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Hello all,
I am checking the following PKGBUILD to see if there possible missing dependencies and debugging.
# Maintainer: Andres Alejandro Navarro Alsina <aanavarroa@unal.edu.co>
# Contributor: GalSim developers team on GitHub
pkgbase=python-galsim-git
pkgname=('python-galsim-git' 'python2-galsim-git' 'galsim-common-git')
pkgver=v2.1.4.r3.68c8695b0
pkgrel=1
pkgdesc=" The modular galaxy image simulation toolkit "
arch=('any')
url="https://github.com/GalSim-developers/GalSim.git"
license=('BSD')
makedepends=('git' 'scons' 'boost-libs' 'fftw' 'tmv-git' 'eigen' 'pybind11' 'python-coord-git' 'python2-coord-git' 'python-future' 'python2-future' 'python-numpy' 'python2-numpy' 'python-astropy' 'python2-astropy')
checkdepends=('python-nose' 'python2-nose')
source=("${pkgbase}::git+${url}")
md5sums=('SKIP')
pkgver() {
cd "${pkgbase}"
printf "%s" "$(git describe --long | sed 's/\([^-]*-\)g/r\1/;s/-/./g')"
}
prepare() {
cp -a $pkgbase{,-py2}
}
build() {
cd "$srcdir"/$pkgbase
scons PREFIX=/usr TMV_DIR=/usr PYBIND11_DIR=/usr/include EIGEN_DIR=/usr/include/eigen3 PYTHON=python
cd "$srcdir"/$pkgbase-py2
scons PREFIX=/usr TMV_DIR=/usr PYBIND11_DIR=/usr/include EIGEN_DIR=/usr/include/eigen3 PYTHON=python2
}
check() {
cd "$srcdir"/$pkgbase/tests
nosetests -v || warning 'Tests failed'
cd "$srcdir"/$pkgbase-py2/tests
nosetests2 -v || warning 'Tests failed'
}
package_python-galsim-git() {
depends=('package_galsim-common-git')
cd $pkgbase
scons PREFIX="${pkgdir}"/usr FINAL_PREFIX=/usr PYTHON=python install
rm -rf "${pkgdir}"/usr/share
rm -f "${pkgdir}"/usr/lib/libgalsim.so
rm -f "${pkgdir}"/usr/lib/libgalsim.so.2.1
install -Dm644 LICENSE "${pkgdir}"/usr/share/licenses/$pkgname/LICENSE
}
package_python2-galsim-git() {
depends=('package_galsim-common-git')
cd $pkgbase-py2
scons PREFIX=$pkgdir/usr FINAL_PREFIX=/usr PYTHON=python2 install
rm -rf "${pkgdir}"/usr/share
rm -f "${pkgdir}"/usr/lib/libgalsim.so
rm -f "${pkgdir}"/usr/lib/libgalsim.so.2.1
for i in galsim galsim_download_cosmos; do mv "$pkgdir"/usr/bin/${i}{,2}; done
install -Dm644 LICENSE "${pkgdir}"/usr/share/licenses/$pkgname/LICENSE
}
package_galsim-common-git() {
depends=()
pkgdesc='common files for python-galsim-git and python2-galsim-git'
cd $pkgbase
install -Dm644 LICENSE "${pkgdir}"/usr/share/licenses/$pkgname/LICENSE
mv "${srcdir}"/$pkgbase/share/ "${pkgdir}"/usr/share/galsim/
install -Dm644 "${srcdir}"/$pkgbase/lib/libgalsim.so "${pkgdir}"/usr/lib/libgalsim.so
install -Dm644 "${srcdir}"/$pkgbase/lib/libgalsim.so.2.1 "${pkgdir}"/usr/lib/libgalsim.so.2.1
}
It compiles perfectly on my environment
[andres@lapalsina python-galsim]$ makepkg -s
==> Making package: python-galsim-git v2.1.4.r3.68c8695b0-1 (Sat 09 Mar 2019 03:56:05 PM -03)
==> Checking runtime dependencies...
==> Checking buildtime dependencies...
==> Retrieving sources...
-> Cloning python-galsim-git git repo...
Cloning into bare repository '/data/andres-arch-packages/python-galsim/python-galsim/python-galsim-git'...
remote: Enumerating objects: 407, done.
remote: Counting objects: 100% (407/407), done.
remote: Compressing objects: 100% (300/300), done.
remote: Total 118204 (delta 239), reused 179 (delta 107), pack-reused 117797
Receiving objects: 100% (118204/118204), 128.24 MiB | 10.98 MiB/s, done.
Resolving deltas: 100% (96978/96978), done.
==> Validating source files with md5sums...
python-galsim-git ... Skipped
==> Extracting sources...
-> Creating working copy of python-galsim-git git repo...
Cloning into 'python-galsim-git'...
done.
==> Starting prepare()...
==> Starting pkgver()...
==> Starting build()...
scons: Reading SConscript files ...
SCons is version 3.0.4 using python version 2.7.15
Python is from /usr/include/python2.7
Using the following (non-default) scons options:
PYTHON = python
PREFIX = /usr
EIGEN_DIR = /usr/include/eigen3
PYBIND11_DIR = /usr/include
TMV_DIR = /usr
These can be edited directly in the file gs_scons.conf.
Type scons -h for a full list of available options.
Using python = /usr/bin/python
Using PYPREFIX generated from PREFIX = /usr/lib/python3.7/site-packages
Using compiler: /usr/bin/g++
compiler version: 8.2.1
Determined that a good number of jobs = 8
Using SSE with flag -msse2
Checking for C++ header file fftw3.h... yes
Checking for correct FFTW linkage... yes
Checking for C++ header file Eigen/Core... yes
Checking if we can build against Python... yes
Building for python version 3.7
Checking if we can build module using Eigen... yes
Eigen version is 3.3.7
Checking if we can build against NumPy... yes
Numpy version is 1.16.2
Checking for astropy.io.fits... yes
Astropy version is 3.1.2
Checking for future... yes
Future version is 0.17.1
Checking for coord... yes
Coord version is 1.1
Checking for pybind11... yes
pybind11 version is 2.2.4
Checking if we can build against PyBind11... yes
Checking if C++ exceptions are propagated up to python... yes
GalSim version 2.1.4
scons: done reading SConscript files.
scons: Building targets ...
