3_6 -pypy -python3_5 -python3_7 -python3_8" [ebuild N ] x11-libs/libX11-1.6.9 USE="ipv6 -doc -static-libs -test" [ebuild N ] dev-python/mock-3.0.5-r1 PYTHON_TARGETS="python2_7 python3_6 -pypy -pypy3 -python3_5 -python3_7 -python3_8" [ebuild N ] x11-libs/libXext-1.3.4 USE="-doc -static-libs" [ebuild N ] x11-libs/libXt-1.2.0 USE="-doc -static-libs -test" [ebuild N ] x11-libs/libXfixes-5.0.3-r1 USE="-static-libs" [ebuild N ] x11-libs/libXrender-0.9.10-r1 USE="-static-libs" [ebuild N ] x11-libs/libXi-1.7.10 USE="-doc -static-libs" [ebuild N ] x11-libs/libXpm-3.5.12-r1 USE="-static-libs" [ebuild N ] x11-libs/libXmu-1.1.3 USE="ipv6 -doc -static-libs" [ebuild N ] x11-libs/libXdamage-1.1.5 USE="-static-libs" [ebuild N ] x11-libs/libXxf86vm-1.1.4-r1 USE="-static-libs" [ebuild N ] x11-libs/libXrandr-1.5.2 USE="-doc -static-libs" [ebuild N ] x11-libs/motif-2.3.8-r1 USE="motif22-compatibility unicode -examples -jpeg -png -static-libs -xft" [ebuild N ] dev-libs/glib-2.60.7 USE="mime -dbus -debug (-fam) -gtk-doc (-selinux) -static-libs -systemtap -test -utils -xattr" [ebuild N ] x11-misc/shared-mime-info-1.10-r1 USE="-test" [ebuild N ] dev-util/desktop-file-utils-0.24 USE="-emacs" [ebuild N ] dev-util/cmake-3.16.0 USE="ncurses -doc -emacs -qt5 -system-jsoncpp -test" [ebuild N ] dev-libs/gobject-introspection-1.60.2 USE="-cairo -doctool -test" PYTHON_SINGLE_TARGET="python3_6 -python3_5 -python3_7" PYTHON_TARGETS="python3_6 -python3_5 -python3_7" [ebuild N ] dev-libs/libsigc++-2.10.1 USE="-doc -static-libs -test" [ebuild N ] sci-libs/lapack-3.8.0 USE="-doc -eselect-ldso -lapacke" [ebuild N ] media-libs/qhull-2015.2 USE="-doc -static-libs" [ebuild N ] sys-devel/llvm-9.0.0 USE="libffi ncurses -debug -doc -exegesis -gold -libedit -test -xar -xml -z3" LLVM_TARGETS="AMDGPU BPF NVPTX (X86) -AArch64 -ARM -Hexagon -Lanai -MSP430 -Mips -PowerPC -RISCV -Sparc -SystemZ -WebAssembly -XCore" [ebuild N ] dev-libs/double-conversion-3.1.4-r1 USE="-static-libs -test" [ebuild N ] media-libs/openjpeg-2.3.1 USE="-doc -static-libs -test" [ebuild N ] media-gfx/graphite2-1.3.13 USE="-perl -test" [ebuild N ] dev-cpp/glibmm-2.60.1 USE="-debug -doc -test" [ebuild N ] media-libs/libjpeg-turbo-2.0.3 USE="-java -static-libs" [ebuild N ] virtual/jpeg-0-r3 USE="-static-libs" [ebuild N ] virtual/lapack-3.8 USE="-eselect-ldso" [ebuild N ] virtual/cblas-3.8 USE="-eselect-ldso" [ebuild N ] virtual/blas-3.8 USE="-eselect-ldso" [ebuild N ] dev-cpp/libxmlpp-2.40.1 USE="-doc" [ebuild N ] dev-python/numpy-1.16.5 USE="lapack -doc -test" PYTHON_TARGETS="python2_7 python3_6 -python3_5 -python3_7" [ebuild N ] media-video/mpeg-tools-1.5b-r5 [ebuild N ] sci-libs/dcmtk-3.6.0 USE="ssl tcpd threads zlib -doc -png -tiff -xml" [ebuild N ] sci-libs/arpack-3.5.0 USE="-doc -examples -mpi" [ebuild N ] sci-libs/ciftilib-1.5.3-r1 USE="-qt5" [ebuild N ] sci-libs/scipy-1.1.0 USE="-doc -sparse -test" PYTHON_TARGETS="python2_7 python3_6 -python3_5 -python3_7" [ebuild N ] dev-python/matplotlib-2.2.4 USE="-cairo -doc -examples -excel -gtk2 -gtk3 -latex -qt5 -test -tk -wxwidgets" PYTHON_TARGETS="python2_7 python3_6 -python3_5 -python3_7" [ebuild N ] sci-libs/itk-5.0.1 USE="-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" [ebuild N ] dev-python/traits-5.1.0 USE="-test" PYTHON_TARGETS="python2_7 python3_6 -python3_5" [ebuild N ] dev-python/numexpr-2.6.9 USE="(-mkl)" PYTHON_TARGETS="python2_7 python3_6 -python3_5 -python3_7" [ebuild N ] sci-libs/nibabel-2.5.1 USE="-dicom -doc -test" PYTHON_TARGETS="python2_7 python3_6 -python3_5" [ebuild N ] dev-python/patsy-0.5.1 USE="-doc -test" PYTHON_TARGETS="python2_7 python3_6 -python3_5 -python3_7" [ebuild N ] dev-python/networkx-2.2 USE="-examples -extras -pandas -scipy -test -xml -yaml" PYTHON_TARGETS="python2_7 python3_6 -python3_5 -python3_7" [ebuild N ] sci-biology/ants-2.3.1_p20191013 USE="-test -vtk" [ebuild N ] sci-libs/scikits_learn-0.19.0-r1 USE="-examples -test" PYTHON_TARGETS="python2_7 python3_6 -python3_5 -python3_7" [ebuild N ] dev-python/bottleneck-1.2.1 USE="-test" PYTHON_TARGETS="python2_7 python3_6 -python3_5 -python3_7" [ebuild N ] dev-python/pandas-0.24.2 USE="-X (-doc) -full-support -minimal -test" PYTHON_TARGETS="python2_7 python3_6 -python3_5 -python3_7" [ebuild N ] dev-python/prov-1.5.0 USE="-test" PYTHON_TARGETS="python2_7 python3_6 -python3_5" [ebuild N ] sci-biology/nilearn-0.5.2 USE="plot -test" PYTHON_TARGETS="python2_7 python3_6 -python3_5" [ebuild N ] dev-python/statsmodels-0.9.0 USE="-doc -examples -test" PYTHON_TARGETS="python2_7 python3_6 -python3_5 -python3_7" [ebuild N ] sci-libs/nipy-0.4.2 PYTHON_TARGETS="python2_7 python3_6 -python3_5" [ebuild N ] sci-libs/pybids-0.5.0 PYTHON_TARGETS="python2_7 python3_6 -python3_5" [ebuild N ] dev-python/seaborn-0.9.0 USE="-test" PYTHON_TARGETS="python2_7 python3_6 -python3_5" [ebuild N ] media-libs/fontconfig-2.13.1-r2 USE="-doc -static-libs" [ebuild N ] app-eselect/eselect-fontconfig-1.1-r1 [ebuild N ] x11-libs/cairo-1.16.0-r3 USE="glib svg -X (-aqua) -debug (-gles2) -opengl -static-libs -utils -valgrind -xcb" [ebuild N ] media-libs/gd-2.2.5-r2 USE="fontconfig jpeg png truetype zlib -static-libs -test -tiff -webp -xpm" CPU_FLAGS_X86="sse" [ebuild N ] x11-libs/libXft-2.3.3 USE="-doc -static-libs" [ebuild N ] dev-lang/tk-8.6.9.1 USE="threads (-aqua) -debug -test -truetype -xscreensaver" [ebuild N ] media-libs/harfbuzz-2.6.4 USE="cairo glib graphite introspection truetype -debug -icu -static-libs -test" [ebuild N ] x11-libs/pango-1.42.4-r2 USE="introspection -X -test" [ebuild N ] media-gfx/graphviz-2.42.3 USE="cairo nls -X -devil -doc -examples -gdk-pixbuf -gtk -gts -guile -java -lasi -pdf -perl -postscript -python -qt5 -ruby -static-libs -svg -tcl" PYTHON_SINGLE_TARGET="python3_6 -python2_7 -python3_5 -python3_7 -python3_8" PYTHON_TARGETS="python2_7 python3_6 -python3_5 -python3_7 -python3_8" [ebuild N ] dev-python/pydot-1.4.1 USE="-test" PYTHON_TARGETS="python2_7 python3_6 -python3_5 -python3_7" [ebuild N ] dev-python/pygraphviz-1.5 USE="-examples -test" PYTHON_TARGETS="python2_7 python3_6 -python3_5 -python3_7" [ebuild N ] sci-libs/nipype-1.1.1-r1 USE="-test" PYTHON_TARGETS="python2_7 python3_6 -python3_5" [ebuild N ] sys-fs/eudev-3.2.9 USE="(-hwdb) -introspection (-kmod) -rule-generator (-selinux) -static-libs -test" [ebuild N ] virtual/udev-217 USE="(-systemd)" [ebuild N ] sys-fs/udev-init-scripts-33 [ebuild N ] sys-apps/hwids-20191025 USE="net pci udev usb" [ebuild N ] x11-libs/libpciaccess-0.16 USE="zlib -static-libs" [ebuild N ] x11-libs/libdrm-2.4.100 USE="-libkms -valgrind" VIDEO_CARDS="amdgpu intel nouveau radeon (-exynos) (-freedreno) (-omap) (-tegra) (-vc4) (-vivante) -vmware" [ebuild N ] media-libs/mesa-19.3.0_rc5 USE="X classic dri3 egl gallium gbm gles2 llvm -d3d9 -debug -gles1 (-libglvnd) -lm-sensors -opencl -osmesa -pax_kernel (-selinux) -test -unwind -vaapi -valgrind -vdpau -vulkan -vulkan-overlay -wayland -xa -xvmc" VIDEO_CARDS="intel nouveau radeon radeonsi (-freedreno) -i915 -i965 -iris (-lima) (-panfrost) -r100 -r200 -r300 -r600 (-vc4) -virgl (-vivante) -vmware" [ebuild N ] virtual/opengl-7.0-r2 [ebuild N ] media-libs/glu-9.0.1 USE="-static-libs" [ebuild N ] x11-libs/libGLw-8.0.0 USE="motif -static-libs" [ebuild N ] sci-biology/fsl-5.0.11 [ebuild N ] sci-biology/afni-19.3.12 [ebuild N ] sci-biology/samri-0.2 USE="atlases -labbookdb -test" PYTHON_TARGETS="python2_7 python3_6 -python3_5"

