ratt-ru / meqtrees

A library for implementing radio astronomical Measurement Equations
http://meqtrees.net
10 stars 2 forks source link

Building dependencies as per meqtrees.net instructions fails: Ubuntu 14.04.3 #867

Closed IanHeywood closed 9 years ago

IanHeywood commented 9 years ago

Another one for the collection:

ianh@nerv:~$ sudo apt-get build-dep -y kittens purr pyxis tigger meqtrees-timba meqtrees-cattery owlcat
Reading package lists... Done
Building dependency tree       
Reading state information... Done
The following NEW packages will be installed:
  build-essential cmake cmake-data debhelper dh-apparmor dpkg-dev libblas-dev
  libblitz0-dev libblitz0ldbl libcasacore-dev libcasacore1 libcfitsio3-dev
  libfftw3-bin libfftw3-dev libfftw3-long3 libfftw3-quad3 libgdbm-dev
  liblapack-dev po-debconf python-all wcslib-dev
0 to upgrade, 21 to newly install, 0 to remove and 1 not to upgrade.
Need to get 19.4 MB of archives.
After this operation, 114 MB of additional disk space will be used.
Get:1 http://au.archive.ubuntu.com/ubuntu/ trusty/main libfftw3-long3 amd64 3.3.3-7ubuntu3 [305 kB]
Get:2 http://au.archive.ubuntu.com/ubuntu/ trusty/main libfftw3-quad3 amd64 3.3.3-7ubuntu3 [548 kB]
Get:3 http://ppa.launchpad.net/radio-astro/main/ubuntu/ trusty/main wcslib-dev amd64 4.25.1-3trusty [297 kB]
Get:4 http://au.archive.ubuntu.com/ubuntu/ trusty-updates/main dpkg-dev all 1.17.5ubuntu5.4 [726 kB]
Get:5 http://au.archive.ubuntu.com/ubuntu/ trusty/main build-essential amd64 11.6ubuntu6 [4,838 B]
Get:6 http://au.archive.ubuntu.com/ubuntu/ trusty/main cmake-data all 2.8.12.2-0ubuntu3 [676 kB]
Get:7 http://au.archive.ubuntu.com/ubuntu/ trusty/main cmake amd64 2.8.12.2-0ubuntu3 [2,618 kB]
Get:8 http://ppa.launchpad.net/ska-sa/main/ubuntu/ trusty/main libblitz0ldbl amd64 1:0.11-1trusty [74.8 kB]
Get:9 http://ppa.launchpad.net/ska-sa/main/ubuntu/ trusty/main libblitz0-dev amd64 1:0.11-1trusty [201 kB]
Get:10 http://au.archive.ubuntu.com/ubuntu/ trusty/main po-debconf all 1.0.16+nmu2ubuntu1 [210 kB]
Get:11 http://au.archive.ubuntu.com/ubuntu/ trusty-updates/main dh-apparmor all 2.8.95~2430-0ubuntu5.3 [12.2 kB]
Get:12 http://au.archive.ubuntu.com/ubuntu/ trusty/main debhelper all 9.20131227ubuntu1 [604 kB]
Get:13 http://au.archive.ubuntu.com/ubuntu/ trusty/main libblas-dev amd64 1.2.20110419-7 [240 kB]
Get:14 http://au.archive.ubuntu.com/ubuntu/ trusty/universe libcfitsio3-dev amd64 3.340-2ubuntu2 [493 kB]
Get:15 http://au.archive.ubuntu.com/ubuntu/ trusty/main libfftw3-bin amd64 3.3.3-7ubuntu3 [32.6 kB]
Get:16 http://ppa.launchpad.net/radio-astro/main/ubuntu/ trusty/main libcasacore1 amd64 1.7.0-2trusty [6,986 kB]
Get:17 http://au.archive.ubuntu.com/ubuntu/ trusty/main libfftw3-dev amd64 3.3.3-7ubuntu3 [2,067 kB]
Get:18 http://au.archive.ubuntu.com/ubuntu/ trusty/main libgdbm-dev amd64 1.8.3-12build1 [24.9 kB]
Get:19 http://au.archive.ubuntu.com/ubuntu/ trusty/main liblapack-dev amd64 3.5.0-2ubuntu1 [1,740 kB]
Get:20 http://au.archive.ubuntu.com/ubuntu/ trusty/main python-all amd64 2.7.5-5ubuntu3 [984 B]
Get:21 http://ppa.launchpad.net/radio-astro/main/ubuntu/ trusty/main libcasacore-dev amd64 1.7.0-2trusty [1,501 kB]
Fetched 19.4 MB in 42s (457 kB/s)                                              
Selecting previously unselected package libfftw3-long3:amd64.
(Reading database ... 206971 files and directories currently installed.)
Preparing to unpack .../libfftw3-long3_3.3.3-7ubuntu3_amd64.deb ...
Unpacking libfftw3-long3:amd64 (3.3.3-7ubuntu3) ...
Selecting previously unselected package libfftw3-quad3:amd64.
Preparing to unpack .../libfftw3-quad3_3.3.3-7ubuntu3_amd64.deb ...
Unpacking libfftw3-quad3:amd64 (3.3.3-7ubuntu3) ...
Selecting previously unselected package dpkg-dev.
Preparing to unpack .../dpkg-dev_1.17.5ubuntu5.4_all.deb ...
