'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 )
Created attachment 296971 [details] An embassy-topo ebuild disabling patches and emerging embassy-topo.
# 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