However, when I use the clean chroot and I pass the requirements to build. It seems that one package python-coord-git were not installed or is not found.
[andres@lapalsina python-galsim]$ makechrootpkg -c -r $CHROOT -I ../../tmv-git/tmv-git/tmv-git-v0.75.r0.fab5df3-1-x86_64.pkg.tar.xz -I ../../python-coord-git/python-coord-git/python-coord-git-v1.0.4.r15.328e54c-1-any.pkg.tar.xz -I ../../python-coord-git/python-coord-git/python2-coord-git-v1.0.4.r15.328e54c-1-any.pkg.tar.xz -I ../../aurrequirements_chroot/python-astropy/requirements/erfa-1.4.0-1-x86_64.pkg.tar.xz -I ../../aurrequirements_chroot/python-astropy/python-astropy-3.1.2-1-x86_64.pkg.tar.xz -I ../../aurrequirements_chroot/python2-astropy/python2-astropy-2.0.12-1-x86_64.pkg.tar.xz
[sudo] password for andres:
Sorry, try again.
[sudo] password for andres:
==> Synchronizing chroot copy [/home/andres/chroot/root] -> [andres]...done
loading packages...
resolving dependencies...
looking for conflicting packages...
Packages (36) blas-3.8.0-2 cblas-3.8.0-2 cfitsio-3.450-1 hdf5-1.10.4-1 lapack-3.8.0-2
libaec-1.0.2-1 libnsl-1.2.0-1 python-3.7.2-3 python-appdirs-1.4.3-2
python-h5py-2.9.0-1 python-jinja-2.10-2 python-markupsafe-1.1.1-1 python-numpy-1.16.2-1
python-packaging-19.0-1 python-pyparsing-2.3.1-1 python-scipy-1.2.1-1
python-setuptools-1:40.8.0-1 python-six-1.12.0-1 python2-2.7.15-4
python2-appdirs-1.4.3-2 python2-h5py-2.9.0-1 python2-jinja-2.10-2
python2-markupsafe-1.1.1-1 python2-numpy-1.16.2-1 python2-packaging-19.0-1
python2-pyparsing-2.3.1-1 python2-scipy-1.2.1-1 python2-setuptools-1:40.8.0-1
python2-six-1.12.0-1 wcslib-6.2-1 erfa-1.4.0-1 python-astropy-3.1.2-1
python-coord-git-v1.0.4.r15.328e54c-1 python2-astropy-2.0.12-1
python2-coord-git-v1.0.4.r15.328e54c-1 tmv-git-v0.75.r0.fab5df3-1
Total Installed Size: 520.19 MiB
:: Proceed with installation? [Y/n]
(36/36) checking keys in keyring [##################################] 100%
(35/36) checking package integrity [##################################] 100%
(35/36) loading package files [##################################] 100%
(36/36) checking for file conflicts [##################################] 100%
(36/36) checking available disk space [##################################] 100%
:: Processing package changes...
( 1/36) installing tmv-git [##################################] 100%
( 2/36) installing python-coord-git [##################################] 100%
( 3/36) installing python2-coord-git [##################################] 100%
( 4/36) installing erfa [##################################] 100%
( 5/36) installing libnsl [##################################] 100%
( 6/36) installing python [##################################] 100%
Optional dependencies for python
python-setuptools [pending]
python-pip
sqlite [installed]
mpdecimal: for decimal
xz: for lzma [installed]
tk: for tkinter
( 7/36) installing blas [##################################] 100%
( 8/36) installing cblas [##################################] 100%
( 9/36) installing lapack [##################################] 100%
(10/36) installing python-numpy [##################################] 100%
Optional dependencies for python-numpy
python-nose: testsuite
openblas: faster linear algebra
(11/36) installing python-scipy [##################################] 100%
Optional dependencies for python-scipy
python-pillow: for image saving module
(12/36) installing libaec [##################################] 100%
(13/36) installing hdf5 [##################################] 100%
(14/36) installing python-six [##################################] 100%
(15/36) installing python-h5py [##################################] 100%
(16/36) installing cfitsio [##################################] 100%
(17/36) installing wcslib [##################################] 100%
(18/36) installing python-appdirs [##################################] 100%
(19/36) installing python-pyparsing [##################################] 100%
(20/36) installing python-packaging [##################################] 100%
(21/36) installing python-setuptools [##################################] 100%
(22/36) installing python-markupsafe [##################################] 100%
(23/36) installing python-jinja [##################################] 100%
(24/36) installing python-astropy [##################################] 100%
(25/36) installing python2 [##################################] 100%
Optional dependencies for python2
tk: for IDLE
python2-setuptools [pending]
python2-pip
(26/36) installing python2-numpy [##################################] 100%
Optional dependencies for python2-numpy
python2-nose: testsuite
openblas: faster linear algebra
(27/36) installing python2-scipy [##################################] 100%
Optional dependencies for python2-scipy
python2-pillow: for image saving module
(28/36) installing python2-six [##################################] 100%
(29/36) installing python2-h5py [##################################] 100%
(30/36) installing python2-appdirs [##################################] 100%
(31/36) installing python2-pyparsing [##################################] 100%
(32/36) installing python2-packaging [##################################] 100%
(33/36) installing python2-setuptools [##################################] 100%
(34/36) installing python2-markupsafe [##################################] 100%
(35/36) installing python2-jinja [##################################] 100%
(36/36) installing python2-astropy [##################################] 100%
:: Running post-transaction hooks...
(1/1) Arming ConditionNeedsUpdate...
==> Making package: python-galsim-git v2.1.4.r3.68c8695b0-1 (Sat Mar 9 16:36:35 2019)
==> Retrieving sources...
-> Updating python-galsim-git git repo...
Fetching origin
==> Validating source files with md5sums...
python-galsim-git ... Skipped
==> Making package: python-galsim-git v2.1.4.r3.68c8695b0-1 (Sat 09 Mar 2019 04:36:38 PM -03)
==> Checking runtime dependencies...
==> Checking buildtime dependencies...
==> Installing missing dependencies...
resolving dependencies...
looking for conflicting packages...
