* Broken URLs
@ 2015-11-12 22:55 Ludovic Courtès
2015-11-20 10:24 ` Ricardo Wurmus
0 siblings, 1 reply; 7+ messages in thread
From: Ludovic Courtès @ 2015-11-12 22:55 UTC (permalink / raw)
To: guix
As discussed today on IRC, commit bd7e1ff adds a timeout on connection
attempts made by ‘guix lint’ for the ‘source’ and ‘home-page’ checkers.
Along with the previous commits, it’s allowed me to run a whole-distro
check with:
guix lint -c source,home-page
It seems to work nicely (it still leaks FDs due to
<http://bugs.gnu.org/20145> but that’s OK since these are eventually
GC’d.)
After letting it run for ~20mn, I’ve collected a whole bunch of URL
issues (below) that I’m sure everyone will rush to fix. :-)
Ludo’.
gnu/packages/audio.scm:272:12: calf-0.0.60: all the source URIs are unreachable:
gnu/packages/audio.scm:272:12: calf-0.0.60: URI http://prdownloads.sourceforge.net/calf/calf/0.0.60/calf-0.0.60.tar.gz not reachable: 404 ("Not Found")
gnu/packages/audio.scm:272:12: calf-0.0.60: URI http://heanet.dl.sourceforge.net/sourceforge/calf/calf/0.0.60/calf-0.0.60.tar.gz not reachable: 404 ("Not Found")
gnu/packages/audio.scm:272:12: calf-0.0.60: URI http://surfnet.dl.sourceforge.net/sourceforge/calf/calf/0.0.60/calf-0.0.60.tar.gz unreachable: Network is unreachable
gnu/packages/audio.scm:272:12: calf-0.0.60: URI http://dfn.dl.sourceforge.net/sourceforge/calf/calf/0.0.60/calf-0.0.60.tar.gz not reachable: 404 ("Not Found")
gnu/packages/audio.scm:272:12: calf-0.0.60: URI http://mesh.dl.sourceforge.net/sourceforge/calf/calf/0.0.60/calf-0.0.60.tar.gz domain not found: Name or service not known
gnu/packages/audio.scm:272:12: calf-0.0.60: URI http://ovh.dl.sourceforge.net/sourceforge/calf/calf/0.0.60/calf-0.0.60.tar.gz domain not found: Name or service not known
gnu/packages/audio.scm:272:12: calf-0.0.60: URI http://osdn.dl.sourceforge.net/sourceforge/calf/calf/0.0.60/calf-0.0.60.tar.gz not reachable: 404 ("Not Found")
gnu/packages/bioinformatics.scm:1115:15: edirect-2.50: URI http://www.ncbi.nlm.nih.gov/books/NBK179288 not reachable: 303 ("See Other")
gnu/packages/bioinformatics.scm:2627:5: sra-tools-2.4.5-5: all the source URIs are unreachable:
gnu/packages/bioinformatics.scm:2627:5: sra-tools-2.4.5-5: URI https://github.com/ncbi/sra-tools/archive/2.4.5-5.tar.gz not reachable: 404 ("Not Found")
gnu/packages/bioinformatics.scm:2419:5: ncbi-vdb-2.4.5-5: all the source URIs are unreachable:
gnu/packages/bioinformatics.scm:2419:5: ncbi-vdb-2.4.5-5: URI https://github.com/ncbi/ncbi-vdb/archive/2.4.5-5.tar.gz not reachable: 404 ("Not Found")
gnu/packages/bioinformatics.scm:2570:12: preseq-1.0.2: all the source URIs are unreachable:
gnu/packages/bioinformatics.scm:2570:12: preseq-1.0.2: URI http://smithlabresearch.org/downloads/preseq-1.0.2.tar.bz2 not reachable: 404 ("Not Found")
gnu/packages/calcurse.scm:46:15: calcurse-4.0.0: URI http://www.calcurse.org unreachable: Connection refused
gnu/packages/calcurse.scm:32:5: calcurse-4.0.0: all the source URIs are unreachable:
gnu/packages/calcurse.scm:32:5: calcurse-4.0.0: URI http://calcurse.org/files/calcurse-4.0.0.tar.gz unreachable: Connection refused
gnu/packages/cdrom.scm:239:12: libcue-1.4.0: all the source URIs are unreachable:
gnu/packages/cdrom.scm:239:12: libcue-1.4.0: URI http://prdownloads.sourceforge.net/libcue/libcue-1.4.0.tar.bz2 not reachable: 404 ("Not Found")
gnu/packages/cdrom.scm:239:12: libcue-1.4.0: URI http://heanet.dl.sourceforge.net/sourceforge/libcue/libcue-1.4.0.tar.bz2 not reachable: 404 ("Not Found")
gnu/packages/cdrom.scm:239:12: libcue-1.4.0: URI http://surfnet.dl.sourceforge.net/sourceforge/libcue/libcue-1.4.0.tar.bz2 unreachable: Network is unreachable
gnu/packages/cdrom.scm:239:12: libcue-1.4.0: URI http://dfn.dl.sourceforge.net/sourceforge/libcue/libcue-1.4.0.tar.bz2 not reachable: 404 ("Not Found")
gnu/packages/cdrom.scm:239:12: libcue-1.4.0: URI http://mesh.dl.sourceforge.net/sourceforge/libcue/libcue-1.4.0.tar.bz2 domain not found: Name or service not known
gnu/packages/cdrom.scm:239:12: libcue-1.4.0: URI http://ovh.dl.sourceforge.net/sourceforge/libcue/libcue-1.4.0.tar.bz2 domain not found: Name or service not known
gnu/packages/cdrom.scm:239:12: libcue-1.4.0: URI http://osdn.dl.sourceforge.net/sourceforge/libcue/libcue-1.4.0.tar.bz2 not reachable: 404 ("Not Found")
gnu/packages/compression.scm:123:14: libtar-1.2.11: URI http://www.feep.net/libtar/ domain not found: Name or service not known
gnu/packages/compression.scm:109:11: libtar-1.2.11: all the source URIs are unreachable:
gnu/packages/compression.scm:109:11: libtar-1.2.11: URI ftp://ftp.feep.net/pub/software/libtar/libtar-1.2.11.tar.gz domain not found: Name or service not known
gnu/packages/cook.scm:77:15: cook-2.34: URI http://miller.emu.id.au/pmiller/software/cook unreachable: Connection timed out
gnu/packages/cook.scm:34:5: cook-2.34: all the source URIs are unreachable:
gnu/packages/cook.scm:34:5: cook-2.34: URI http://miller.emu.id.au/pmiller/software/cook/cook-2.34.tar.gz unreachable: Connection timed out
gnu/packages/crypto.scm:30:12: libsodium-1.0.0: all the source URIs are unreachable:
gnu/packages/crypto.scm:30:12: libsodium-1.0.0: URI http://download.libsodium.org/libsodium/releases/libsodium-1.0.0.tar.gz not reachable: 404 ("Not Found")