Unpacking dpkg-dev (1.17.5ubuntu5.4) ...
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Preparing to unpack .../build-essential_11.6ubuntu6_amd64.deb ...
Unpacking build-essential (11.6ubuntu6) ...
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Preparing to unpack .../cmake-data_2.8.12.2-0ubuntu3_all.deb ...
Unpacking cmake-data (2.8.12.2-0ubuntu3) ...
Selecting previously unselected package cmake.
Preparing to unpack .../cmake_2.8.12.2-0ubuntu3_amd64.deb ...
Unpacking cmake (2.8.12.2-0ubuntu3) ...
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Unpacking po-debconf (1.0.16+nmu2ubuntu1) ...
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Preparing to unpack .../dh-apparmor_2.8.95~2430-0ubuntu5.3_all.deb ...
Unpacking dh-apparmor (2.8.95~2430-0ubuntu5.3) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../debhelper_9.20131227ubuntu1_all.deb ...
Unpacking debhelper (9.20131227ubuntu1) ...
Selecting previously unselected package libblas-dev.
Preparing to unpack .../libblas-dev_1.2.20110419-7_amd64.deb ...
Unpacking libblas-dev (1.2.20110419-7) ...
Selecting previously unselected package libcfitsio3-dev.
Preparing to unpack .../libcfitsio3-dev_3.340-2ubuntu2_amd64.deb ...
Unpacking libcfitsio3-dev (3.340-2ubuntu2) ...
Selecting previously unselected package libfftw3-bin.
Preparing to unpack .../libfftw3-bin_3.3.3-7ubuntu3_amd64.deb ...
Unpacking libfftw3-bin (3.3.3-7ubuntu3) ...
Selecting previously unselected package libfftw3-dev:amd64.
Preparing to unpack .../libfftw3-dev_3.3.3-7ubuntu3_amd64.deb ...
Unpacking libfftw3-dev:amd64 (3.3.3-7ubuntu3) ...
Selecting previously unselected package libgdbm-dev.
Preparing to unpack .../libgdbm-dev_1.8.3-12build1_amd64.deb ...
Unpacking libgdbm-dev (1.8.3-12build1) ...
Selecting previously unselected package liblapack-dev.
Preparing to unpack .../liblapack-dev_3.5.0-2ubuntu1_amd64.deb ...
Unpacking liblapack-dev (3.5.0-2ubuntu1) ...
Selecting previously unselected package python-all.
Preparing to unpack .../python-all_2.7.5-5ubuntu3_amd64.deb ...
Unpacking python-all (2.7.5-5ubuntu3) ...
Selecting previously unselected package wcslib-dev.
Preparing to unpack .../wcslib-dev_4.25.1-3trusty_amd64.deb ...
Unpacking wcslib-dev (4.25.1-3trusty) ...
Selecting previously unselected package libblitz0ldbl.
Preparing to unpack .../libblitz0ldbl_1%3a0.11-1trusty_amd64.deb ...
Unpacking libblitz0ldbl (1:0.11-1trusty) ...
Selecting previously unselected package libblitz0-dev.
Preparing to unpack .../libblitz0-dev_1%3a0.11-1trusty_amd64.deb ...
Unpacking libblitz0-dev (1:0.11-1trusty) ...
Selecting previously unselected package libcasacore1.
Preparing to unpack .../libcasacore1_1.7.0-2trusty_amd64.deb ...
Unpacking libcasacore1 (1.7.0-2trusty) ...
Selecting previously unselected package libcasacore-dev.
Preparing to unpack .../libcasacore-dev_1.7.0-2trusty_amd64.deb ...
Unpacking libcasacore-dev (1.7.0-2trusty) ...
dpkg: error processing archive /var/cache/apt/archives/libcasacore-dev_1.7.0-2trusty_amd64.deb (--unpack):
 trying to overwrite '/usr/lib/libcasa_components.so', which is also in package casarest 1.3.1-2trusty
Processing triggers for man-db (2.6.7.1-1ubuntu1) ...
Processing triggers for doc-base (0.10.5) ...
Processing 1 added doc-base file...
Processing triggers for install-info (5.2.0.dfsg.1-2) ...
Errors were encountered while processing:
 /var/cache/apt/archives/libcasacore-dev_1.7.0-2trusty_amd64.deb
E: Sub-process /usr/bin/dpkg returned an error code (1)
E: Failed to process build dependencies
ianh@nerv:~$ 
gijzelaerr commented 9 years ago

hm, one of the packages you install depends on casacore 1.7, which conflicts with casarest.

can you try to install the packages one by one and see which one depends on casacore 1.7? I thought I updated all packages, but something went wrong there.