Packages (13) perl-error-0.17027-1 perl-mailtools-2.20-2 perl-timedate-2.30-5 boost-libs-1.69.0-1
eigen-3.3.7-1 fftw-3.3.8-1 git-2.21.0-1 pybind11-2.2.4-5 python-future-0.17.1-1
python-nose-1.3.7-4 python2-future-0.17.1-1 python2-nose-1.3.7-4 scons-3.0.4-1
Total Installed Size: 75.62 MiB
:: Proceed with installation? [Y/n]
(13/13) checking keys in keyring [##################################] 100%
(13/13) checking package integrity [##################################] 100%
(13/13) loading package files [##################################] 100%
(13/13) checking for file conflicts [##################################] 100%
(13/13) checking available disk space [##################################] 100%
:: Processing package changes...
( 1/13) installing perl-error [##################################] 100%
( 2/13) installing perl-timedate [##################################] 100%
( 3/13) installing perl-mailtools [##################################] 100%
( 4/13) installing git [##################################] 100%
Optional dependencies for git
tk: gitk and git gui
perl-libwww: git svn
perl-term-readkey: git svn and interactive.singlekey setting
perl-mime-tools: git send-email
perl-net-smtp-ssl: git send-email TLS support
perl-authen-sasl: git send-email TLS support
perl-mediawiki-api: git mediawiki support
perl-datetime-format-iso8601: git mediawiki support
perl-lwp-protocol-https: git mediawiki https support
perl-cgi: gitweb (web interface) support
python2: various helper scripts [installed]
subversion: git svn
gnome-keyring: GNOME keyring credential helper
libsecret: libsecret credential helper [installed]
( 5/13) installing scons [##################################] 100%
( 6/13) installing boost-libs [##################################] 100%
Optional dependencies for boost-libs
openmpi: for mpi support
( 7/13) installing fftw [##################################] 100%
( 8/13) installing eigen [##################################] 100%
( 9/13) installing pybind11 [##################################] 100%
Optional dependencies for pybind11
python: to target bindings supporting python 3 [installed]
python2: to target bindings supporting python 2 [installed]
(10/13) installing python-future [##################################] 100%
Optional dependencies for python-future
python-setuptools: futurize and pasteurize scripts [installed]
(11/13) installing python2-future [##################################] 100%
Optional dependencies for python2-future
python2-setuptools: futurize2 and pasteurize2 scripts [installed]
(12/13) installing python-nose [##################################] 100%
(13/13) installing python2-nose [##################################] 100%
:: Running post-transaction hooks...
(1/5) Warn about old perl modules
(2/5) Reloading system manager configuration...
Skipped: Current root is not booted.
(3/5) Creating system user accounts...
Creating group git with gid 977.
Creating user git (git daemon user) with uid 977 and gid 977.
(4/5) Arming ConditionNeedsUpdate...
(5/5) Updating the info directory file...
==> Retrieving sources...
==> WARNING: Skipping all source file integrity checks.
==> Extracting sources...
-> Creating working copy of python-galsim-git git repo...
Cloning into 'python-galsim-git'...
done.
==> Starting prepare()...
==> Starting pkgver()...
==> Starting build()...
scons: Reading SConscript files ...
SCons is version 3.0.4 using python version 2.7.15
Python is from /usr/include/python2.7
Using the following (non-default) scons options:
PYTHON = python
PREFIX = /usr
EIGEN_DIR = /usr/include/eigen3
PYBIND11_DIR = /usr/include
TMV_DIR = /usr
These can be edited directly in the file gs_scons.conf.
Type scons -h for a full list of available options.
Using python = /usr/bin/python
Using PYPREFIX generated from PREFIX = /usr/lib/python3.7/site-packages
Using compiler: /usr/bin/g++
compiler version: 8.2.1
Determined that a good number of jobs = 8
Using SSE with flag -msse2
Checking for C++ header file fftw3.h... yes
Checking for correct FFTW linkage... yes
Checking for C++ header file Eigen/Core... yes
Checking if we can build against Python... yes
Building for python version 3.7
Checking if we can build module using Eigen... yes
Eigen version is 3.3.7
Checking if we can build against NumPy... yes
Numpy version is 1.16.2
Checking for astropy.io.fits... yes
Astropy version is 3.1.2
Checking for future... yes
Future version is 0.17.1
Checking for coord...
Unable to import coord using the python executable:
/usr/bin/python
Please fix the above error(s) and rerun scons.
Note: you may want to look through the file INSTALL.md for advice.
Also, if you are having trouble, please check the INSTALL FAQ at
https://github.com/GalSim-developers/GalSim/wiki/Installation%20FAQ
If nothing there seems helpful, feel free to post an issue here:
https://github.com/GalSim-developers/GalSim/issues
describing the problem along with the particulars of your system and
configuration. Include a copy of the above output to the screen, and
post and copy of the file gs_error.txt, which will help people diagnose
the problem.
==> ERROR: A failure occurred in build().
Aborting...
==> ERROR: Build failed, check /home/andres/chroot/andres/build
What could I be missing?
cheers.
Last edited by andalenavals (2019-03-12 21:24:36)
Offline
python-coord-git is an AUR package, clean chroot building only uses packages from the repos in pacman.conf by default.
You can add the package temporarily, see https://wiki.archlinux.org/index.php/De … d_packages
Last edited by Lone_Wolf (2019-03-10 12:16:44)
Disliking systemd intensely, but not satisfied with alternatives so focusing on taming systemd.
(A works at time B) && (time C > time B ) ≠ (A works at time C)
Offline
python-coord-git is an AUR package, clean chroot building only uses packages from the repos in pacman.conf by default.
Is the command they are using not enough?
makechrootpkg -c -r $CHROOT -I ../../tmv-git/tmv-git/tmv-git-v0.75.r0.fab5df3-1-x86_64.pkg.tar.xz -I ../../python-coord-git/python-coord-git/python-coord-git-v1.0.4.r15.328e54c-1-any.pkg.tar.xz -I ../../python-coord-git/python-coord-git/python2-coord-git-v1.0.4.r15.328e54c-1-any.pkg.tar.xz -I ../../aurrequirements_chroot/python-astropy/requirements/erfa-1.4.0-1-x86_64.pkg.tar.xz -I ../../aurrequirements_chroot/python-astropy/python-astropy-3.1.2-1-x86_64.pkg.tar.xz -I ../../aurrequirements_chroot/python2-astropy/python2-astropy-2.0.12-1-x86_64.pkg.tar.xz
The output goes on to show
( 2/36) installing python-coord-git [##################################] 100%
( 3/36) installing python2-coord-git [##################################] 100%
it looks to me something in the scons detection script fails when it tries 'import coord' in a spawned python.