gnu/packages/databases.scm:446:5: perl-dbix-class-0.082810: all the source URIs are unreachable:
gnu/packages/databases.scm:446:5: perl-dbix-class-0.082810: URI http://cpan.enstimac.fr/authors/id/R/RI/RIBASUSHI/DBIx-Class-0.082810.tar.gz not reachable: 404 ("Not Found")
gnu/packages/databases.scm:442:2: perl-dbix-class-0.082810: URI ftp://ftp.ciril.fr/pub/cpan/authors/id/R/RI/RIBASUSHI/DBIx-Class-0.082810.tar.gz not reachable: 550 ("DBIx-Class-0.082810.tar.gz: No such file or directory")
gnu/packages/databases.scm:442:2: perl-dbix-class-0.082810: URI ftp://artfiles.org/cpan.org/authors/id/R/RI/RIBASUSHI/DBIx-Class-0.082810.tar.gz not reachable: 550 ("DBIx-Class-0.082810.tar.gz: No such file or directory")
gnu/packages/databases.scm:446:5: perl-dbix-class-0.082810: URI http://www.cpan.org/authors/id/R/RI/RIBASUSHI/DBIx-Class-0.082810.tar.gz not reachable: 404 ("Not Found")
gnu/packages/databases.scm:442:2: perl-dbix-class-0.082810: URI ftp://cpan.rinet.ru/pub/mirror/CPAN/authors/id/R/RI/RIBASUSHI/DBIx-Class-0.082810.tar.gz not reachable: 550 ("DBIx-Class-0.082810.tar.gz: No such file or directory.")
gnu/packages/databases.scm:446:5: perl-dbix-class-0.082810: URI http://cpan.cu.be/authors/id/R/RI/RIBASUSHI/DBIx-Class-0.082810.tar.gz not reachable: 404 ("Not Found")
gnu/packages/databases.scm:446:5: perl-dbix-class-0.082810: URI ftp://cpan.inode.at/authors/id/R/RI/RIBASUSHI/DBIx-Class-0.082810.tar.gz unreachable: Protocol not supported
gnu/packages/databases.scm:442:2: perl-dbix-class-0.082810: URI ftp://cpan.iht.co.il/authors/id/R/RI/RIBASUSHI/DBIx-Class-0.082810.tar.gz not reachable: 550 ("Could not get file size.")
gnu/packages/databases.scm:442:2: perl-dbix-class-0.082810: URI ftp://ftp.osuosl.org/pub/CPAN/authors/id/R/RI/RIBASUSHI/DBIx-Class-0.082810.tar.gz not reachable: 550 ("Could not get file size.")
gnu/packages/databases.scm:442:2: perl-dbix-class-0.082810: URI ftp://ftp.nara.wide.ad.jp/pub/CPAN/authors/id/R/RI/RIBASUSHI/DBIx-Class-0.082810.tar.gz not reachable: 550 ("DBIx-Class-0.082810.tar.gz: No such file or directory")
gnu/packages/databases.scm:446:5: perl-dbix-class-0.082810: URI http://mirrors.163.com/cpan/authors/id/R/RI/RIBASUSHI/DBIx-Class-0.082810.tar.gz not reachable: 404 ("Not Found")
gnu/packages/databases.scm:442:2: perl-dbix-class-0.082810: URI ftp://cpan.mirror.ac.za/authors/id/R/RI/RIBASUSHI/DBIx-Class-0.082810.tar.gz not reachable: 550 ("Can't check for file existence")
gnu/packages/ghostscript.scm:84:11: psutils-17: all the source URIs are unreachable:
gnu/packages/ghostscript.scm:81:2: psutils-17: URI ftp://ftp.knackered.org/pub/psutils/psutils.tar.gz not reachable: 550 ("psutils.tar.gz: Operation not permitted")
gnu/packages/gnome.scm:3292:15: gusb-0.2.6: URI https://github/hughsie/libgusb domain not found: Name or service not known
gnu/packages/graphics.scm:304:15: agg-2.5: URI http://antigrain.com not reachable: 404 ("Not Found")
gnu/packages/graphics.scm:272:12: agg-2.5: all the source URIs are unreachable:
gnu/packages/graphics.scm:272:12: agg-2.5: URI http://www.antigrain.com/agg-2.5.tar.gz not reachable: 404 ("Not Found")
gnu/packages/gstreamer.scm:73:15: orc-0.4.24: URI http://code.entropywave.com/orc/ domain not found: Name or service not known
gnu/packages/hugs.scm:30:5: hugs-Sep2006: all the source URIs are unreachable:
gnu/packages/hugs.scm:30:5: hugs-Sep2006: URI http://cvs.haskell.org/Hugs/downloads/2006-09/hugs98-plus-Sep2006.tar.gz not reachable: 404 ("Not Found")
gnu/packages/image.scm:468:15: giblib-1.2.4: URI http://linuxbrit.co.uk/software/ not reachable: 403 ("Forbidden")
gnu/packages/image.scm:456:12: giblib-1.2.4: all the source URIs are unreachable:
gnu/packages/image.scm:456:12: giblib-1.2.4: URI http://linuxbrit.co.uk/downloads/giblib-1.2.4.tar.gz not reachable: 403 ("Forbidden")
gnu/packages/java.scm:139:12: ant-1.9.4: all the source URIs are unreachable:
gnu/packages/java.scm:139:12: ant-1.9.4: URI https://www.apache.org/dist/ant/source/apache-ant-1.9.4-src.tar.gz not reachable: 404 ("Not Found")
gnu/packages/language.scm:77:5: perl-lingua-en-inflect-number-1.11: all the source URIs are unreachable:
gnu/packages/language.scm:77:5: perl-lingua-en-inflect-number-1.11: URI http://cpan.enstimac.fr/authors/id/N/NE/NEILB/Lingua-EN-Inflect-Number-1.11.tar.gz not reachable: 404 ("Not Found")
gnu/packages/language.scm:73:2: perl-lingua-en-inflect-number-1.11: URI ftp://ftp.ciril.fr/pub/cpan/authors/id/N/NE/NEILB/Lingua-EN-Inflect-Number-1.11.tar.gz not reachable: 550 ("Lingua-EN-Inflect-Number-1.11.tar.gz: No such file or directory")
gnu/packages/language.scm:73:2: perl-lingua-en-inflect-number-1.11: URI ftp://artfiles.org/cpan.org/authors/id/N/NE/NEILB/Lingua-EN-Inflect-Number-1.11.tar.gz not reachable: 550 ("Lingua-EN-Inflect-Number-1.11.tar.gz: No such file or directory")
gnu/packages/language.scm:77:5: perl-lingua-en-inflect-number-1.11: URI http://www.cpan.org/authors/id/N/NE/NEILB/Lingua-EN-Inflect-Number-1.11.tar.gz not reachable: 404 ("Not Found")
gnu/packages/language.scm:73:2: perl-lingua-en-inflect-number-1.11: URI ftp://cpan.rinet.ru/pub/mirror/CPAN/authors/id/N/NE/NEILB/Lingua-EN-Inflect-Number-1.11.tar.gz not reachable: 550 ("Lingua-EN-Inflect-Number-1.11.tar.gz: No such file or directory.")