The 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)

=dev-lang/python-2.7.17:2.7 sqlite

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)

=dev-lang/python-3.6.9:3.6 sqlite

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)

=media-libs/gd-2.2.5-r2 truetype png jpeg fontconfig

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)

=sci-biology/fsl-5.0.11 FSL newmat

required by sci-biology/samri-0.2::science[atlases]

required by samri (argument)

=sci-biology/mouse-brain-atlases-0.5.3 fairuse

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.

  • In order to avoid wasting time, backtracking has terminated early
  • due to the above autounmask change(s). The --autounmask-backtrack=y
  • option can be used to force further backtracking, but there is no
  • guarantee that it will produce a solution.

!!! The following updates are masked by LICENSE changes:

  • sci-libs/dcmtk-3.6.4-r1::gentoo (masked by: OFFIS license(s)) 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:

  • dev-python/numpy-1.16.1::gentoo (Change USE: +lapack)
  • sci-libs/scikits_learn-0.19.0-r1::gentoo (Change USE: -python_targets_python2_7) (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])_

salma1601 avatar Nov 30 '19 06:11 salma1601

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-continue

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:

echo 'ACCEPT_LICENSE="*"' >> /etc/portage/make.conf

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:

echo 'ACCEPT_KEYWORDS="~amd64"' >> /etc/portage/make.conf

After 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-continue

Let me know if there are further issues. We're happy to include such helpful tips in the README.

TheChymera avatar Nov 30 '19 18:11 TheChymera

Dear @TheChymera Thank you very much for your help and reactivity. I tried the first command emerge -v samri --autounmask-continue, and it looks like there is an error with UTF8 and dev-util/meson-0.52.0. Can I follow the rest of the commands ?

Emerging (46 of 217) dev-util/meson-0.52.0::gentoo

  • meson-0.52.0.tar.gz BLAKE2B SHA512 size ;-) ... [ ok ]

Unpacking source... Unpacking meson-0.52.0.tar.gz to /home/salma/gentoo/var/tmp/portage/dev-util/meson-0.52.0/work Source unpacked in /home/salma/gentoo/var/tmp/portage/dev-util/meson-0.52.0/work Preparing source in /home/salma/gentoo/var/tmp/portage/dev-util/meson-0.52.0/work/meson-0.52.0 ... Source prepared. Configuring source in /home/salma/gentoo/var/tmp/portage/dev-util/meson-0.52.0/work/meson-0.52.0 ...

  • Could not find a UTF-8 locale. This may trigger build failures in
  • some python packages. Please ensure that a UTF-8 locale is listed in
  • /etc/locale.gen and run locale-gen.

Source configured. Compiling source in /home/salma/gentoo/var/tmp/portage/dev-util/meson-0.52.0/work/meson-0.52.0 ...