Offline
Oops, missed that OP already used that.
Disliking systemd intensely, but not satisfied with alternatives so focusing on taming systemd.
(A works at time B) && (time C > time B ) ≠ (A works at time C)
Offline
Just skimming through this on my phone, if the issue is that a dep from the AUR is needed, one solution is to keep a local repo INSIDE the chroot from which it will pull deps. See clean-chroot-manager from the AUR.
CPU-optimized Linux-ck packages @ Repo-ck • AUR packages • Zsh and other configs
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File "/usr/lib/python3.7/site-packages/coord/__init__.py", line 24, in <module>
import os,cffi,glob
ModuleNotFoundError: No module named 'cffi'
not the cause but
python-coord-git /usr/lib/python3.7/site-packages/coord/_coord.cpython-37m-x86_64-linux-gnu.so
why is a package of arch=any including a .so?
Offline
Just skimming through this on my phone, if the issue is that a dep from the AUR is needed, one solution is to keep a local repo INSIDE the chroot from which it will pull deps. See clean-chroot-manager from the AUR.
The issue is that when I try makechrootpkg providing python-coord-git dependency using -I flag and all the tar balls that the package demands, scons cannot build the package, despite they seem correctly installed by pacman. On the other hand makepkg build the package without problems, so I suspect that there must be something in mi local installation that I am missing to include in the CHROOT, no idea if it is a package or a particular configuration.
As a early comment said "the scons detection script fails when it tries 'import coord' in a spawned python"
why is a package of arch=any including a .so?
Why not? sorry but I do not get what could it be a problem.
By the way just tried
arch=('i686' 'x86_64')
[andres@lapalsina python-galsim] $ makechrootpkg -c -r $CHROOT -I ../../tmv-git/tmv-git/tmv-git-v0.75.r0.fab5df3-1-x86_64.pkg.tar.xz -I ../../python-coord-git/python-coord-git/python-coord-git-v1.0.4.r15.328e54c-1-x86_64.pkg.tar.xz -I ../../python-coord-git/python-coord-git/python2-coord-git-v1.0.4.r15.328e54c-1-x86_64.pkg.tar.xz -I ../../aurrequirements_chroot/python-astropy/requirements/erfa-1.4.0-1-x86_64.pkg.tar.xz -I ../../aurrequirements_chroot/python-astropy/python-astropy-3.1.2-1-x86_64.pkg.tar.xz -I ../../aurrequirements_chroot/python2-astropy/python2-astropy-2.0.12-1-x86_64.pkg.tar.xz
and the problem is still there.
Thank you guys, for helping me out.
Last edited by andalenavals (2019-03-10 23:55:04)
Offline
file usr/lib/python3.7/site-packages/coord/_coord.cpython-37m-x86_64-linux-gnu.so
usr/lib/python3.7/site-packages/coord/_coord.cpython-37m-x86_64-linux-gnu.so: ELF 64-bit LSB shared object, x86-64, version 1 (SYSV), dynamically linked, BuildID[sha1]=090645dd5114a5fd829c08de9534ad013c742850, stripped
Edit:
I was not clear enough when I wrote
File "/usr/lib/python3.7/site-packages/coord/__init__.py", line 24, in <module> import os,cffi,glob ModuleNotFoundError: No module named 'cffi'
not the cause but
python-coord-git /usr/lib/python3.7/site-packages/coord/_coord.cpython-37m-x86_64-linux-gnu.so
why is a package of arch=any including a .so?
The cause was 'ModuleNotFoundError: No module named 'cffi'
"not the cause but" was referring to the .so inclusion
Add python-cffi as a depends of python-coord-git and python2-cffi as a depends of python2-coord-git
extra-x86_64-build -- -I ../python-astropy/python-astropy-3.1.2-1-x86_64.pkg.tar.xz -I ../python2-astropy/python2-astropy-2.0.12-1-x86_64.pkg.tar.xz -I ../erfa/erfa-1.4.0-1-x86_64.pkg.tar.xz -I ../python-coord-git/python-coord-git-v1.0.4.r15.328e54c-1-x86_64.pkg.tar.xz -I ../python-coord-git/python2-coord-git-v1.0.4.r15.328e54c-1-x86_64.pkg.tar.xz -I ../tmv-git/tmv-git-v0.75.r0.fab5df3-1-x86_64.pkg.tar.xz
:: Synchronizing package databases...
core is up to date
extra is up to date
community is up to date
:: Starting full system upgrade...
there is nothing to do
==> Building in chroot for [extra] (x86_64)...
==> Synchronizing chroot copy [/var/lib/archbuild/extra-x86_64/root] -> [testuser]...done
loading packages...
resolving dependencies...
looking for conflicting packages...
Packages (42) blas-3.8.0-2 cblas-3.8.0-2 cfitsio-3.450-1 hdf5-1.10.4-1
lapack-3.8.0-2 libaec-1.0.2-1 libnsl-1.2.0-1 python-3.7.2-3
python-appdirs-1.4.3-2 python-cffi-1.12.2-1 python-h5py-2.9.0-1
python-jinja-2.10-2 python-markupsafe-1.1.1-1
python-numpy-1.16.2-1 python-packaging-19.0-1 python-ply-3.11-2
python-pycparser-2.19-1 python-pyparsing-2.3.1-1
python-scipy-1.2.1-1 python-setuptools-1:40.8.0-1
python-six-1.12.0-1 python2-2.7.15-4 python2-appdirs-1.4.3-2
python2-cffi-1.12.2-1 python2-h5py-2.9.0-1 python2-jinja-2.10-2
python2-markupsafe-1.1.1-1 python2-numpy-1.16.2-1
python2-packaging-19.0-1 python2-ply-3.11-2
python2-pycparser-2.19-1 python2-pyparsing-2.3.1-1
python2-scipy-1.2.1-1 python2-setuptools-1:40.8.0-1
python2-six-1.12.0-1 wcslib-6.2-1 erfa-1.4.0-1
python-astropy-3.1.2-1 python-coord-git-v1.0.4.r15.328e54c-1
python2-astropy-2.0.12-1 python2-coord-git-v1.0.4.r15.328e54c-1
tmv-git-v0.75.r0.fab5df3-1
Total Installed Size: 525.57 MiB
:: Proceed with installation? [Y/n]
(42/42) checking keys in keyring [######################] 100%
(40/42) checking package integrity [######################] 100%
(40/42) loading package files [######################] 100%
(42/42) checking for file conflicts [######################] 100%
:: Processing package changes...