gnu/packages/language.scm:77:5: perl-lingua-en-inflect-number-1.11: URI http://cpan.cu.be/authors/id/N/NE/NEILB/Lingua-EN-Inflect-Number-1.11.tar.gz not reachable: 404 ("Not Found")
gnu/packages/language.scm:77:5: perl-lingua-en-inflect-number-1.11: URI ftp://cpan.inode.at/authors/id/N/NE/NEILB/Lingua-EN-Inflect-Number-1.11.tar.gz unreachable: Protocol not supported
gnu/packages/language.scm:73:2: perl-lingua-en-inflect-number-1.11: URI ftp://cpan.iht.co.il/authors/id/N/NE/NEILB/Lingua-EN-Inflect-Number-1.11.tar.gz not reachable: 550 ("Could not get file size.")
gnu/packages/language.scm:73:2: perl-lingua-en-inflect-number-1.11: URI ftp://ftp.osuosl.org/pub/CPAN/authors/id/N/NE/NEILB/Lingua-EN-Inflect-Number-1.11.tar.gz not reachable: 550 ("Could not get file size.")
gnu/packages/language.scm:73:2: perl-lingua-en-inflect-number-1.11: URI ftp://ftp.nara.wide.ad.jp/pub/CPAN/authors/id/N/NE/NEILB/Lingua-EN-Inflect-Number-1.11.tar.gz not reachable: 550 ("Lingua-EN-Inflect-Number-1.11.tar.gz: No such file or directory")
gnu/packages/language.scm:77:5: perl-lingua-en-inflect-number-1.11: URI http://mirrors.163.com/cpan/authors/id/N/NE/NEILB/Lingua-EN-Inflect-Number-1.11.tar.gz not reachable: 404 ("Not Found")
gnu/packages/language.scm:73:2: perl-lingua-en-inflect-number-1.11: URI ftp://cpan.mirror.ac.za/authors/id/N/NE/NEILB/Lingua-EN-Inflect-Number-1.11.tar.gz not reachable: 550 ("Can't check for file existence")
gnu/packages/language.scm:33:5: perl-lingua-en-findnumber-1.30: all the source URIs are unreachable:
gnu/packages/language.scm:33:5: perl-lingua-en-findnumber-1.30: URI http://cpan.enstimac.fr/authors/id/N/NE/NEILB/Lingua-EN-FindNumber-1.30.tar.gz not reachable: 404 ("Not Found")
gnu/packages/language.scm:29:2: perl-lingua-en-findnumber-1.30: URI ftp://ftp.ciril.fr/pub/cpan/authors/id/N/NE/NEILB/Lingua-EN-FindNumber-1.30.tar.gz not reachable: 550 ("Lingua-EN-FindNumber-1.30.tar.gz: No such file or directory")
gnu/packages/language.scm:29:2: perl-lingua-en-findnumber-1.30: URI ftp://artfiles.org/cpan.org/authors/id/N/NE/NEILB/Lingua-EN-FindNumber-1.30.tar.gz not reachable: 550 ("Lingua-EN-FindNumber-1.30.tar.gz: No such file or directory")
gnu/packages/language.scm:33:5: perl-lingua-en-findnumber-1.30: URI http://www.cpan.org/authors/id/N/NE/NEILB/Lingua-EN-FindNumber-1.30.tar.gz not reachable: 404 ("Not Found")
gnu/packages/language.scm:29:2: perl-lingua-en-findnumber-1.30: URI ftp://cpan.rinet.ru/pub/mirror/CPAN/authors/id/N/NE/NEILB/Lingua-EN-FindNumber-1.30.tar.gz not reachable: 550 ("Lingua-EN-FindNumber-1.30.tar.gz: No such file or directory.")
gnu/packages/language.scm:33:5: perl-lingua-en-findnumber-1.30: URI http://cpan.cu.be/authors/id/N/NE/NEILB/Lingua-EN-FindNumber-1.30.tar.gz not reachable: 404 ("Not Found")
gnu/packages/language.scm:33:5: perl-lingua-en-findnumber-1.30: URI ftp://cpan.inode.at/authors/id/N/NE/NEILB/Lingua-EN-FindNumber-1.30.tar.gz unreachable: Protocol not supported
gnu/packages/language.scm:29:2: perl-lingua-en-findnumber-1.30: URI ftp://cpan.iht.co.il/authors/id/N/NE/NEILB/Lingua-EN-FindNumber-1.30.tar.gz not reachable: 550 ("Could not get file size.")
gnu/packages/language.scm:29:2: perl-lingua-en-findnumber-1.30: URI ftp://ftp.osuosl.org/pub/CPAN/authors/id/N/NE/NEILB/Lingua-EN-FindNumber-1.30.tar.gz not reachable: 550 ("Could not get file size.")
