Unable to install breqn and cadabra on Arch Linux

darkmav · 2012-05-31 14:40:11

Hi,

I am running Arch Linux (64-bit) on my Dell XPS 15 laptop. I use LaTeX for all my scientific typesetting. When I was running Fedora on this system earlier, I used Cadabra, an open source symbolic manipulation program suited to calculations in quantum field theory. I tried to install cadabra in Arch using yaourt, but I get the following error message:

[root@krypton ~]# yaourt cadabra
1 aur/cadabra 1.29-1 (2)
    Cadabra is a computer algebra system (CAS)
2 aur/modglue 1.16-2 (1)
    Modglue library for Cadabra computer algebra system (CAS)
==> Enter n° of packages to be installed (ex: 1 2 3 or 1-3)
==> -------------------------------------------------------
==> 1


==> Downloading cadabra PKGBUILD from AUR...
x PKGBUILD
x cadabra.install


First Submitted: Wed, 16 Sep 2009 08:01:06 +0000	
cadabra 1.29-1 
( Unsupported package: Potentially dangerous ! )
==> Edit PKGBUILD ? [Y/n] ("A" to abort)
==> ------------------------------------
==> n

==> cadabra dependencies:
 - conlie (building from AUR)
 - modglue>=1.16 (building from AUR)
 - breqn (building from AUR)


==> Edit cadabra.install ? [Y/n] ("A" to abort)
==> -------------------------------------------
==> n

==> Continue building cadabra ? [Y/n]
==> ---------------------------------
==> 
==> Building and installing package
==> Install or build missing dependencies for cadabra:

==> Downloading breqn PKGBUILD from AUR...
x breqn.install
x PKGBUILD


First Submitted: Wed, 16 Sep 2009 08:00:09 +0000	
breqn 1.2b-2 
( Unsupported package: Potentially dangerous ! )
==> Edit PKGBUILD ? [Y/n] ("A" to abort)
==> ------------------------------------
==> n

==> breqn dependencies:
 - texlive-bin (already installed)
 - texlive-core (already installed)


==> Edit breqn.install ? [Y/n] ("A" to abort)
==> -----------------------------------------
==> n

==> Continue building breqn ? [Y/n]
==> -------------------------------
==> 
==> Building and installing package
==> WARNING: Building package as root is dangerous.
 Please run yaourt as a non-privileged user.
==> Making package: breqn 1.2b-2 (Thu May 31 20:10:59 IST 2012)
==> Checking runtime dependencies...
==> Checking buildtime dependencies...
==> Retrieving Sources...
  -> Downloading mh.zip...
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 2196k  100 2196k    0     0  74677      0  0:00:30  0:00:30 --:--:-- 73748
==> Validating source files with md5sums...
    mh.zip ... FAILED
==> ERROR: One or more files did not pass the validity check!
==> ERROR: Makepkg was unable to build breqn.
==> Restart building breqn ? [y/N]
==> ------------------------------
==>

Surprisingly, a search on google did not reveal anything useful. Apparently the problem is validating the package 'breqn' which is a prerequisite for cadabra, but fails to install through yaourt because of some md5 checksum validation error (as I understand). And it seems there is no override for this in yaourt.

Any suggestions to help me get cadabra to work will be greatly appreciated.

Thanks in advance!

References:

1. http://aur.archlinux.org/packages.php?ID=30207

2. http://cadabra.phi-sci.com/

Last edited by darkmav (2012-05-31 14:41:57)

ewaller · 2012-05-31 15:07:47

Your problem is that the file the PKGBUILD is downloading is not the same one that the creator of the PKGBUILD was working with.

an md5sum is a hash (a fingerprint, if you will) of the file. When the PKGBUILD was created, that fingerprint was included in the file. That yours does not match means one of two things:

1. The file you downloaded was either corrupt, or has been tampered with, or
2. The file you downloaded has been updated by the author, but the PKGBUILD has not been updated.

If it is case 1, stop. If it is case 2, you can do the following:

The Cadabra PKGBUILD was updated last June (almost a year ago). You can either post a comment to the AUR and see if the maintainer will fix it, or you can fix the PKGBUILD yourself and (hopefully) post the changes back to the AUR as a comment.

# Contributor: Dariusz 'quasi' Panchyrz <quasi@aur.archlinux.org>

pkgname=cadabra
pkgver=1.29
pkgrel=1
pkgdesc="Cadabra is a computer algebra system (CAS)"
arch=('i686' 'x86_64')
url="http://cadabra.phi-sci.com/"
license=('GPL')
depends=('conlie' 'modglue>=1.16' 'breqn')
install=$pkgname.install
source=(http://cadabra.phi-sci.com/$pkgname-$pkgver.tar.gz)
md5sums=('ea6e64535e6a9abe8810e5baa6a579a8')

build() {

  cd $startdir/src/$pkgname-$pkgver/
  ./configure --prefix=$startdir/pkg/usr/
  make || return 1
  make install || return 1


}

Notice the md5sums entry in the PKGBUILD above. It needs to be updated in accordance with this article and then built on your machine using makepkg. I strongly suggest you not user a helper for this, but rather use the methods described here

Last edited by ewaller (2012-05-31 15:09:09)

WorMzy · 2012-05-31 15:14:57

That error could mean that a] the source file (mh.zip) is corrupted (either on the server, or on your local machine), b] the source file has changed on the server and the PKGBUILD is now out of date.