  • python3_6: running distutils-r1_run_phase distutils-r1_python_compile python3.6 setup.py build -j 3 Traceback (most recent call last): File "setup.py", line 24, in from setuptools import setup File "/home/salma/gentoo/usr/lib64/python3.6/site-packages/setuptools/init.py", line 18, in import setuptools.version File "/home/salma/gentoo/usr/lib64/python3.6/site-packages/setuptools/version.py", line 1, in import pkg_resources File "/home/salma/gentoo/usr/lib64/python3.6/site-packages/pkg_resources/init.py", line 35, in import plistlib File "/home/salma/gentoo/usr/lib64/python3.6/plistlib.py", line 65, in from xml.parsers.expat import ParserCreate File "/home/salma/gentoo/usr/lib64/python3.6/xml/parsers/expat.py", line 4, in from pyexpat import * ImportError: /home/salma/gentoo/usr/lib64/python3.6/lib-dynload/pyexpat.cpython-36m-x86_64-linux-gnu.so: undefined symbol: XML_SetHashSalt
  • ERROR: dev-util/meson-0.52.0::gentoo failed (compile phase):
  • (no error message)
  • Call stack:
  • ebuild.sh, line  125:  Called src_compile
  • environment, line 2855: Called distutils-r1_src_compile
  • environment, line 942: Called _distutils-r1_run_foreach_impl 'distutils-r1_python_compile'
  • environment, line 447: Called python_foreach_impl 'distutils-r1_run_phase' 'distutils-r1_python_compile'
  • environment, line 2388: Called multibuild_foreach_variant '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'distutils-r1_python_compile'
  • environment, line 1767: Called _multibuild_run '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'distutils-r1_python_compile'
  • environment, line 1765: Called _python_multibuild_wrapper 'distutils-r1_run_phase' 'distutils-r1_python_compile'
  • environment, line 649: Called distutils-r1_run_phase 'distutils-r1_python_compile'
  • environment, line 933: Called distutils-r1_python_compile
  • environment, line 801: Called esetup.py 'build' '-j' '3'
  • environment, line 1311: Called die
  • The specific snippet of code:
  •   "${@}" || die "${die_args[@]}";
  • If you need support, post the output of emerge --info '=dev-util/meson-0.52.0::gentoo',
  • the complete build log and the output of emerge -pqv '=dev-util/meson-0.52.0::gentoo'.
  • The complete build log is located at '/home/salma/gentoo/var/tmp/portage/dev-util/meson-0.52.0/temp/build.log'.
  • The ebuild environment file is located at '/home/salma/gentoo/var/tmp/portage/dev-util/meson-0.52.0/temp/environment'.
  • Working directory: '/home/salma/gentoo/var/tmp/portage/dev-util/meson-0.52.0/work/meson-0.52.0'
  • S: '/home/salma/gentoo/var/tmp/portage/dev-util/meson-0.52.0/work/meson-0.52.0'

Failed to emerge dev-util/meson-0.52.0, Log file:

'/home/salma/gentoo/var/tmp/portage/dev-util/meson-0.52.0/temp/build.log'

  • Messages for package sci-libs/itk-5.0.1:

  • To tune ITK to make the best use of working memory you can set

  • ITK_COMPUTER_MEMORY_SIZE=XX

  • in make.conf, default is 1 (unit is GB)

  • Messages for package sys-fs/eudev-3.2.9:

  • As of 2013-01-29, eudev-3.2.9 provides the new interface renaming functionality,

  • as described in the URL below:

  • https://www.freedesktop.org/wiki/Software/systemd/PredictableNetworkInterfaceNames

  • This functionality is enabled BY DEFAULT because eudev has no means of synchronizing

  • between the default or user-modified choice of sys-fs/udev. If you wish to disable

  • this new iface naming, please be sure that /etc/udev/rules.d/80-net-name-slot.rules

  • exists: touch /etc/udev/rules.d/80-net-name-slot.rules

  • Messages for package media-fonts/liberation-fonts-2.00.5:

  • The following fontconfig configuration files have been installed:

  • 60-liberation.conf

  • Use eselect fontconfig to enable/disable them.

  • Messages for package dev-python/backports-1.0:

  • Could not find a UTF-8 locale. This may trigger build failures in

  • some python packages. Please ensure that a UTF-8 locale is listed in

  • /etc/locale.gen and run locale-gen.

  • Messages for package dev-python/olefile-0.46:

  • Could not find a UTF-8 locale. This may trigger build failures in

  • some python packages. Please ensure that a UTF-8 locale is listed in

  • /etc/locale.gen and run locale-gen.

  • Messages for package dev-python/mpmath-1.1.0:

  • Could not find a UTF-8 locale. This may trigger build failures in

  • some python packages. Please ensure that a UTF-8 locale is listed in

  • /etc/locale.gen and run locale-gen.

  • Messages for package dev-python/ptyprocess-0.5.2:

  • Could not find a UTF-8 locale. This may trigger build failures in

  • some python packages. Please ensure that a UTF-8 locale is listed in

  • /etc/locale.gen and run locale-gen.

  • Messages for package dev-python/functools32-3.2.3:

  • Could not find a UTF-8 locale. This may trigger build failures in

  • some python packages. Please ensure that a UTF-8 locale is listed in

  • /etc/locale.gen and run locale-gen.