gnu/packages/language.scm:29:2: perl-lingua-en-findnumber-1.30: URI ftp://ftp.nara.wide.ad.jp/pub/CPAN/authors/id/N/NE/NEILB/Lingua-EN-FindNumber-1.30.tar.gz not reachable: 550 ("Lingua-EN-FindNumber-1.30.tar.gz: No such file or directory")
gnu/packages/language.scm:33:5: perl-lingua-en-findnumber-1.30: URI http://mirrors.163.com/cpan/authors/id/N/NE/NEILB/Lingua-EN-FindNumber-1.30.tar.gz not reachable: 404 ("Not Found")
gnu/packages/language.scm:29:2: perl-lingua-en-findnumber-1.30: URI ftp://cpan.mirror.ac.za/authors/id/N/NE/NEILB/Lingua-EN-FindNumber-1.30.tar.gz not reachable: 550 ("Can't check for file existence")
gnu/packages/libreoffice.scm:681:5: libreoffice-5.0.0.2: all the source URIs are unreachable:
gnu/packages/libreoffice.scm:681:5: libreoffice-5.0.0.2: URI http://download.documentfoundation.org/libreoffice/src/5.0.0/libreoffice-5.0.0.2.tar.xz not reachable: 404 ("Not Found")
gnu/packages/linux.scm:1590:15: eudev-3.1.5: URI http://www.gentoo.org/proj/en/eudev/ not reachable: 404 ("Not Found")
gnu/packages/linux.scm:1313:15: unionfs-fuse-0.26: URI http://podgorny.cz/moin/UnionFsFuse not reachable: 404 ("NOT FOUND")
gnu/packages/linux.scm:1302:12: unionfs-fuse-0.26: all the source URIs are unreachable:
gnu/packages/linux.scm:1302:12: unionfs-fuse-0.26: URI http://podgorny.cz/unionfs-fuse/releases/unionfs-fuse-0.26.tar.xz not reachable: 404 ("NOT FOUND")
gnu/packages/linux.scm:1340:2: unionfs-fuse-static-0.26: URI http://podgorny.cz/moin/UnionFsFuse not reachable: 404 ("NOT FOUND")
gnu/packages/linux.scm:1343:12: unionfs-fuse-static-0.26: all the source URIs are unreachable:
gnu/packages/linux.scm:1343:12: unionfs-fuse-static-0.26: URI http://podgorny.cz/unionfs-fuse/releases/unionfs-fuse-0.26.tar.xz not reachable: 404 ("NOT FOUND")
gnu/packages/linux.scm:1497:15: kbd-2.0.2: URI ftp://ftp.kernel.org/pub/linux/utils/kbd/ unreachable: Protocol not supported
gnu/packages/linux.scm:1873:15: lm-sensors-3.3.5: URI http://www.lm-sensors.org/ unreachable: Connection refused
gnu/packages/linux.scm:1812:12: lm-sensors-3.3.5: all the source URIs are unreachable:
gnu/packages/linux.scm:1812:12: lm-sensors-3.3.5: URI http://dl.lm-sensors.org/lm-sensors/releases/lm_sensors-3.3.5.tar.bz2 unreachable: Connection refused
gnu/packages/linux.scm:1902:15: i2c-tools-3.1.1: URI http://www.lm-sensors.org/wiki/I2CTools unreachable: Connection refused
gnu/packages/linux.scm:1885:12: i2c-tools-3.1.1: all the source URIs are unreachable:
gnu/packages/linux.scm:1885:12: i2c-tools-3.1.1: URI http://dl.lm-sensors.org/i2c-tools/releases/i2c-tools-3.1.1.tar.bz2 unreachable: Connection refused
gnu/packages/lsof.scm:33:11: lsof-4.88: all the source URIs are unreachable:
gnu/packages/lsof.scm:33:11: lsof-4.88: URI ftp://lsof.itap.purdue.edu/pub/tools/unix/lsof/lsof_4.88.tar.bz2 unreachable: Protocol not supported
gnu/packages/lsof.scm:33:11: lsof-4.88: URI ftp://lsof.itap.purdue.edu/pub/tools/unix/lsof/OLD/lsof_4.88.tar.bz2 unreachable: Protocol not supported
gnu/packages/lsof.scm:30:2: lsof-4.88: URI ftp://ftp.fu-berlin.de/pub/unix/tools/lsof/lsof_4.88.tar.bz2 not reachable: 550 ("lsof_4.88.tar.bz2: No such file or directory")
gnu/packages/lsof.scm:30:2: lsof-4.88: URI ftp://sunsite.ualberta.ca/pub/Mirror/lsof/lsof_4.88.tar.bz2 not reachable: 550 ("Could not get file size.")
gnu/packages/lynx.scm:37:12: lynx-2.8.8rel.2: all the source URIs are unreachable:
gnu/packages/lynx.scm:37:12: lynx-2.8.8rel.2: URI http://lynx.isc.org/lynx2.8.8/lynx2.8.8rel.2.tar.bz2 not reachable: 404 ("Not Found")
gnu/packages/mail.scm:598:5: exim-4.85: all the source URIs are unreachable:
gnu/packages/mail.scm:594:2: exim-4.85: URI ftp://ftp.exim.org/pub/exim/exim4/exim-4.85.tar.bz2 not reachable: 550 ("Could not get file size.")
gnu/packages/mail.scm:828:5: perl-email-mime-1.929: all the source URIs are unreachable:
gnu/packages/mail.scm:828:5: perl-email-mime-1.929: URI http://cpan.enstimac.fr/authors/id/R/RJ/RJBS/Email-MIME-1.929.tar.gz not reachable: 404 ("Not Found")
gnu/packages/mail.scm:824:2: perl-email-mime-1.929: URI ftp://ftp.ciril.fr/pub/cpan/authors/id/R/RJ/RJBS/Email-MIME-1.929.tar.gz not reachable: 550 ("Email-MIME-1.929.tar.gz: No such file or directory")
gnu/packages/mail.scm:824:2: perl-email-mime-1.929: URI ftp://artfiles.org/cpan.org/authors/id/R/RJ/RJBS/Email-MIME-1.929.tar.gz not reachable: 550 ("Email-MIME-1.929.tar.gz: No such file or directory")
gnu/packages/mail.scm:828:5: perl-email-mime-1.929: URI http://www.cpan.org/authors/id/R/RJ/RJBS/Email-MIME-1.929.tar.gz not reachable: 404 ("Not Found")
gnu/packages/mail.scm:824:2: perl-email-mime-1.929: URI ftp://cpan.rinet.ru/pub/mirror/CPAN/authors/id/R/RJ/RJBS/Email-MIME-1.929.tar.gz not reachable: 550 ("Email-MIME-1.929.tar.gz: No such file or directory.")