In the case of a], try redownloading the source files. If you get the same error again, check that you can extract the the contents of the file; if you can't, contact the developer and let them know; if you can, then it's probably not corrupted, so move to b].

In the case of b], I recommend that you check the developer's website to confirm that the source package has been changed (to make sure that it hasn't been maliciously tampered with), then browse to the directory containing the PKGBUILD, and run

makepkg -g >> PKGBUILD

to generated new md5sums and append them to the end of the PKGBUILD (which overrides the old md5s). Then run

makepkg -sri

Also, flag the aur package as out of date and make a comment containing the reason why it's out of date, and, ideally, the correct md5sum.

Pres · 2012-05-31 15:16:26

ewaller is correct, but he pointed you to the wrong package. The breqn package is the one that's failing and needs to be modified.

Also I'll point out that you are running yaourt as root (and therefore makepkg as root), which is a bad idea.

ewaller · 2012-05-31 15:23:20

Pres wrote:

ewaller is correct, but he pointed you to the wrong package. The breqn package is the one that's failing and needs to be modified.

Good catch.

breqn was updated in November. There are no comments on it ,either.

Last edited by ewaller (2012-05-31 15:56:17)

darkmav · 2012-06-04 17:48:50

WorMzy wrote:

That error could mean that a] the source file (mh.zip) is corrupted (either on the server, or on your local machine), b] the source file has changed on the server and the PKGBUILD is now out of date.
In the case of a], try redownloading the source files. If you get the same error again, check that you can extract the the contents of the file; if you can't, contact the developer and let them know; if you can, then it's probably not corrupted, so move to b].
In the case of b], I recommend that you check the developer's website to confirm that the source package has been changed (to make sure that it hasn't been maliciously tampered with), then browse to the directory containing the PKGBUILD, and run
makepkg -g >> PKGBUILD
to generated new md5sums and append them to the end of the PKGBUILD (which overrides the old md5s). Then run
makepkg -sri
Also, flag the aur package as out of date and make a comment containing the reason why it's out of date, and, ideally, the correct md5sum.

Thanks for the replies everyone. I tried what you suggested, but this does not help. I am yet to contact the developer, but it seems this problem is specific to Arch Linux, even though cadabra is on the AUR.

Pres · 2012-06-04 18:03:10

The problem is that the file the breqn PKGBUILD is pointing at has been updated on the server, however the md5sum in the PKGBUILD has not been updated to reflect this.

You can check the server yourself to verify.

darkmav · 2012-06-04 18:22:25

Pres wrote:

The problem is that the file the breqn PKGBUILD is pointing at has been updated on the server, however the md5sum in the PKGBUILD has not been updated to reflect this.
You can check the server yourself to verify.

That may be so, but being relatively new to this distribution, and also being somewhat hard pressed for time (I need to use Cadabra for a project), I do not know what to do. Maybe I will have to consider installing Ubuntu in a virtual box environment just to run Cadabra.

Pres · 2012-06-04 18:28:45

Here's the PKGBUILD for breqn:

# Contributor: Dariusz 'quasi' Panchyrz <quasi@aur.archlinux.org>

pkgname=breqn
pkgver=1.2b
pkgrel=2
pkgdesc="Automatic line breaking of displayed equations."
arch=('i686' 'x86_64')
url="http://www.ctan.org/tex-archive/help/Catalogue/entries/breqn.html"
license=('LPPL')
depends=('texlive-bin' 'texlive-core')
install=$pkgname.install
source=(ftp://cam.ctan.org/tex-archive/macros/latex/contrib/mh.zip)
md5sums=('6ae7bdc1d723dfe1cbb549a4c3b310d9')
build() {

  mkdir -p $startdir/pkg/usr/share/texmf/tex/latex/breqn
  mkdir -p $startdir/pkg/usr/share/doc/breqn

  cd $startdir/src/mh

  for i in *.dtx
  do
    tex --output-directory=$startdir/pkg/usr/share/texmf/tex/latex/breqn/ $i
  done

  for i in *.pdf
  do
    cp $i $startdir/pkg/usr/share/doc/breqn
  done

}

Grab the mh.zip file listed there. Run md5sum on the file to get an md5 hash of it. Then replace the hash in the md5sums array with the new one and build it.

Probably a good idea to figure out why the file was updated first, however. Was it a version bump?

Once you fix this, post in the comments section for breqn to alert the maintainer of this change.

Arch Linux

#1 2012-05-31 14:40:11

Unable to install breqn and cadabra on Arch Linux

#2 2012-05-31 15:07:47

Re: Unable to install breqn and cadabra on Arch Linux

#3 2012-05-31 15:14:57

Re: Unable to install breqn and cadabra on Arch Linux

#4 2012-05-31 15:16:26

Re: Unable to install breqn and cadabra on Arch Linux

#5 2012-05-31 15:23:20

Re: Unable to install breqn and cadabra on Arch Linux

#6 2012-06-04 17:48:50

Re: Unable to install breqn and cadabra on Arch Linux

#7 2012-06-04 18:03:10

Re: Unable to install breqn and cadabra on Arch Linux

#8 2012-06-04 18:22:25

Re: Unable to install breqn and cadabra on Arch Linux

#9 2012-06-04 18:28:45

Re: Unable to install breqn and cadabra on Arch Linux

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