  • Messages for package dev-python/subprocess32-3.5.4:

  • Could not find a UTF-8 locale. This may trigger build failures in

  • some python packages. Please ensure that a UTF-8 locale is listed in

  • /etc/locale.gen and run locale-gen.

  • Messages for package media-fonts/stix-fonts-2.0.0:

  • The following fontconfig configuration files have been installed:

  • 61-stix.conf

  • Use eselect fontconfig to enable/disable them.

  • Messages for package dev-libs/boost-1.71.0:

  • Boost.Regex is extremely ABI sensitive. If you get errors such as

  • undefined reference to `boost::re_detail_107100::cpp_regex_traits_implementation

  • <char>::transform_primary[abi:cxx11](char const*, char const*) const'

  • Then you need you need to recompile Boost and all its reverse dependencies

  • using the same toolchain. In general, every change of the C++ toolchain

  • requires a complete rebuild of the boost-dependent ecosystem.

  • See for instance https://bugs.gentoo.org/638138

  • Messages for package dev-python/six-1.13.0:

  • Could not find a UTF-8 locale. This may trigger build failures in

  • some python packages. Please ensure that a UTF-8 locale is listed in

  • /etc/locale.gen and run locale-gen.

  • Messages for package dev-util/meson-0.52.0:

  • Could not find a UTF-8 locale. This may trigger build failures in

  • some python packages. Please ensure that a UTF-8 locale is listed in

  • /etc/locale.gen and run locale-gen.

  • ERROR: dev-util/meson-0.52.0::gentoo failed (compile phase):

  • (no error message)

  • Call stack:

  • ebuild.sh, line  125:  Called src_compile

  • environment, line 2855: Called distutils-r1_src_compile

  • environment, line 942: Called _distutils-r1_run_foreach_impl 'distutils-r1_python_compile'

  • environment, line 447: Called python_foreach_impl 'distutils-r1_run_phase' 'distutils-r1_python_compile'

  • environment, line 2388: Called multibuild_foreach_variant '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'distutils-r1_python_compile'

  • environment, line 1767: Called _multibuild_run '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'distutils-r1_python_compile'

  • environment, line 1765: Called _python_multibuild_wrapper 'distutils-r1_run_phase' 'distutils-r1_python_compile'

  • environment, line 649: Called distutils-r1_run_phase 'distutils-r1_python_compile'

  • environment, line 933: Called distutils-r1_python_compile

  • environment, line 801: Called esetup.py 'build' '-j' '3'

  • environment, line 1311: Called die

  • The specific snippet of code:

  •   "${@}" || die "${die_args[@]}";

  • If you need support, post the output of emerge --info '=dev-util/meson-0.52.0::gentoo',

  • the complete build log and the output of emerge -pqv '=dev-util/meson-0.52.0::gentoo'.

  • The complete build log is located at '/home/salma/gentoo/var/tmp/portage/dev-util/meson-0.52.0/temp/build.log'.

  • The ebuild environment file is located at '/home/salma/gentoo/var/tmp/portage/dev-util/meson-0.52.0/temp/environment'.

  • Working directory: '/home/salma/gentoo/var/tmp/portage/dev-util/meson-0.52.0/work/meson-0.52.0'

  • S: '/home/salma/gentoo/var/tmp/portage/dev-util/meson-0.52.0/work/meson-0.52.0'

  • GNU info directory index is up-to-date.

  • IMPORTANT: config file '/home/salma/gentoo/etc/hosts' needs updating.

  • See the CONFIGURATION FILES and CONFIGURATION FILES UPDATE TOOLS

  • sections of the emerge man page to learn how to update config files.

salma1601 avatar Dec 01 '19 17:12 salma1601

Dear @salma1601 can you please paste the output of locale?

TheChymera avatar Dec 02 '19 18:12 TheChymera

Dear @TheChymera here is the output of locale

LANG= LC_CTYPE="POSIX" LC_NUMERIC="POSIX" LC_TIME="POSIX" LC_COLLATE="POSIX" LC_MONETARY="POSIX" LC_MESSAGES="POSIX" LC_PAPER="POSIX" LC_NAME="POSIX" LC_ADDRESS="POSIX" LC_TELEPHONE="POSIX" LC_MEASUREMENT="POSIX" LC_IDENTIFICATION="POSIX" LC_ALL=

salma1601 avatar Dec 02 '19 20:12 salma1601

Please uncomment one of the lines in /etc/locale.gen, e.g. en_US.UTF-8 UTF-8, and then run:

locale-gen
source /etc/profile

If you encounter further issues, please consult the localization guide. In the end, locale should return something like:

LANG=en_US.utf8
LC_CTYPE="en_US.utf8"
LC_NUMERIC=en_US.utf8
LC_TIME=en_US.utf8
LC_COLLATE="en_US.utf8"
LC_MONETARY=en_US.utf8
LC_MESSAGES="en_US.utf8"
LC_PAPER=en_US.utf8
LC_NAME="en_US.utf8"
LC_ADDRESS="en_US.utf8"
LC_TELEPHONE="en_US.utf8"
LC_MEASUREMENT=en_US.utf8
LC_IDENTIFICATION="en_US.utf8"
LC_ALL=

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.