gnu/packages/mail.scm:828:5: perl-email-mime-1.929: URI http://cpan.cu.be/authors/id/R/RJ/RJBS/Email-MIME-1.929.tar.gz not reachable: 404 ("Not Found")
gnu/packages/mail.scm:828:5: perl-email-mime-1.929: URI ftp://cpan.inode.at/authors/id/R/RJ/RJBS/Email-MIME-1.929.tar.gz unreachable: Protocol not supported
gnu/packages/mail.scm:824:2: perl-email-mime-1.929: URI ftp://cpan.iht.co.il/authors/id/R/RJ/RJBS/Email-MIME-1.929.tar.gz not reachable: 550 ("Could not get file size.")
gnu/packages/mail.scm:824:2: perl-email-mime-1.929: URI ftp://ftp.osuosl.org/pub/CPAN/authors/id/R/RJ/RJBS/Email-MIME-1.929.tar.gz not reachable: 550 ("Could not get file size.")
gnu/packages/mail.scm:824:2: perl-email-mime-1.929: URI ftp://ftp.nara.wide.ad.jp/pub/CPAN/authors/id/R/RJ/RJBS/Email-MIME-1.929.tar.gz not reachable: 550 ("Email-MIME-1.929.tar.gz: No such file or directory")
gnu/packages/mail.scm:828:5: perl-email-mime-1.929: URI http://mirrors.163.com/cpan/authors/id/R/RJ/RJBS/Email-MIME-1.929.tar.gz not reachable: 404 ("Not Found")
gnu/packages/mail.scm:824:2: perl-email-mime-1.929: URI ftp://cpan.mirror.ac.za/authors/id/R/RJ/RJBS/Email-MIME-1.929.tar.gz not reachable: 550 ("Can't check for file existence")
gnu/packages/make-bootstrap.scm:602:2: static-binaries-tarball-0: invalid value for home page
gnu/packages/maths.scm:1645:15: atlas-3.10.2: URI http://math-atlas.sourceforge.net/ unreachable: Connection timed out
gnu/packages/messaging.scm:413:15: python2-nbxmpp-0.5.3: URI http://python-nbxmpp.gajim.org not reachable: 500 ("Internal Server Error")
gnu/packages/messaging.scm:413:15: python-nbxmpp-0.5.3: URI http://python-nbxmpp.gajim.org not reachable: 500 ("Internal Server Error")
gnu/packages/moreutils.scm:32:12: moreutils-0.55: all the source URIs are unreachable:
gnu/packages/moreutils.scm:32:12: moreutils-0.55: URI http://ftp.de.debian.org/debian/pool/main/m/moreutils/moreutils_0.55.orig.tar.gz not reachable: 404 ("Not Found")
gnu/packages/moreutils.scm:32:12: moreutils-0.55: URI http://ftp.fr.debian.org/debian/pool/main/m/moreutils/moreutils_0.55.orig.tar.gz not reachable: 404 ("Not Found")
gnu/packages/moreutils.scm:32:12: moreutils-0.55: URI http://ftp.debian.org/debian/pool/main/m/moreutils/moreutils_0.55.orig.tar.gz not reachable: 404 ("Not Found")
gnu/packages/mp3.scm:416:12: mpc123-0.2.4: all the source URIs are unreachable:
gnu/packages/mp3.scm:416:12: mpc123-0.2.4: URI http://prdownloads.sourceforge.net/mpc123/version%200.2.4/mpc123-0.2.4.tar.gz not reachable: 404 ("Not Found")
gnu/packages/mp3.scm:416:12: mpc123-0.2.4: URI http://heanet.dl.sourceforge.net/sourceforge/mpc123/version%200.2.4/mpc123-0.2.4.tar.gz not reachable: 404 ("Not Found")
gnu/packages/mp3.scm:416:12: mpc123-0.2.4: URI http://surfnet.dl.sourceforge.net/sourceforge/mpc123/version%200.2.4/mpc123-0.2.4.tar.gz unreachable: Network is unreachable
gnu/packages/mp3.scm:416:12: mpc123-0.2.4: URI http://dfn.dl.sourceforge.net/sourceforge/mpc123/version%200.2.4/mpc123-0.2.4.tar.gz not reachable: 404 ("Not Found")
gnu/packages/mp3.scm:416:12: mpc123-0.2.4: URI http://mesh.dl.sourceforge.net/sourceforge/mpc123/version%200.2.4/mpc123-0.2.4.tar.gz domain not found: Name or service not known
gnu/packages/mp3.scm:416:12: mpc123-0.2.4: URI http://ovh.dl.sourceforge.net/sourceforge/mpc123/version%200.2.4/mpc123-0.2.4.tar.gz domain not found: Name or service not known
gnu/packages/mp3.scm:416:12: mpc123-0.2.4: URI http://osdn.dl.sourceforge.net/sourceforge/mpc123/version%200.2.4/mpc123-0.2.4.tar.gz not reachable: 404 ("Not Found")
gnu/packages/ocaml.scm:286:12: hevea-2.23: all the source URIs are unreachable:
gnu/packages/ocaml.scm:286:12: hevea-2.23: URI http://hevea.inria.fr/distri/hevea-2.23.tar.gz not reachable: 404 ("Not Found")
gnu/packages/patchutils.scm:154:5: colordiff-1.0.13: all the source URIs are unreachable:
gnu/packages/patchutils.scm:154:5: colordiff-1.0.13: URI http://www.colordiff.org/colordiff-1.0.13.tar.gz not reachable: 404 ("Not Found")
gnu/packages/perl.scm:5004:5: perl-test-mocktime-0.13: all the source URIs are unreachable:
gnu/packages/perl.scm:5004:5: perl-test-mocktime-0.13: URI http://cpan.enstimac.fr/authors/id/D/DD/DDICK/Test-MockTime-0.13.tar.gz not reachable: 404 ("Not Found")
gnu/packages/perl.scm:5000:2: perl-test-mocktime-0.13: URI ftp://ftp.ciril.fr/pub/cpan/authors/id/D/DD/DDICK/Test-MockTime-0.13.tar.gz not reachable: 550 ("Test-MockTime-0.13.tar.gz: No such file or directory")
gnu/packages/perl.scm:5000:2: perl-test-mocktime-0.13: URI ftp://artfiles.org/cpan.org/authors/id/D/DD/DDICK/Test-MockTime-0.13.tar.gz not reachable: 550 ("Test-MockTime-0.13.tar.gz: No such file or directory")
gnu/packages/perl.scm:5004:5: perl-test-mocktime-0.13: URI http://www.cpan.org/authors/id/D/DD/DDICK/Test-MockTime-0.13.tar.gz not reachable: 404 ("Not Found")
gnu/packages/perl.scm:5000:2: perl-test-mocktime-0.13: URI ftp://cpan.rinet.ru/pub/mirror/CPAN/authors/id/D/DD/DDICK/Test-MockTime-0.13.tar.gz not reachable: 550 ("Test-MockTime-0.13.tar.gz: No such file or directory.")