( 1/42) installing libnsl [######################] 100%
( 2/42) installing python [######################] 100%
Optional dependencies for python
python-setuptools [pending]
python-pip
sqlite [installed]
mpdecimal: for decimal
xz: for lzma [installed]
tk: for tkinter
( 3/42) installing blas [######################] 100%
( 4/42) installing cblas [######################] 100%
( 5/42) installing lapack [######################] 100%
( 6/42) installing python-numpy [######################] 100%
Optional dependencies for python-numpy
python-nose: testsuite
openblas: faster linear algebra
( 7/42) installing python-scipy [######################] 100%
Optional dependencies for python-scipy
python-pillow: for image saving module
( 8/42) installing libaec [######################] 100%
( 9/42) installing hdf5 [######################] 100%
(10/42) installing python-six [######################] 100%
(11/42) installing python-h5py [######################] 100%
(12/42) installing cfitsio [######################] 100%
(13/42) installing wcslib [######################] 100%
(14/42) installing erfa [######################] 100%
(15/42) installing python-appdirs [######################] 100%
(16/42) installing python-pyparsing [######################] 100%
(17/42) installing python-packaging [######################] 100%
(18/42) installing python-setuptools [######################] 100%
(19/42) installing python-markupsafe [######################] 100%
(20/42) installing python-jinja [######################] 100%
(21/42) installing python-astropy [######################] 100%
(22/42) installing python2 [######################] 100%
Optional dependencies for python2
tk: for IDLE
python2-setuptools [pending]
python2-pip
(23/42) installing python2-numpy [######################] 100%
Optional dependencies for python2-numpy
python2-nose: testsuite
openblas: faster linear algebra
(24/42) installing python2-scipy [######################] 100%
Optional dependencies for python2-scipy
python2-pillow: for image saving module
(25/42) installing python2-six [######################] 100%
(26/42) installing python2-h5py [######################] 100%
(27/42) installing python2-appdirs [######################] 100%
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(29/42) installing python2-packaging [######################] 100%
(30/42) installing python2-setuptools [######################] 100%
(31/42) installing python2-markupsafe [######################] 100%
(32/42) installing python2-jinja [######################] 100%
(33/42) installing python2-astropy [######################] 100%
(34/42) installing python-ply [######################] 100%
(35/42) installing python-pycparser [######################] 100%
(36/42) installing python-cffi [######################] 100%
(37/42) installing python-coord-git [######################] 100%
(38/42) installing python2-ply [######################] 100%
(39/42) installing python2-pycparser [######################] 100%
(40/42) installing python2-cffi [######################] 100%
(41/42) installing python2-coord-git [######################] 100%
(42/42) installing tmv-git [######################] 100%
:: Running post-transaction hooks...
(1/1) Arming ConditionNeedsUpdate...
==> Making package: python-galsim-git v2.1.4.r3.68c8695b0-1 (Mon Mar 11 00:52:20 2019)
==> Retrieving sources...
-> Updating python-galsim-git git repo...
Fetching origin
==> Validating source files with md5sums...
python-galsim-git ... Skipped
==> Making package: python-galsim-git v2.1.4.r3.68c8695b0-1 (Mon 11 Mar 2019 12:52:22 AM UTC)
==> Checking runtime dependencies...
==> Checking buildtime dependencies...
==> Installing missing dependencies...
resolving dependencies...
looking for conflicting packages...
Packages (13) perl-error-0.17027-1 perl-mailtools-2.20-2 perl-timedate-2.30-5 boost-libs-1.69.0-1 eigen-3.3.7-1 fftw-3.3.8-1 git-2.21.0-1 pybind11-2.2.4-5 python-future-0.17.1-1
python-nose-1.3.7-4 python2-future-0.17.1-1 python2-nose-1.3.7-4 scons-3.0.4-1
Total Installed Size: 75.62 MiB
:: Proceed with installation? [Y/n]
(13/13) checking keys in keyring [####################################################################] 100%
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:: Processing package changes...
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( 2/13) installing perl-timedate [####################################################################] 100%
( 3/13) installing perl-mailtools [####################################################################] 100%
( 4/13) installing git [####################################################################] 100%
Optional dependencies for git
tk: gitk and git gui
perl-libwww: git svn
perl-term-readkey: git svn and interactive.singlekey setting
perl-mime-tools: git send-email
perl-net-smtp-ssl: git send-email TLS support
perl-authen-sasl: git send-email TLS support
perl-mediawiki-api: git mediawiki support
perl-datetime-format-iso8601: git mediawiki support
perl-lwp-protocol-https: git mediawiki https support
perl-cgi: gitweb (web interface) support
python2: various helper scripts [installed]
subversion: git svn
gnome-keyring: GNOME keyring credential helper
libsecret: libsecret credential helper [installed]
( 5/13) installing scons [####################################################################] 100%
( 6/13) installing boost-libs [####################################################################] 100%
Optional dependencies for boost-libs
openmpi: for mpi support
( 7/13) installing fftw [####################################################################] 100%
( 8/13) installing eigen [####################################################################] 100%
( 9/13) installing pybind11 [####################################################################] 100%
Optional dependencies for pybind11
python: to target bindings supporting python 3 [installed]
python2: to target bindings supporting python 2 [installed]
(10/13) installing python-future [####################################################################] 100%
Optional dependencies for python-future
python-setuptools: futurize and pasteurize scripts [installed]
(11/13) installing python2-future [####################################################################] 100%
Optional dependencies for python2-future
python2-setuptools: futurize2 and pasteurize2 scripts [installed]
(12/13) installing python-nose [####################################################################] 100%
(13/13) installing python2-nose [####################################################################] 100%
:: Running post-transaction hooks...