TheChymera avatar Dec 03 '19 03:12 TheChymera

Dear @TheChymera I enabled the chymeric overlay but there is still some problem with dev-lang/python-3.6.9. I am posting the whole traceback

make: *** [Makefile:603: sharedmods] Error 1

  • ERROR: dev-lang/python-3.6.9::gentoo failed (compile phase):
  • emake failed
  • If you need support, post the output of emerge --info '=dev-lang/python-3.6.9::gentoo',
  • the complete build log and the output of emerge -pqv '=dev-lang/python-3.6.9::gentoo'.
  • The complete build log is located at '/home/salma/gentoo/var/tmp/portage/dev-lang/python-3.6.9/temp/build.log'.
  • The ebuild environment file is located at '/home/salma/gentoo/var/tmp/portage/dev-lang/python-3.6.9/temp/environment'.
  • Working directory: '/home/salma/gentoo/var/tmp/portage/dev-lang/python-3.6.9/work/Python-3.6.9'
  • S: '/home/salma/gentoo/var/tmp/portage/dev-lang/python-3.6.9/work/Python-3.6.9'

Failed to emerge dev-lang/python-3.6.9, Log file:

'/home/salma/gentoo/var/tmp/portage/dev-lang/python-3.6.9/temp/build.log'

  • Messages for package sci-libs/itk-5.0.1:
  • To tune ITK to make the best use of working memory you can set
  • ITK_COMPUTER_MEMORY_SIZE=XX
  • in make.conf, default is 1 (unit is GB)
  • Messages for package sys-fs/eudev-3.2.9:
  • As of 2013-01-29, eudev-3.2.9 provides the new interface renaming functionality,
  • as described in the URL below:
  • https://www.freedesktop.org/wiki/Software/systemd/PredictableNetworkInterfaceNames
  • This functionality is enabled BY DEFAULT because eudev has no means of synchronizing
  • between the default or user-modified choice of sys-fs/udev. If you wish to disable
  • this new iface naming, please be sure that /etc/udev/rules.d/80-net-name-slot.rules
  • exists: touch /etc/udev/rules.d/80-net-name-slot.rules
  • Messages for package sys-apps/texinfo-6.7:
  • This package will overwrite one or more files that may belong to other
  • packages (see list below). You can use a command such as `portageq
  • owners / ` to identify the installed package that owns a
  • file. If portageq reports that only one package owns a file then do
  • NOT file a bug report. A bug report is only useful if it identifies at
  • least two or more packages that are known to install the same file(s).
  • If a collision occurs and you can not explain where the file came from
  • then you should simply ignore the collision since there is not enough
  • information to determine if a real problem exists. Please do NOT file
  • a bug report at https://bugs.gentoo.org/ unless you report exactly
  • which two packages install the same file(s). See
  • https://wiki.gentoo.org/wiki/Knowledge_Base:Blockers for tips on how
  • to solve the problem. And once again, please do NOT file a bug report
  • unless you have completely understood the above message.
  • Detected file collision(s):
  • /home/salma/gentoo/usr/bin/install-info

  • /home/salma/gentoo/usr/bin/makeinfo
  • Searching all installed packages for file collisions...
  • Press Ctrl-C to Stop
  • None of the installed packages claim the file(s).
  • Package 'sys-apps/texinfo-6.7' merged despite file collisions. If
  • necessary, refer to your elog messages for the whole content of the
  • above message.
  • Messages for package dev-lang/python-3.6.9:
  • ERROR: dev-lang/python-3.6.9::gentoo failed (compile phase):
  • emake failed
  • If you need support, post the output of emerge --info '=dev-lang/python-3.6.9::gentoo',
  • the complete build log and the output of emerge -pqv '=dev-lang/python-3.6.9::gentoo'.
  • The complete build log is located at '/home/salma/gentoo/var/tmp/portage/dev-lang/python-3.6.9/temp/build.log'.
  • The ebuild environment file is located at '/home/salma/gentoo/var/tmp/portage/dev-lang/python-3.6.9/temp/environment'.
  • Working directory: '/home/salma/gentoo/var/tmp/portage/dev-lang/python-3.6.9/work/Python-3.6.9'
  • S: '/home/salma/gentoo/var/tmp/portage/dev-lang/python-3.6.9/work/Python-3.6.9'
  • GNU info directory index is up-to-date.
  • IMPORTANT: config file '/home/salma/gentoo/etc/hosts' needs updating.
  • See the CONFIGURATION FILES and CONFIGURATION FILES UPDATE TOOLS
  • sections of the emerge man page to learn how to update config files.

salma1601 avatar Dec 03 '19 11:12 salma1601

Dear @salma1601 , the relevant errors are contained within the /home/salma/gentoo/var/tmp/portage/dev-lang/python-3.6.9/temp/build.log file. Can you please upload it here?