gnu/packages/perl.scm:5004:5: perl-test-mocktime-0.13: URI http://cpan.cu.be/authors/id/D/DD/DDICK/Test-MockTime-0.13.tar.gz not reachable: 404 ("Not Found")
gnu/packages/perl.scm:5004:5: perl-test-mocktime-0.13: URI ftp://cpan.inode.at/authors/id/D/DD/DDICK/Test-MockTime-0.13.tar.gz unreachable: Protocol not supported
gnu/packages/perl.scm:5000:2: perl-test-mocktime-0.13: URI ftp://cpan.iht.co.il/authors/id/D/DD/DDICK/Test-MockTime-0.13.tar.gz not reachable: 550 ("Could not get file size.")
gnu/packages/perl.scm:5000:2: perl-test-mocktime-0.13: URI ftp://ftp.osuosl.org/pub/CPAN/authors/id/D/DD/DDICK/Test-MockTime-0.13.tar.gz not reachable: 550 ("Could not get file size.")
gnu/packages/perl.scm:5000:2: perl-test-mocktime-0.13: URI ftp://ftp.nara.wide.ad.jp/pub/CPAN/authors/id/D/DD/DDICK/Test-MockTime-0.13.tar.gz not reachable: 550 ("Test-MockTime-0.13.tar.gz: No such file or directory")
gnu/packages/perl.scm:5004:5: perl-test-mocktime-0.13: URI http://mirrors.163.com/cpan/authors/id/D/DD/DDICK/Test-MockTime-0.13.tar.gz not reachable: 404 ("Not Found")
gnu/packages/perl.scm:5000:2: perl-test-mocktime-0.13: URI ftp://cpan.mirror.ac.za/authors/id/D/DD/DDICK/Test-MockTime-0.13.tar.gz not reachable: 550 ("Can't check for file existence")
gnu/packages/perl.scm:3211:5: perl-moosex-getopt-0.65: all the source URIs are unreachable:
gnu/packages/perl.scm:3211:5: perl-moosex-getopt-0.65: URI http://cpan.enstimac.fr/authors/id/E/ET/ETHER/MooseX-Getopt-0.65.tar.gz not reachable: 404 ("Not Found")
gnu/packages/perl.scm:3207:2: perl-moosex-getopt-0.65: URI ftp://ftp.ciril.fr/pub/cpan/authors/id/E/ET/ETHER/MooseX-Getopt-0.65.tar.gz not reachable: 550 ("MooseX-Getopt-0.65.tar.gz: No such file or directory")
gnu/packages/perl.scm:3207:2: perl-moosex-getopt-0.65: URI ftp://artfiles.org/cpan.org/authors/id/E/ET/ETHER/MooseX-Getopt-0.65.tar.gz not reachable: 550 ("MooseX-Getopt-0.65.tar.gz: No such file or directory")
gnu/packages/perl.scm:3211:5: perl-moosex-getopt-0.65: URI http://www.cpan.org/authors/id/E/ET/ETHER/MooseX-Getopt-0.65.tar.gz not reachable: 404 ("Not Found")
gnu/packages/perl.scm:3207:2: perl-moosex-getopt-0.65: URI ftp://cpan.rinet.ru/pub/mirror/CPAN/authors/id/E/ET/ETHER/MooseX-Getopt-0.65.tar.gz not reachable: 550 ("MooseX-Getopt-0.65.tar.gz: No such file or directory.")
gnu/packages/perl.scm:3211:5: perl-moosex-getopt-0.65: URI http://cpan.cu.be/authors/id/E/ET/ETHER/MooseX-Getopt-0.65.tar.gz not reachable: 404 ("Not Found")
gnu/packages/perl.scm:3211:5: perl-moosex-getopt-0.65: URI ftp://cpan.inode.at/authors/id/E/ET/ETHER/MooseX-Getopt-0.65.tar.gz unreachable: Protocol not supported
gnu/packages/perl.scm:3207:2: perl-moosex-getopt-0.65: URI ftp://cpan.iht.co.il/authors/id/E/ET/ETHER/MooseX-Getopt-0.65.tar.gz not reachable: 550 ("Could not get file size.")
gnu/packages/perl.scm:3207:2: perl-moosex-getopt-0.65: URI ftp://ftp.osuosl.org/pub/CPAN/authors/id/E/ET/ETHER/MooseX-Getopt-0.65.tar.gz not reachable: 550 ("Could not get file size.")
