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Bug 396065 - [science-overlay] embassy-topo fails to emerge due to wrong filesize
Summary: [science-overlay] embassy-topo fails to emerge due to wrong filesize
Status: RESOLVED OBSOLETE
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Assignee: Gentoo Science Related Packages
URL:
Whiteboard:
Keywords:
Depends on:
Blocks:
 
Reported: 2011-12-26 11:36 UTC by Juergen Rose
Modified: 2015-03-28 17:51 UTC (History)
0 users

See Also:
Package list:
Runtime testing required: ---


Attachments
An embassy-topo ebuild disabling patches and emerging embassy-topo. (embassy-topo-2.0.0.ebuild,389 bytes, text/plain)
2011-12-26 11:38 UTC, Juergen Rose
Details

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Description Juergen Rose 2011-12-26 11:36:57 UTC
'emerge embassy' fails with:

root@lynx:/usr/local/portage/sci-biology(68)# emerge -vD embassy

These are the packages that would be merged, in order:

Calculating dependencies... done!
[ebuild  N     ] sci-biology/embassy-topo-2.0.0  USE="X mysql pdf png postgres -static-libs" 378 kB [1]
...
>>> Starting parallel fetch

>>> Emerging (1 of 6) sci-biology/embassy-topo-2.0.0 from science
 * Fetching files in the background. To view fetch progress, run
 * `tail -f /var/log/emerge-fetch.log` in another terminal.
>>> Downloading 'http://linux.rz.ruhr-uni-bochum.de/download/gentoo-mirror/distfiles/embassy-topo-2.0.0.tar.gz'
--2011-12-26 12:31:56--  http://linux.rz.ruhr-uni-bochum.de/download/gentoo-mirror/distfiles/embassy-topo-2.0.0.tar.gz
Resolving linux.rz.ruhr-uni-bochum.de (linux.rz.ruhr-uni-bochum.de)... 134.147.32.114
Connecting to linux.rz.ruhr-uni-bochum.de (linux.rz.ruhr-uni-bochum.de)|134.147.32.114|:80... connected.
HTTP request sent, awaiting response... 404 Not Found
2011-12-26 12:31:57 ERROR 404: Not Found.

>>> Downloading 'http://ftp-stud.fht-esslingen.de/pub/Mirrors/gentoo/distfiles/embassy-topo-2.0.0.tar.gz'
--2011-12-26 12:31:57--  http://ftp-stud.fht-esslingen.de/pub/Mirrors/gentoo/distfiles/embassy-topo-2.0.0.tar.gz
Resolving ftp-stud.fht-esslingen.de (ftp-stud.fht-esslingen.de)... 129.143.116.10
Connecting to ftp-stud.fht-esslingen.de (ftp-stud.fht-esslingen.de)|129.143.116.10|:80... connected.
HTTP request sent, awaiting response... 404 Not Found
2011-12-26 12:31:57 ERROR 404: Not Found.

>>> Downloading 'ftp://ftp.wh2.tu-dresden.de/pub/mirrors/gentoo/distfiles/embassy-topo-2.0.0.tar.gz'
--2011-12-26 12:31:57--  ftp://ftp.wh2.tu-dresden.de/pub/mirrors/gentoo/distfiles/embassy-topo-2.0.0.tar.gz
           => `/usr/portage_lynx/distfiles/embassy-topo-2.0.0.tar.gz'
Resolving ftp.wh2.tu-dresden.de (ftp.wh2.tu-dresden.de)... 141.30.228.4
Connecting to ftp.wh2.tu-dresden.de (ftp.wh2.tu-dresden.de)|141.30.228.4|:21... connected.
Logging in as anonymous ... Logged in!
==> SYST ... done.    ==> PWD ... done.
==> TYPE I ... done.  ==> CWD (1) /pub/mirrors/gentoo/distfiles ... done.
==> SIZE embassy-topo-2.0.0.tar.gz ... done.
==> PASV ... done.    ==> RETR embassy-topo-2.0.0.tar.gz ... 
No such file `embassy-topo-2.0.0.tar.gz'.

>>> Downloading 'ftp://sunsite.informatik.rwth-aachen.de/pub/Linux/gentoo/distfiles/embassy-topo-2.0.0.tar.gz'
--2011-12-26 12:32:00--  ftp://sunsite.informatik.rwth-aachen.de/pub/Linux/gentoo/distfiles/embassy-topo-2.0.0.tar.gz
           => `/usr/portage_lynx/distfiles/embassy-topo-2.0.0.tar.gz'
Resolving sunsite.informatik.rwth-aachen.de (sunsite.informatik.rwth-aachen.de)... 137.226.34.227
Connecting to sunsite.informatik.rwth-aachen.de (sunsite.informatik.rwth-aachen.de)|137.226.34.227|:21... connected.
Logging in as anonymous ... Logged in!
==> SYST ... done.    ==> PWD ... done.
==> TYPE I ... done.  ==> CWD (1) /pub/Linux/gentoo/distfiles ... done.
==> SIZE embassy-topo-2.0.0.tar.gz ... done.
==> PASV ... done.    ==> RETR embassy-topo-2.0.0.tar.gz ... 
No such file `embassy-topo-2.0.0.tar.gz'.