TheChymera avatar Dec 03 '19 18:12 TheChymera

Dear @TheChymera , here is the log file build.log

salma1601 avatar Dec 03 '19 20:12 salma1601

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 emerge --oneshot dev-libs/expat and thereafter emerge -vaDNu world?

TheChymera avatar Dec 04 '19 05:12 TheChymera

@salma1601 what script did you use to set up the prefix installation?

TheChymera avatar Dec 04 '19 05:12 TheChymera

@TheChymera I used the bootstrp-prefix.sh script https://gitweb.gentoo.org/repo/proj/prefix.git/plain/scripts/bootstrap-prefix.sh

salma1601 avatar Dec 04 '19 07:12 salma1601

@TheChymera I tried the emerge --oneshot dev-libs/expat followed by emerge -vaDNu world but there is still a failiure with the dev-lang build.log

salma1601 avatar Dec 04 '19 12:12 salma1601

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: https://github.com/sqlmapproject/sqlmap/issues/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 LD_LIBRARY_PATH? If so, could you temporarily disable them, re-log into your prefix, and try anew?

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!

TheChymera avatar Dec 05 '19 02:12 TheChymera

dear @TheChymera , thank you for your support ! You are right, I have changed my LD_LIBRARY_PATH in my .bashrc to match some software requirements. After unsetting it and retrying the install, things go better and the dev-lang failiure is gone. Now the emerge reached 114 of 166, failing for sci-libs/dcmtk-3.6.0::science. Could it be because I already have dcmtk installed on my machine ? build.log

salma1601 avatar Dec 05 '19 10:12 salma1601

@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 =dcmtk-3.6.0. This is a comparatively old version, the current version is considerably newer (you can browse all available Gentoo packages with eix, to install it type emerge eix):

chymera@darkhost ~ $ eix dcmtk -v
* sci-libs/dcmtk
     Available versions:  (~)3.6.0[1] (~)3.6.3 (~)3.6.4-r1
     IUSE (all versions): doc png ssl tcpd +threads tiff xml zlib
     Installed versions:  Version:   3.6.4-r1
                          Date:      23:53:08 20/11/19
                          USE:       png ssl tcpd threads tiff xml zlib -doc
                          DEPEND:    ${RDEPEND} media-gfx/graphviz
                          RDEPEND:   dev-libs/icu:0/65.1= virtual/jpeg:0 media-libs/libpng:* dev-libs/openssl:0/1.1= sys-apps/tcp-wrappers media-libs/tiff:0 dev-libs/libxml2:2 sys-libs/zlib
                          BDEPEND:   dev-util/ninja >=dev-util/cmake-3.9.6
                          SRC_URI:   
                          EAPI:      7
     Best versions/slot:  (~)3.6.4-r1
     Homepage:            https://dicom.offis.de/dcmtk.php.en
     Find open bugs:      https://bugs.gentoo.org/buglist.cgi?quicksearch=sci-libs%2Fdcmtk
     Description:         The DICOM Toolkit
     License:             OFFIS

[1] "science" /var/db/repos/science

What command are you using to get this error?

TheChymera avatar Dec 05 '19 21:12 TheChymera

You are right! Actually it was a licence issue because I run the command echo 'ACCEPT_LICENSE="*"' >> /etc/portage/make.conf only the first time. I ran it again, and the dcmtk failiure is solved :)

Now the emerge fails at step 10 of 47 with sci-libs/nipy-0.4.2::science, appearently there is an issue with nibabel ? build.log

salma1601 avatar Dec 06 '19 08:12 salma1601

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 eix nibabel say?

Not least of all, echo 'ACCEPT_LICENSE="*"' >> /etc/portage/make.conf was part of the instructions I gave you before I realized this was Prefix. It should be echo 'ACCEPT_LICENSE="*"' >> /home/salma/gentoo/etc/portage/make.conf unless prefix auto-assigns / to /home/salma/gentoo, which I somewhat doubt and can't check, since I don't have a Prefix machine. Could you just look at the file and see if the license definition is in there?

TheChymera avatar Dec 06 '19 14:12 TheChymera

@TheChymera licence is OK and this is the output of eix nibabel

[I] sci-libs/nibabel
     Available versions:  2.0.1[1] 2.1.0[1] 2.3.0[1] 2.3.1[1] 2.5.1[1] 2.5.1[2] **9999*l[1] {dicom doc test PYTHON_TARGETS="python2_7 python3_5 python3_6 python3_7"}
     Installed versions:  2.5.1[2](10:56:22 PM 12/05/2019)(-dicom -doc -test PYTHON_TARGETS="python2_7 python3_6 -python3_5 -python3_7")
     Homepage:            http://nipy.org/nibabel/
     Description:         Access a cacophony of neuro-imaging file formats

[1] "science" /home/salma/gentoo/var/db/repos/science
[2] "chymeric" /home/salma/gentoo/var/db/repos/chymeric

salma1601 avatar Dec 06 '19 17:12 salma1601

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?