gnu/packages/perl.scm:3207:2: perl-moosex-getopt-0.65: URI ftp://ftp.nara.wide.ad.jp/pub/CPAN/authors/id/E/ET/ETHER/MooseX-Getopt-0.65.tar.gz not reachable: 550 ("MooseX-Getopt-0.65.tar.gz: No such file or directory")
gnu/packages/perl.scm:3211:5: perl-moosex-getopt-0.65: URI http://mirrors.163.com/cpan/authors/id/E/ET/ETHER/MooseX-Getopt-0.65.tar.gz not reachable: 404 ("Not Found")
gnu/packages/perl.scm:3207:2: perl-moosex-getopt-0.65: URI ftp://cpan.mirror.ac.za/authors/id/E/ET/ETHER/MooseX-Getopt-0.65.tar.gz not reachable: 550 ("Can't check for file existence")
gnu/packages/perl.scm:3704:5: perl-namespace-clean-0.25: all the source URIs are unreachable:
gnu/packages/perl.scm:3704:5: perl-namespace-clean-0.25: URI http://cpan.enstimac.fr/authors/id/R/RI/RIBASUSHI/namespace-clean-0.25.tar.gz not reachable: 404 ("Not Found")
gnu/packages/perl.scm:3700:2: perl-namespace-clean-0.25: URI ftp://ftp.ciril.fr/pub/cpan/authors/id/R/RI/RIBASUSHI/namespace-clean-0.25.tar.gz not reachable: 550 ("namespace-clean-0.25.tar.gz: No such file or directory")
gnu/packages/perl.scm:3700:2: perl-namespace-clean-0.25: URI ftp://artfiles.org/cpan.org/authors/id/R/RI/RIBASUSHI/namespace-clean-0.25.tar.gz not reachable: 550 ("namespace-clean-0.25.tar.gz: No such file or directory")
gnu/packages/perl.scm:3704:5: perl-namespace-clean-0.25: URI http://www.cpan.org/authors/id/R/RI/RIBASUSHI/namespace-clean-0.25.tar.gz not reachable: 404 ("Not Found")
gnu/packages/perl.scm:3700:2: perl-namespace-clean-0.25: URI ftp://cpan.rinet.ru/pub/mirror/CPAN/authors/id/R/RI/RIBASUSHI/namespace-clean-0.25.tar.gz not reachable: 550 ("namespace-clean-0.25.tar.gz: No such file or directory.")
gnu/packages/perl.scm:3704:5: perl-namespace-clean-0.25: URI http://cpan.cu.be/authors/id/R/RI/RIBASUSHI/namespace-clean-0.25.tar.gz not reachable: 404 ("Not Found")
gnu/packages/perl.scm:3704:5: perl-namespace-clean-0.25: URI ftp://cpan.inode.at/authors/id/R/RI/RIBASUSHI/namespace-clean-0.25.tar.gz unreachable: Protocol not supported
gnu/packages/perl.scm:3700:2: perl-namespace-clean-0.25: URI ftp://cpan.iht.co.il/authors/id/R/RI/RIBASUSHI/namespace-clean-0.25.tar.gz not reachable: 550 ("Could not get file size.")
gnu/packages/perl.scm:3700:2: perl-namespace-clean-0.25: URI ftp://ftp.osuosl.org/pub/CPAN/authors/id/R/RI/RIBASUSHI/namespace-clean-0.25.tar.gz not reachable: 550 ("Could not get file size.")
gnu/packages/perl.scm:3700:2: perl-namespace-clean-0.25: URI ftp://ftp.nara.wide.ad.jp/pub/CPAN/authors/id/R/RI/RIBASUSHI/namespace-clean-0.25.tar.gz not reachable: 550 ("namespace-clean-0.25.tar.gz: No such file or directory")
gnu/packages/perl.scm:3704:5: perl-namespace-clean-0.25: URI http://mirrors.163.com/cpan/authors/id/R/RI/RIBASUSHI/namespace-clean-0.25.tar.gz not reachable: 404 ("Not Found")
gnu/packages/perl.scm:3700:2: perl-namespace-clean-0.25: URI ftp://cpan.mirror.ac.za/authors/id/R/RI/RIBASUSHI/namespace-clean-0.25.tar.gz not reachable: 550 ("Can't check for file existence")
gnu/packages/perl.scm:4756:5: perl-test-cleannamespaces-0.16: all the source URIs are unreachable:
gnu/packages/perl.scm:4756:5: perl-test-cleannamespaces-0.16: URI http://cpan.enstimac.fr/authors/id/E/ET/ETHER/Test-CleanNamespaces-0.16.tar.gz not reachable: 404 ("Not Found")
gnu/packages/perl.scm:4752:2: perl-test-cleannamespaces-0.16: URI ftp://ftp.ciril.fr/pub/cpan/authors/id/E/ET/ETHER/Test-CleanNamespaces-0.16.tar.gz not reachable: 550 ("Test-CleanNamespaces-0.16.tar.gz: No such file or directory")
gnu/packages/perl.scm:4752:2: perl-test-cleannamespaces-0.16: URI ftp://artfiles.org/cpan.org/authors/id/E/ET/ETHER/Test-CleanNamespaces-0.16.tar.gz not reachable: 550 ("Test-CleanNamespaces-0.16.tar.gz: No such file or directory")
gnu/packages/perl.scm:4756:5: perl-test-cleannamespaces-0.16: URI http://www.cpan.org/authors/id/E/ET/ETHER/Test-CleanNamespaces-0.16.tar.gz not reachable: 404 ("Not Found")
gnu/packages/perl.scm:4752:2: perl-test-cleannamespaces-0.16: URI ftp://cpan.rinet.ru/pub/mirror/CPAN/authors/id/E/ET/ETHER/Test-CleanNamespaces-0.16.tar.gz not reachable: 550 ("Test-CleanNamespaces-0.16.tar.gz: No such file or directory.")
gnu/packages/perl.scm:4756:5: perl-test-cleannamespaces-0.16: URI http://cpan.cu.be/authors/id/E/ET/ETHER/Test-CleanNamespaces-0.16.tar.gz not reachable: 404 ("Not Found")
gnu/packages/perl.scm:4756:5: perl-test-cleannamespaces-0.16: URI ftp://cpan.inode.at/authors/id/E/ET/ETHER/Test-CleanNamespaces-0.16.tar.gz unreachable: Protocol not supported
gnu/packages/perl.scm:4752:2: perl-test-cleannamespaces-0.16: URI ftp://cpan.iht.co.il/authors/id/E/ET/ETHER/Test-CleanNamespaces-0.16.tar.gz not reachable: 550 ("Could not get file size.")
gnu/packages/perl.scm:4752:2: perl-test-cleannamespaces-0.16: URI ftp://ftp.osuosl.org/pub/CPAN/authors/id/E/ET/ETHER/Test-CleanNamespaces-0.16.tar.gz not reachable: 550 ("Could not get file size.")