IanHeywood commented 9 years ago

Looks like

sudo apt-get build-dep -y meqtrees-timba

is the offender.

Cheers.

gijzelaerr commented 9 years ago

can't replicate the problem.

what is the content of /etc/apt/sources.list.d/radio-astro-main-trusty.list and did you do a apt-get update before the build-dep command?

IanHeywood commented 9 years ago

I did an apt-get update as part of the Launchpad preparations.

ianh@nerv:~$ more /etc/apt/sources.list.d/radio-astro-main-trusty.list
deb http://ppa.launchpad.net/radio-astro/main/ubuntu trusty main
# deb-src http://ppa.launchpad.net/radio-astro/main/ubuntu trusty main
gijzelaerr commented 9 years ago

uncomment the commented line or do sudo add-apt-repository -s ppa:radio-astro/main, update and try again.

you forgot to add the -s flag, which adds the PPA as a source repo. Is that not in the documentation?

gijzelaerr commented 9 years ago

also, it looks like you still have the old ska-sa repo enabed, please remove that from your /etc/apt/sources.list.d folder.

IanHeywood commented 9 years ago

Uncommenting the line has fixed it.

The -s flag is in the documentation for the "build from source" section but not in the "install binaries" section, which might have caused the trouble. Also, the old ska-sa repro is the one that is pointed to in the "build from source" instructions so that might need changing.

I guess the lack of a -s flag in the binaries section (unless it should be there) combined with the old repo in the from source section was the problem. This is a brand new VM so there are no hangovers from previous builds.

Cheers.

IanHeywood commented 9 years ago

A new problem at the next step:

ianh@nerv:~$ sudo apt-get install -y libcasacore-dev
Reading package lists... Done
Building dependency tree       
Reading state information... Done
The following packages were automatically installed and are no longer required:
  libboost-filesystem1.54.0 libboost-regex1.54.0 libboost-thread1.54.0
  libcasacore2 libgsl0ldbl liblog4cplus-1.0-4 libmeqtrees-timba0
  meqtrees-timba python-kittens python-meqtrees-timba python-purr python-pywcs
  python-tigger
Use 'apt-get autoremove' to remove them.
The following NEW packages will be installed:
  libcasacore-dev
0 to upgrade, 1 to newly install, 0 to remove and 1 not to upgrade.
19 not fully installed or removed.
Need to get 0 B/1,501 kB of archives.
After this operation, 11.9 MB of additional disk space will be used.
(Reading database ... 208460 files and directories currently installed.)
Preparing to unpack .../libcasacore-dev_1.7.0-2trusty_amd64.deb ...
Unpacking libcasacore-dev (1.7.0-2trusty) ...
dpkg: error processing archive /var/cache/apt/archives/libcasacore-dev_1.7.0-2trusty_amd64.deb (--unpack):
 trying to overwrite '/usr/lib/libcasa_components.so', which is also in package casarest 1.3.1-2trusty
Errors were encountered while processing:
 /var/cache/apt/archives/libcasacore-dev_1.7.0-2trusty_amd64.deb
E: Sub-process /usr/bin/dpkg returned an error code (1)
gijzelaerr commented 9 years ago

Can you update the doc or give a link so i can modify.

you are installing the development files for casacore 1.7 (libcasacore-dev) which is there for historical reasons, I suggest you install libcasacore2-dev

IanHeywood commented 9 years ago

Thanks, libcasacore2-dev has installed successfully.

The binary documentation that may or may not need the -s flag is here:

(https://github.com/ska-sa/meqtrees/wiki/UbuntuPackages)[https://github.com/ska-sa/meqtrees/wiki/UbuntuPackages]

and the build from source documentation that has the old ska-sa repository and the historical libcasacore-dev item is here:

(https://github.com/ska-sa/meqtrees/wiki/UbuntuPackages)[https://github.com/ska-sa/meqtrees/wiki/UbuntuPackages]

gijzelaerr commented 9 years ago

those are both the same link

gijzelaerr commented 9 years ago

found and fixed

IanHeywood commented 9 years ago

I obviously haven't mastered markdown either. I going to blame the fact that I'm having to use Ctrl+C, Shift+Ctrl+C and Cmd+C for copying depending on what window I'm in.

Cheers.