(1/5) Warn about old perl modules
(2/5) Reloading system manager configuration...
Skipped: Current root is not booted.
(3/5) Creating system user accounts...
Creating group git with gid 977.
Creating user git (git daemon user) with uid 977 and gid 977.
(4/5) Arming ConditionNeedsUpdate...
(5/5) Updating the info directory file...
==> Retrieving sources...
==> WARNING: Skipping all source file integrity checks.
==> Extracting sources...
-> Creating working copy of python-galsim-git git repo...
Cloning into 'python-galsim-git'...
done.
==> Starting prepare()...
==> Starting pkgver()...
==> Starting build()...
scons: Reading SConscript files ...
SCons is version 3.0.4 using python version 2.7.15
Python is from /usr/include/python2.7
Using the following (non-default) scons options:
PYTHON = python
PREFIX = /usr
EIGEN_DIR = /usr/include/eigen3
PYBIND11_DIR = /usr/include
TMV_DIR = /usr
These can be edited directly in the file gs_scons.conf.
Type scons -h for a full list of available options.
Using python = /usr/bin/python
Using PYPREFIX generated from PREFIX = /usr/lib/python3.7/site-packages
Using compiler: /usr/bin/g++
compiler version: 8.2.1
Determined that a good number of jobs = 8
Using SSE with flag -msse2
Checking for C++ header file fftw3.h... yes
Checking for correct FFTW linkage... yes
Checking for C++ header file Eigen/Core... yes
Checking if we can build against Python... yes
Building for python version 3.7
Checking if we can build module using Eigen... yes
Eigen version is 3.3.7
Checking if we can build against NumPy... yes
Numpy version is 1.16.2
Checking for astropy.io.fits... yes
Astropy version is 3.1.2
Checking for future... yes
Future version is 0.17.1
Checking for coord... yes
Coord version is 1.1
Checking for pybind11... yes
pybind11 version is 2.2.4
Checking if we can build against PyBind11... yes
Checking if C++ exceptions are propagated up to python... yes
GalSim version 2.1.4
scons: done reading SConscript files.
scons: Building targets ...
Last edited by loqs (2019-03-11 01:02:20)
Offline
file usr/lib/python3.7/site-packages/coord/_coord.cpython-37m-x86_64-linux-gnu.so usr/lib/python3.7/site-packages/coord/_coord.cpython-37m-x86_64-linux-gnu.so: ELF 64-bit LSB shared object, x86-64, version 1 (SYSV), dynamically linked, BuildID[sha1]=090645dd5114a5fd829c08de9534ad013c742850, stripped
Edit:
I was not clear enough when I wroteloqs wrote:File "/usr/lib/python3.7/site-packages/coord/__init__.py", line 24, in <module> import os,cffi,glob ModuleNotFoundError: No module named 'cffi'
not the cause but
python-coord-git /usr/lib/python3.7/site-packages/coord/_coord.cpython-37m-x86_64-linux-gnu.so
why is a package of arch=any including a .so?
The cause was 'ModuleNotFoundError: No module named 'cffi'
"not the cause but" was referring to the .so inclusionAdd python-cffi as a depends of python-coord-git and python2-cffi as a depends of python2-coord-git
extra-x86_64-build -- -I ../python-astropy/python-astropy-3.1.2-1-x86_64.pkg.tar.xz -I ../python2-astropy/python2-astropy-2.0.12-1-x86_64.pkg.tar.xz -I ../erfa/erfa-1.4.0-1-x86_64.pkg.tar.xz -I ../python-coord-git/python-coord-git-v1.0.4.r15.328e54c-1-x86_64.pkg.tar.xz -I ../python-coord-git/python2-coord-git-v1.0.4.r15.328e54c-1-x86_64.pkg.tar.xz -I ../tmv-git/tmv-git-v0.75.r0.fab5df3-1-x86_64.pkg.tar.xz :: Synchronizing package databases... core is up to date extra is up to date community is up to date :: Starting full system upgrade... there is nothing to do ==> Building in chroot for [extra] (x86_64)... ==> Synchronizing chroot copy [/var/lib/archbuild/extra-x86_64/root] -> [testuser]...done loading packages... resolving dependencies... looking for conflicting packages... Packages (42) blas-3.8.0-2 cblas-3.8.0-2 cfitsio-3.450-1 hdf5-1.10.4-1 lapack-3.8.0-2 libaec-1.0.2-1 libnsl-1.2.0-1 python-3.7.2-3 python-appdirs-1.4.3-2 python-cffi-1.12.2-1 python-h5py-2.9.0-1 python-jinja-2.10-2 python-markupsafe-1.1.1-1 python-numpy-1.16.2-1 python-packaging-19.0-1 python-ply-3.11-2 python-pycparser-2.19-1 python-pyparsing-2.3.1-1 python-scipy-1.2.1-1 python-setuptools-1:40.8.0-1 python-six-1.12.0-1 python2-2.7.15-4 python2-appdirs-1.4.3-2 python2-cffi-1.12.2-1 python2-h5py-2.9.0-1 python2-jinja-2.10-2 python2-markupsafe-1.1.1-1 python2-numpy-1.16.2-1 python2-packaging-19.0-1 python2-ply-3.11-2 python2-pycparser-2.19-1 python2-pyparsing-2.3.1-1 python2-scipy-1.2.1-1 python2-setuptools-1:40.8.0-1 python2-six-1.12.0-1 wcslib-6.2-1 erfa-1.4.0-1 python-astropy-3.1.2-1 python-coord-git-v1.0.4.r15.328e54c-1 python2-astropy-2.0.12-1 python2-coord-git-v1.0.4.r15.328e54c-1 tmv-git-v0.75.r0.fab5df3-1 Total Installed Size: 525.57 MiB :: Proceed with installation? [Y/n] (42/42) checking keys in keyring [######################] 100% (40/42) checking package integrity [######################] 100% (40/42) loading package files [######################] 100% (42/42) checking for file conflicts [######################] 100% :: Processing package changes... ( 1/42) installing libnsl [######################] 100% ( 2/42) installing python [######################] 100% Optional dependencies for python python-setuptools [pending] python-pip sqlite [installed] mpdecimal: for decimal xz: for lzma [installed] tk: for tkinter ( 3/42) installing blas [######################] 100% ( 4/42) installing cblas [######################] 100% ( 5/42) installing lapack [######################] 100% ( 6/42) installing python-numpy [######################] 100% Optional dependencies for python-numpy python-nose: testsuite openblas: faster linear algebra ( 7/42) installing python-scipy [######################] 100% Optional dependencies for python-scipy python-pillow: for image saving module ( 8/42) installing libaec [######################] 100% ( 9/42) installing hdf5 [######################] 100% (10/42) installing python-six [######################] 100% (11/42) installing python-h5py [######################] 100% (12/42) installing cfitsio [######################] 100% (13/42) installing wcslib [######################] 100% (14/42) installing erfa [######################] 100% (15/42) installing python-appdirs [######################] 100% (16/42) installing python-pyparsing [######################] 100% (17/42) installing python-packaging [######################] 100% (18/42) installing python-setuptools [######################] 100% (19/42) installing python-markupsafe [######################] 100% (20/42) installing python-jinja [######################] 100% (21/42) installing python-astropy [######################] 100% (22/42) installing python2 [######################] 100% Optional dependencies for python2 tk: for IDLE python2-setuptools [pending] python2-pip (23/42) installing python2-numpy [######################] 100% Optional dependencies for python2-numpy python2-nose: testsuite openblas: faster linear algebra (24/42) installing python2-scipy [######################] 100% Optional dependencies for python2-scipy python2-pillow: for