TheChymera avatar Dec 06 '19 17:12 TheChymera

Yes I do have nibabel because I already use it with other nipy libraries. Here is the output of python -c "import nibabel; print(nibabel.__version__, nibabel.__file__)"

2.5.1 /home/salma/miniconda3/lib/python3.7/site-packages/nibabel/init.py

salma1601 avatar Dec 06 '19 17:12 salma1601

@salma1601 but I assume this is outside of Prefix? So the way Prefix works, is it creates its own system inside of /home/salma/gentoo. It's basically like a container but without the device mapping overhead.

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 python -c "import nibabel; print(nibabel.__version__, nibabel.__file__)" inside Prefix, it means that your PYTHONPATH is similarly edited as LD_LIBRARY_PATH was before. So maybe try to clean that up?

TheChymera avatar Dec 06 '19 17:12 TheChymera

OK I understand better. Actually I have miniconda3 binaries added to my PATH in my ~/.bashrc. So I unset my PYTHONPATH removed from PATH all paths pointing outside gentoo directory and rerun the emerge but it is still failing at the same point build.log and the output of python -c "import nibabel; print(nibabel.__version__, nibabel.__file__)" is now

2.5.1 /home/salma/gentoo/usr/lib64/python3.6/site-packages/nibabel/init.py

salma1601 avatar Dec 06 '19 18:12 salma1601

@salma1601 hm.... yes, looks like it's properly accessible now. The error message seems to come from the package's setup.py and not from Portage, meaning that it's trying to check for the package itself, in excess of what Portage does. And somehow it's not managing to...

Maybe this is Python-version contingent (though, again, Portage should be handling all of this automatically, and based on your eix output, it definitely has). At any rate, try:

python2.7 -c "import nibabel; print(nibabel.__version__, nibabel.__file__)"
python3.6 -c "import nibabel; print(nibabel.__version__, nibabel.__file__)"

And please post the output of:

eselect python list

TheChymera avatar Dec 06 '19 20:12 TheChymera

@TheChymera here are the outputs python2.7 -c "import nibabel; print(nibabel.__version__, nibabel.__file__)"

Traceback (most recent call last): File "", line 1, in File "/home/salma/gentoo/usr/lib64/python2.7/site-packages/nibabel/init.py", line 62, in from . import analyze as ana File "/home/salma/gentoo/usr/lib64/python2.7/site-packages/nibabel/analyze.py", line 87, in from .volumeutils import (native_code, swapped_code, make_dt_codes, File "/home/salma/gentoo/usr/lib64/python2.7/site-packages/nibabel/volumeutils.py", line 23, in from .openers import Opener, BZ2File File "/home/salma/gentoo/usr/lib64/python2.7/site-packages/nibabel/openers.py", line 14, in from bz2file import BZ2File ImportError: No module named bz2file

python3.6 -c "import nibabel; print(nibabel.__version__, nibabel.__file__)"

2.5.1 /home/salma/gentoo/usr/lib64/python3.6/site-packages/nibabel/init.py

eselect python list

Available Python interpreters, in order of preference: [1] python3.6 [2] python2.7 (fallback)

salma1601 avatar Dec 06 '19 21:12 salma1601

@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 eix bz2file whether it is already installed, if not, emerge it with emerge -v1 bz2file. This will emerge it only once but not add it to the world package set, this is useful because you only want to get it as a quick fix. If this solves the issue, let me know, and I will add it to the dependency list for all users to benefit from (and to act as a permanent fix).

TheChymera avatar Dec 06 '19 21:12 TheChymera

Now it is failing because of my DCMTK outside prefix ! build.log

salma1601 avatar Dec 07 '19 06:12 salma1601

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 :-/ https://github.com/gentoo/gentoo/commit/3494cfeb45b8fefd8a39d3ffdbde30a5423a3740

I am working on updating this package, so it should be back in order soon.

TheChymera avatar Dec 08 '19 00:12 TheChymera

@salma1601 I believe I have fixed it. Try running eix-sync && emerge -vaDNu world.

TheChymera avatar Dec 08 '19 00:12 TheChymera

@TheChymera I think you did fix it! Now failing for ANTs :) build.log

salma1601 avatar Dec 08 '19 07:12 salma1601

It seems to nit find ITK. can you paste the output of: eix itk and equery f itk?

TheChymera avatar Dec 08 '19 22:12 TheChymera