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Bug 396063 - [science-overlay] embassy-mse fails to emerge due to wrong filesize
Summary: [science-overlay] embassy-mse 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 11:07 UTC by Juergen Rose
Modified: 2015-03-28 17:51 UTC (History)
0 users

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


Attachments
An embassy-mse ebuild which disables patches and compiles embassy-mse (embassy-mse-3.0.0.ebuild,563 bytes, text/plain)
2011-12-26 11:09 UTC, Juergen Rose
Details

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Description Juergen Rose 2011-12-26 11:07:37 UTC
'emerge embassy' fails with:

root@lynx:/usr/local/portage/sci-biology(40)# emerge -vD embassy

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

Calculating dependencies... done!
[ebuild  N     ] sci-biology/embassy-mse-3.0.0  USE="X mysql ncurses pdf png postgres -static-libs" 426 kB [1]
...
>>> Starting parallel fetch

>>> Emerging (1 of 12) sci-biology/embassy-mse-3.0.0 from local
 * 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-mse-3.0.0.tar.gz'
--2011-12-26 12:02:26--  http://linux.rz.ruhr-uni-bochum.de/download/gentoo-mirror/distfiles/embassy-mse-3.0.0.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 12:02:26 ERROR 404: Not Found.

>>> Downloading 'http://ftp-stud.fht-esslingen.de/pub/Mirrors/gentoo/distfiles/embassy-mse-3.0.0.tar.gz'
--2011-12-26 12:02:26--  http://ftp-stud.fht-esslingen.de/pub/Mirrors/gentoo/distfiles/embassy-mse-3.0.0.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 12:02:26 ERROR 404: Not Found.

>>> Downloading 'ftp://ftp.wh2.tu-dresden.de/pub/mirrors/gentoo/distfiles/embassy-mse-3.0.0.tar.gz'
--2011-12-26 12:02:26--  ftp://ftp.wh2.tu-dresden.de/pub/mirrors/gentoo/distfiles/embassy-mse-3.0.0.tar.gz
           => `/usr/portage_lynx/distfiles/embassy-mse-3.0.0.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-mse-3.0.0.tar.gz ... done.
==> PASV ... done.    ==> RETR embassy-mse-3.0.0.tar.gz ... 
No such file `embassy-mse-3.0.0.tar.gz'.

>>> Downloading 'ftp://sunsite.informatik.rwth-aachen.de/pub/Linux/gentoo/distfiles/embassy-mse-3.0.0.tar.gz'
--2011-12-26 12:02:28--  ftp://sunsite.informatik.rwth-aachen.de/pub/Linux/gentoo/distfiles/embassy-mse-3.0.0.tar.gz
           => `/usr/portage_lynx/distfiles/embassy-mse-3.0.0.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-mse-3.0.0.tar.gz ... done.
==> PASV ... done.    ==> RETR embassy-mse-3.0.0.tar.gz ... 
No such file `embassy-mse-3.0.0.tar.gz'.

>>> Downloading 'ftp://ftp.tu-clausthal.de/pub/linux/gentoo/distfiles/embassy-mse-3.0.0.tar.gz'
--2011-12-26 12:02:29--  ftp://ftp.tu-clausthal.de/pub/linux/gentoo/distfiles/embassy-mse-3.0.0.tar.gz
           => `/usr/portage_lynx/distfiles/embassy-mse-3.0.0.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-mse-3.0.0.tar.gz ... done.
==> PASV ... done.    ==> RETR embassy-mse-3.0.0.tar.gz ... 
No such file `embassy-mse-3.0.0.tar.gz'.

>>> Downloading 'ftp://ftp.easynet.nl/mirror/gentoo/distfiles/embassy-mse-3.0.0.tar.gz'
--2011-12-26 12:02:29--  ftp://ftp.easynet.nl/mirror/gentoo/distfiles/embassy-mse-3.0.0.tar.gz
           => `/usr/portage_lynx/distfiles/embassy-mse-3.0.0.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/MSE-3.0.0.tar.gz'
--2011-12-26 12:02:30--  ftp://emboss.open-bio.org/pub/EMBOSS/MSE-3.0.0.tar.gz
           => `/usr/portage_lynx/distfiles/embassy-mse-3.0.0.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 MSE-3.0.0.tar.gz ... 454487
==> PASV ... done.    ==> RETR MSE-3.0.0.tar.gz ... done.
Length: 454487 (444K) (unauthoritative)

100%[======================================>] 454,487      160K/s   in 2.8s    

2011-12-26 12:02:35 (160 KB/s) - `/usr/portage_lynx/distfiles/embassy-mse-3.0.0.tar.gz' saved [454487]

!!! Fetched file: embassy-mse-3.0.0.tar.gz VERIFY FAILED!
!!! Reason: Filesize does not match recorded size
!!! Got:      454487
!!! Expected: 435315
Refetching... File renamed to '/usr/portage_lynx/distfiles/embassy-mse-3.0.0.tar.gz._checksum_failure_.QQD0Gt'

!!! Couldn't download 'embassy-mse-3.0.0.tar.gz'. Aborting.


After deleting the Manifest I could download ftp://emboss.open-bio.org/pub/EMBOSS/MSE-3.0.0.tar.gz, but the patch failed:

>>> Emerging (1 of 12) sci-biology/embassy-mse-3.0.0 from local
 * embassy-mse-3.0.0.tar.gz RMD160 SHA1 SHA256 size ;-) ...                                                                                                                       [ ok ]
>>> Unpacking source...
>>> Unpacking embassy-mse-3.0.0.tar.gz to /var/tmp/portage/sci-biology/embassy-mse-3.0.0/work
>>> Source unpacked in /var/tmp/portage/sci-biology/embassy-mse-3.0.0/work
>>> Preparing source in /var/tmp/portage/sci-biology/embassy-mse-3.0.0/work/MSE-3.0.0 ...
 * Applying embassy-mse-3.0.0.patch ...

 * Failed Patch: embassy-mse-3.0.0.patch !
 *  ( /usr/local/portage/sci-biology/embassy-mse/files/embassy-mse-3.0.0.patch )
 * 
 * Include in your bugreport the contents of:
 * 
 *   /var/tmp/portage/sci-biology/embassy-mse-3.0.0/temp/embassy-mse-3.0.0.patch.out

 * ERROR: sci-biology/embassy-mse-3.0.0 failed (prepare phase):
 *   Failed Patch: embassy-mse-3.0.0.patch!
Comment 1 Juergen Rose 2011-12-26 11:09:29 UTC
Created attachment 296967 [details]
An embassy-mse ebuild which disables patches and compiles embassy-mse
Comment 2 Justin Lecher gentoo-dev 2012-02-20 14:33:56 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