image saving module (25/42) installing python2-six [######################] 100% (26/42) installing python2-h5py [######################] 100% (27/42) installing python2-appdirs [######################] 100% (28/42) installing python2-pyparsing [######################] 100% (29/42) installing python2-packaging [######################] 100% (30/42) installing python2-setuptools [######################] 100% (31/42) installing python2-markupsafe [######################] 100% (32/42) installing python2-jinja [######################] 100% (33/42) installing python2-astropy [######################] 100% (34/42) installing python-ply [######################] 100% (35/42) installing python-pycparser [######################] 100% (36/42) installing python-cffi [######################] 100% (37/42) installing python-coord-git [######################] 100% (38/42) installing python2-ply [######################] 100% (39/42) installing python2-pycparser [######################] 100% (40/42) installing python2-cffi [######################] 100% (41/42) installing python2-coord-git [######################] 100% (42/42) installing tmv-git [######################] 100% :: Running post-transaction hooks... (1/1) Arming ConditionNeedsUpdate... ==> Making package: python-galsim-git v2.1.4.r3.68c8695b0-1 (Mon Mar 11 00:52:20 2019) ==> Retrieving sources... -> Updating python-galsim-git git repo... Fetching origin ==> Validating source files with md5sums... python-galsim-git ... Skipped ==> Making package: python-galsim-git v2.1.4.r3.68c8695b0-1 (Mon 11 Mar 2019 12:52:22 AM UTC) ==> Checking runtime dependencies... ==> Checking buildtime dependencies... ==> Installing missing dependencies... resolving dependencies... looking for conflicting packages... Packages (13) perl-error-0.17027-1 perl-mailtools-2.20-2 perl-timedate-2.30-5 boost-libs-1.69.0-1 eigen-3.3.7-1 fftw-3.3.8-1 git-2.21.0-1 pybind11-2.2.4-5 python-future-0.17.1-1 python-nose-1.3.7-4 python2-future-0.17.1-1 python2-nose-1.3.7-4 scons-3.0.4-1 Total Installed Size: 75.62 MiB :: Proceed with installation? [Y/n] (13/13) checking keys in keyring [####################################################################] 100% (13/13) checking package integrity [####################################################################] 100% (13/13) loading package files [####################################################################] 100% (13/13) checking for file conflicts [####################################################################] 100% :: Processing package changes... ( 1/13) installing perl-error [####################################################################] 100% ( 2/13) installing perl-timedate [####################################################################] 100% ( 3/13) installing perl-mailtools [####################################################################] 100% ( 4/13) installing git [####################################################################] 100% Optional dependencies for git tk: gitk and git gui perl-libwww: git svn perl-term-readkey: git svn and interactive.singlekey setting perl-mime-tools: git send-email perl-net-smtp-ssl: git send-email TLS support perl-authen-sasl: git send-email TLS support perl-mediawiki-api: git mediawiki support perl-datetime-format-iso8601: git mediawiki support perl-lwp-protocol-https: git mediawiki https support perl-cgi: gitweb (web interface) support python2: various helper scripts [installed] subversion: git svn gnome-keyring: GNOME keyring credential helper libsecret: libsecret credential helper [installed] ( 5/13) installing scons [####################################################################] 100% ( 6/13) installing boost-libs [####################################################################] 100% Optional dependencies for boost-libs openmpi: for mpi support ( 7/13) installing fftw [####################################################################] 100% ( 8/13) installing eigen [####################################################################] 100% ( 9/13) installing pybind11 [####################################################################] 100% Optional dependencies for pybind11 python: to target bindings supporting python 3 [installed] python2: to target bindings supporting python 2 [installed] (10/13) installing python-future [####################################################################] 100% Optional dependencies for python-future python-setuptools: futurize and pasteurize scripts [installed] (11/13) installing python2-future [####################################################################] 100% Optional dependencies for python2-future python2-setuptools: futurize2 and pasteurize2 scripts [installed] (12/13) installing python-nose [####################################################################] 100% (13/13) installing python2-nose [####################################################################] 100% :: Running post-transaction hooks... (1/5) Warn about old perl modules (2/5) Reloading system manager configuration... Skipped: Current root is not booted. (3/5) Creating system user accounts... Creating group git with gid 977. Creating user git (git daemon user) with uid 977 and gid 977. (4/5) Arming ConditionNeedsUpdate... (5/5) Updating the info directory file... ==> Retrieving sources... ==> WARNING: Skipping all source file integrity checks. ==> Extracting sources... -> Creating working copy of python-galsim-git git repo... Cloning into 'python-galsim-git'... done. ==> Starting prepare()... ==> Starting pkgver()... ==> Starting build()... scons: Reading SConscript files ... SCons is version 3.0.4 using python version 2.7.15 Python is from /usr/include/python2.7 Using the following (non-default) scons options: PYTHON = python PREFIX = /usr EIGEN_DIR = /usr/include/eigen3 PYBIND11_DIR = /usr/include TMV_DIR = /usr These can be edited directly in the file gs_scons.conf. Type scons -h for a full list of available options. Using python = /usr/bin/python Using PYPREFIX generated from PREFIX = /usr/lib/python3.7/site-packages Using compiler: /usr/bin/g++ compiler version: 8.2.1 Determined that a good number of jobs = 8 Using SSE with flag -msse2 Checking for C++ header file fftw3.h... yes Checking for correct FFTW linkage... yes Checking for C++ header file Eigen/Core... yes Checking if we can build against Python... yes Building for python version 3.7 Checking if we can build module using Eigen... yes Eigen version is 3.3.7 Checking if we can build against NumPy... yes Numpy version is 1.16.2 Checking for astropy.io.fits... yes Astropy version is 3.1.2 Checking for future... yes Future version is 0.17.1 Checking for coord... yes Coord version is 1.1 Checking for pybind11... yes pybind11 version is 2.2.4 Checking if we can build against PyBind11... yes Checking if C++ exceptions are propagated up to python... yes GalSim version 2.1.4 scons: done reading SConscript files. scons: Building targets ...