>>> Downloading 'ftp://ftp.tu-clausthal.de/pub/linux/gentoo/distfiles/embassy-topo-2.0.0.tar.gz'
--2011-12-26 12:32:01--  ftp://ftp.tu-clausthal.de/pub/linux/gentoo/distfiles/embassy-topo-2.0.0.tar.gz
           => `/usr/portage_lynx/distfiles/embassy-topo-2.0.0.tar.gz'
Resolving ftp.tu-clausthal.de (ftp.tu-clausthal.de)... 139.174.2.36
Connecting to ftp.tu-clausthal.de (ftp.tu-clausthal.de)|139.174.2.36|:21... connected.
Logging in as anonymous ... Logged in!
==> SYST ... done.    ==> PWD ... done.
==> TYPE I ... done.  ==> CWD (1) /pub/linux/gentoo/distfiles ... done.
==> SIZE embassy-topo-2.0.0.tar.gz ... done.
==> PASV ... done.    ==> RETR embassy-topo-2.0.0.tar.gz ... 
No such file `embassy-topo-2.0.0.tar.gz'.

>>> Downloading 'ftp://ftp.easynet.nl/mirror/gentoo/distfiles/embassy-topo-2.0.0.tar.gz'
--2011-12-26 12:32:01--  ftp://ftp.easynet.nl/mirror/gentoo/distfiles/embassy-topo-2.0.0.tar.gz
           => `/usr/portage_lynx/distfiles/embassy-topo-2.0.0.tar.gz'
Resolving ftp.easynet.nl (ftp.easynet.nl)... 195.86.128.57
Connecting to ftp.easynet.nl (ftp.easynet.nl)|195.86.128.57|:21... failed: Connection refused.
>>> Downloading 'ftp://emboss.open-bio.org/pub/EMBOSS/TOPO-2.0.0.tar.gz'
--2011-12-26 12:32:02--  ftp://emboss.open-bio.org/pub/EMBOSS/TOPO-2.0.0.tar.gz
           => `/usr/portage_lynx/distfiles/embassy-topo-2.0.0.tar.gz'
Resolving emboss.open-bio.org (emboss.open-bio.org)... 208.94.50.58
Connecting to emboss.open-bio.org (emboss.open-bio.org)|208.94.50.58|:21... connected.
Logging in as anonymous ... Logged in!
==> SYST ... done.    ==> PWD ... done.
==> TYPE I ... done.  ==> CWD (1) /pub/EMBOSS ... done.
==> SIZE TOPO-2.0.0.tar.gz ... 411485
==> PASV ... done.    ==> RETR TOPO-2.0.0.tar.gz ... done.
Length: 411485 (402K) (unauthoritative)

100%[======================================>] 411,485      158K/s   in 2.5s    

2011-12-26 12:32:06 (158 KB/s) - `/usr/portage_lynx/distfiles/embassy-topo-2.0.0.tar.gz' saved [411485]

!!! Fetched file: embassy-topo-2.0.0.tar.gz VERIFY FAILED!
!!! Reason: Filesize does not match recorded size
!!! Got:      411485
!!! Expected: 386287


After deleting the Manifest I could download ftp://emboss.open-bio.org/pub/EMBOSS/TOPO-2.0.0.tar.gz, but embassy-topo-2.0.0.patch failed:


>>> Emerging (1 of 6) sci-biology/embassy-topo-2.0.0 from local
 * embassy-topo-2.0.0.tar.gz RMD160 SHA1 SHA256 size ;-) ...                                                                                                                      [ ok ]
>>> Unpacking source...
>>> Unpacking embassy-topo-2.0.0.tar.gz to /var/tmp/portage/sci-biology/embassy-topo-2.0.0/work
>>> Source unpacked in /var/tmp/portage/sci-biology/embassy-topo-2.0.0/work
>>> Preparing source in /var/tmp/portage/sci-biology/embassy-topo-2.0.0/work/TOPO-2.0.0 ...
 * Applying embassy-topo-2.0.0.patch ...

 * Failed Patch: embassy-topo-2.0.0.patch !
 *  ( /usr/local/portage/sci-biology/embassy-topo/files/embassy-topo-2.0.0.patch )
Comment 1 Juergen Rose 2011-12-26 11:38:25 UTC
Created attachment 296971 [details]
An embassy-topo ebuild disabling patches and emerging embassy-topo.
Comment 2 Justin Lecher gentoo-dev 2012-02-20 14:33:52 UTC
# Justin Lecher <jlec@gentoo.org> (20 Feb 2012)
# They are broken in one or the other way
# Need to be bumped to emboss-6.4.0
sci-biology/emboss::science
sci-biology/embassy::science
sci-biology/embassy-cbstools::science
sci-biology/embassy-domainatrix::science
sci-biology/embassy-domalign::science
sci-biology/embassy-domsearch::science
sci-biology/embassy-emnu::science
sci-biology/embassy-esim4::science
sci-biology/embassy-hmmer::science
sci-biology/embassy-iprscan::science
sci-biology/embassy-mse::science
sci-biology/embassy-phylipnew::science
sci-biology/embassy-signature::science
sci-biology/embassy-structure::science
sci-biology/embassy-topo::science
sci-biology/embassy-vienna::science