Bug 396057 – [science-overlay] embassy-phylipnew-3.69 fails to emerge due to wrong filesize

• Product: Gentoo Linux
• Status: RESOLVED OBSOLETE

[Description Juergen Rose 2011-12-26 10:49:44 UTC]

'emerge -vD embassy' fails with:
...
root@lynx:/usr/local/portage/sci-biology(23)# emerge -vD embassy
These are the packages that would be merged, in order:
Calculating dependencies... done!
[ebuild  N     ] sci-biology/embassy-phylipnew-3.69  USE="X mysql pdf png postgres -static-libs" 1,629 kB [1]
...
>>> Starting parallel fetch

>>> Emerging (1 of 13) sci-biology/embassy-phylipnew-3.69 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-phylipnew-3.69.tar.gz'
--2011-12-26 11:44:24--  http://linux.rz.ruhr-uni-bochum.de/download/gentoo-mirror/distfiles/embassy-phylipnew-3.69.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 11:44:24 ERROR 404: Not Found.

>>> Downloading 'http://ftp-stud.fht-esslingen.de/pub/Mirrors/gentoo/distfiles/embassy-phylipnew-3.69.tar.gz'
--2011-12-26 11:44:24--  http://ftp-stud.fht-esslingen.de/pub/Mirrors/gentoo/distfiles/embassy-phylipnew-3.69.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 11:44:25 ERROR 404: Not Found.

>>> Downloading 'ftp://ftp.wh2.tu-dresden.de/pub/mirrors/gentoo/distfiles/embassy-phylipnew-3.69.tar.gz'
--2011-12-26 11:44:25--  ftp://ftp.wh2.tu-dresden.de/pub/mirrors/gentoo/distfiles/embassy-phylipnew-3.69.tar.gz
           => `/usr/portage_lynx/distfiles/embassy-phylipnew-3.69.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-phylipnew-3.69.tar.gz ... done.
==> PASV ... done.    ==> RETR embassy-phylipnew-3.69.tar.gz ... 
No such file `embassy-phylipnew-3.69.tar.gz'.

>>> Downloading 'ftp://sunsite.informatik.rwth-aachen.de/pub/Linux/gentoo/distfiles/embassy-phylipnew-3.69.tar.gz'
--2011-12-26 11:44:27--  ftp://sunsite.informatik.rwth-aachen.de/pub/Linux/gentoo/distfiles/embassy-phylipnew-3.69.tar.gz
           => `/usr/portage_lynx/distfiles/embassy-phylipnew-3.69.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-phylipnew-3.69.tar.gz ... done.
==> PASV ... done.    ==> RETR embassy-phylipnew-3.69.tar.gz ... 
No such file `embassy-phylipnew-3.69.tar.gz'.

>>> Downloading 'ftp://ftp.tu-clausthal.de/pub/linux/gentoo/distfiles/embassy-phylipnew-3.69.tar.gz'
--2011-12-26 11:44:28--  ftp://ftp.tu-clausthal.de/pub/linux/gentoo/distfiles/embassy-phylipnew-3.69.tar.gz
           => `/usr/portage_lynx/distfiles/embassy-phylipnew-3.69.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-phylipnew-3.69.tar.gz ... done.
==> PASV ... done.    ==> RETR embassy-phylipnew-3.69.tar.gz ... 
No such file `embassy-phylipnew-3.69.tar.gz'.

>>> Downloading 'ftp://ftp.easynet.nl/mirror/gentoo/distfiles/embassy-phylipnew-3.69.tar.gz'
--2011-12-26 11:44:29--  ftp://ftp.easynet.nl/mirror/gentoo/distfiles/embassy-phylipnew-3.69.tar.gz
           => `/usr/portage_lynx/distfiles/embassy-phylipnew-3.69.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/PHYLIPNEW-3.69.tar.gz'
--2011-12-26 11:44:29--  ftp://emboss.open-bio.org/pub/EMBOSS/PHYLIPNEW-3.69.tar.gz
           => `/usr/portage_lynx/distfiles/embassy-phylipnew-3.69.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 PHYLIPNEW-3.69.tar.gz ... 1693200
==> PASV ... done.    ==> RETR PHYLIPNEW-3.69.tar.gz ... done.
Length: 1693200 (1.6M) (unauthoritative)

100%[======================================>] 1,693,200    177K/s   in 9.6s    

2011-12-26 11:44:41 (172 KB/s) - `/usr/portage_lynx/distfiles/embassy-phylipnew-3.69.tar.gz' saved [1693200]

!!! Fetched file: embassy-phylipnew-3.69.tar.gz VERIFY FAILED!
!!! Reason: Filesize does not match recorded size
!!! Got:      1693200
!!! Expected: 1667760
Refetching... File renamed to '/usr/portage_lynx/distfiles/embassy-phylipnew-3.69.tar.gz._checksum_failure_.tLErVD'

!!! Couldn't download 'embassy-phylipnew-3.69.tar.gz'. Aborting.


After deleting the Manifest I could download ftp://emboss.open-bio.org/pub/EMBOSS/PHYLIPNEW-3.69.tar.gz, but the patch failed:

>>> Emerging (1 of 13) sci-biology/embassy-phylipnew-3.69 from local
 * embassy-phylipnew-3.69.tar.gz RMD160 SHA1 SHA256 size ;-) ...                                                                                                                  [ ok ]
>>> Unpacking source...
>>> Unpacking embassy-phylipnew-3.69.tar.gz to /var/tmp/portage/sci-biology/embassy-phylipnew-3.69/work
>>> Source unpacked in /var/tmp/portage/sci-biology/embassy-phylipnew-3.69/work
>>> Preparing source in /var/tmp/portage/sci-biology/embassy-phylipnew-3.69/work/PHYLIPNEW-3.69 ...
 * Applying embassy-phylipnew-3.69.patch ...

 * Failed Patch: embassy-phylipnew-3.69.patch !
 *  ( /usr/local/portage/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.patch )
 * 
 * Include in your bugreport the contents of:
 * 
 *   /var/tmp/portage/sci-biology/embassy-phylipnew-3.69/temp/embassy-phylipnew-3.69.patch.out

 * ERROR: sci-biology/embassy-phylipnew-3.69 failed (prepare phase):
 *   Failed Patch: embassy-phylipnew-3.69.patch!

[Comment 1 Juergen Rose 2011-12-26 10:57:28 UTC]

Created attachment 296965 [details]
An embassy-phylipnew ebuild which solved the issue

[Comment 2 Justin Lecher (RETIRED) 2012-02-20 14:34:00 UTC]

# Justin Lecher <[e-mail]> (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