Could you tell me a litle more about how do you come up with this solution?
Because I tested the PKGBUILD of python-coord-git in a clean chroot, and no problems were reported at least for the check() tests. So now I wondering if I should put python-future, python-numpy and python-setuptools in the dependences rather than makedepends.
# This is an example PKGBUILD file. Use this as a start to creating your own,
# and remove these comments. For more information, see 'man PKGBUILD'.
# NOTE: Please fill out the license field for your package! If it is unknown,
# then please put 'unknown'.
# Maintainer: Andres Alejandro Navarro Alsina <aanavarroa@unal.edu.co>
# Contributor: M. Jarvis
pkgbase=python-coord-git
pkgname=('python-coord-git' 'python2-coord-git')
pkgver=v1.0.4.r15.328e54c
pkgrel=1
pkgdesc=" Coord is a Python module that provides basic functionality related to angles and celestial coordinatesw"
arch=('i686' 'x86_64')
url="https://github.com/LSSTDESC/Coord.git"
license=('BSD')
makedepends=('git' 'python' 'python-cffi' 'python-numpy' 'python-future' 'python2' 'python2-cffi' 'python2-numpy' 'python2-future' 'python-setuptools' 'python2-setuptools')
checkdepends=('python-nose' 'python2-nose' 'python-astropy' 'python2-astropy')
source=("${pkgbase}::git+${url}")
md5sums=('SKIP')
pkgver() {
cd "${pkgbase}"
printf "%s" "$(git describe --long --tags | sed 's/\([^-]*-\)g/r\1/;s/-/./g')"
}
prepare() {
cp -a $pkgbase{,-py2}
}
build() {
cd "$srcdir"/$pkgbase
python setup.py build
cd "$srcdir"/$pkgbase-py2
python2 setup.py build
}
check() {
cd "$srcdir"/$pkgbase
nosetests -v || warning 'Tests failed'
cd "$srcdir"/$pkgbase-py2
nosetests2 -v || warning 'Tests2 failed'
}
package_python-coord-git() {
depends=('glibc')
cd $pkgbase
python setup.py install --root=${pkgdir} --prefix=/usr --optimize=1
install -Dm644 LICENSE "${pkgdir}"/usr/share/licenses/$pkgname/LICENSE
}
package_python2-coord-git() {
depends=('glibc')
cd $pkgbase-py2
python2 setup.py install --root=${pkgdir} --prefix=/usr --optimize=1
install -Dm644 LICENSE "${pkgdir}"/usr/share/licenses/$pkgname/LICENSE
}
EDIT:
Thank you very much @loqs that was the solution!
I just build the tarball, and it is working just right.
Other wierd thing is that namcap, shows python-cffi as an not needed dependency
or might I am not running it properly.
[andres@lapalsina python-coord-git]$ namcap PKGBUILD python-coord-git-v1.0.4.r15.328e54c-1-x86_64.pkg.tar.xz
python-coord-git W: Unused shared library '/usr/lib/libpthread.so.0' by file ('usr/lib/python3.7/site-packages/coord/_coord.cpython-37m-x86_64-linux-gnu.so')
python-coord-git W: Dependency glibc included but already satisfied
python-coord-git W: Dependency included and not needed ('python-cffi')
Last edited by andalenavals (2019-03-11 01:50:28)
Offline
I looked at https://github.com/GalSim-developers/Ga … ruct#L1801 which showed the test was 'import coord'
I added python -c 'import coord' to the start of build()
build() {
cd "$srcdir"/$pkgbase
python -c 'import coord'
scons PREFIX=/usr TMV_DIR=/usr PYBIND11_DIR=/usr/include EIGEN_DIR=/usr/include/eigen3 PYTHON=python
cd "$srcdir"/$pkgbase-py2
scons PREFIX=/usr TMV_DIR=/usr PYBIND11_DIR=/usr/include EIGEN_DIR=/usr/include/eigen3 PYTHON=python2
}
That produced the error referencing cffi.
Offline
I looked at https://github.com/GalSim-developers/Ga … ruct#L1801 which showed the test was 'import coord'
I added python -c 'import coord' to the start of build()build() { cd "$srcdir"/$pkgbase python -c 'import coord' scons PREFIX=/usr TMV_DIR=/usr PYBIND11_DIR=/usr/include EIGEN_DIR=/usr/include/eigen3 PYTHON=python cd "$srcdir"/$pkgbase-py2 scons PREFIX=/usr TMV_DIR=/usr PYBIND11_DIR=/usr/include EIGEN_DIR=/usr/include/eigen3 PYTHON=python2 }
That produced the error referencing cffi.
Really smart!
Offline