gnu/packages/perl.scm:4752:2: perl-test-cleannamespaces-0.16: URI ftp://ftp.nara.wide.ad.jp/pub/CPAN/authors/id/E/ET/ETHER/Test-CleanNamespaces-0.16.tar.gz not reachable: 550 ("Test-CleanNamespaces-0.16.tar.gz: No such file or directory")
gnu/packages/perl.scm:4756:5: perl-test-cleannamespaces-0.16: URI http://mirrors.163.com/cpan/authors/id/E/ET/ETHER/Test-CleanNamespaces-0.16.tar.gz not reachable: 404 ("Not Found")
gnu/packages/perl.scm:4752:2: perl-test-cleannamespaces-0.16: URI ftp://cpan.mirror.ac.za/authors/id/E/ET/ETHER/Test-CleanNamespaces-0.16.tar.gz not reachable: 550 ("Can't check for file existence")
gnu/packages/perl.scm:5184:5: perl-test-sharedfork-0.29: all the source URIs are unreachable:
gnu/packages/perl.scm:5184:5: perl-test-sharedfork-0.29: URI http://cpan.enstimac.fr/authors/id/E/EX/EXODIST/Test-SharedFork-0.29.tar.gz not reachable: 404 ("Not Found")
gnu/packages/perl.scm:5180:2: perl-test-sharedfork-0.29: URI ftp://ftp.ciril.fr/pub/cpan/authors/id/E/EX/EXODIST/Test-SharedFork-0.29.tar.gz not reachable: 550 ("Test-SharedFork-0.29.tar.gz: No such file or directory")
gnu/packages/perl.scm:5180:2: perl-test-sharedfork-0.29: URI ftp://artfiles.org/cpan.org/authors/id/E/EX/EXODIST/Test-SharedFork-0.29.tar.gz not reachable: 550 ("Test-SharedFork-0.29.tar.gz: No such file or directory")
gnu/packages/perl.scm:5184:5: perl-test-sharedfork-0.29: URI http://www.cpan.org/authors/id/E/EX/EXODIST/Test-SharedFork-0.29.tar.gz not reachable: 404 ("Not Found")
gnu/packages/perl.scm:5180:2: perl-test-sharedfork-0.29: URI ftp://cpan.rinet.ru/pub/mirror/CPAN/authors/id/E/EX/EXODIST/Test-SharedFork-0.29.tar.gz not reachable: 550 ("Test-SharedFork-0.29.tar.gz: No such file or directory.")
gnu/packages/perl.scm:5184:5: perl-test-sharedfork-0.29: URI http://cpan.cu.be/authors/id/E/EX/EXODIST/Test-SharedFork-0.29.tar.gz not reachable: 404 ("Not Found")
gnu/packages/perl.scm:5184:5: perl-test-sharedfork-0.29: URI ftp://cpan.inode.at/authors/id/E/EX/EXODIST/Test-SharedFork-0.29.tar.gz unreachable: Protocol not supported
gnu/packages/perl.scm:5180:2: perl-test-sharedfork-0.29: URI ftp://cpan.iht.co.il/authors/id/E/EX/EXODIST/Test-SharedFork-0.29.tar.gz not reachable: 550 ("Could not get file size.")
gnu/packages/perl.scm:5180:2: perl-test-sharedfork-0.29: URI ftp://ftp.osuosl.org/pub/CPAN/authors/id/E/EX/EXODIST/Test-SharedFork-0.29.tar.gz not reachable: 550 ("Could not get file size.")
gnu/packages/perl.scm:5180:2: perl-test-sharedfork-0.29: URI ftp://ftp.nara.wide.ad.jp/pub/CPAN/authors/id/E/EX/EXODIST/Test-SharedFork-0.29.tar.gz not reachable: 550 ("Test-SharedFork-0.29.tar.gz: No such file or directory")
gnu/packages/perl.scm:5184:5: perl-test-sharedfork-0.29: URI http://mirrors.163.com/cpan/authors/id/E/EX/EXODIST/Test-SharedFork-0.29.tar.gz not reachable: 404 ("Not Found")
gnu/packages/perl.scm:5180:2: perl-test-sharedfork-0.29: URI ftp://cpan.mirror.ac.za/authors/id/E/EX/EXODIST/Test-SharedFork-0.29.tar.gz not reachable: 550 ("Can't check for file existence")
gnu/packages/perl.scm:4485:5: perl-svg-2.63: all the source URIs are unreachable:
gnu/packages/perl.scm:4485:5: perl-svg-2.63: URI http://cpan.enstimac.fr/authors/id/S/SZ/SZABGAB/SVG-2.63.tar.gz not reachable: 404 ("Not Found")
gnu/packages/perl.scm:4481:2: perl-svg-2.63: URI ftp://ftp.ciril.fr/pub/cpan/authors/id/S/SZ/SZABGAB/SVG-2.63.tar.gz not reachable: 550 ("SVG-2.63.tar.gz: No such file or directory")
gnu/packages/perl.scm:4481:2: perl-svg-2.63: URI ftp://artfiles.org/cpan.org/authors/id/S/SZ/SZABGAB/SVG-2.63.tar.gz not reachable: 550 ("SVG-2.63.tar.gz: No such file or directory")
gnu/packages/perl.scm:4485:5: perl-svg-2.63: URI http://www.cpan.org/authors/id/S/SZ/SZABGAB/SVG-2.63.tar.gz not reachable: 404 ("Not Found")
gnu/packages/perl.scm:4481:2: perl-svg-2.63: URI ftp://cpan.rinet.ru/pub/mirror/CPAN/authors/id/S/SZ/SZABGAB/SVG-2.63.tar.gz not reachable: 550 ("SVG-2.63.tar.gz: No such file or directory.")
gnu/packages/perl.scm:4485:5: perl-svg-2.63: URI http://cpan.cu.be/authors/id/S/SZ/SZABGAB/SVG-2.63.tar.gz not reachable: 404 ("Not Found")
gnu/packages/perl.scm:4485:5: perl-svg-2.63: URI ftp://cpan.inode.at/authors/id/S/SZ/SZABGAB/SVG-2.63.tar.gz unreachable: Protocol not supported
gnu/packages/perl.scm:4481:2: perl-svg-2.63: URI ftp://cpan.iht.co.il/authors/id/S/SZ/SZABGAB/SVG-2.63.tar.gz not reachable: 550 ("Could not get file size.")
gnu/packages/perl.scm:4481:2: perl-svg-2.63: URI ftp://ftp.osuosl.org/pub/CPAN/authors/id/S/SZ/SZABGAB/SVG-2.63.tar.gz not reachable: 550 ("Could not get file size.")
gnu/packages/perl.scm:4481:2: perl-svg-2.63: URI ftp://ftp.nara.wide.ad.jp/pub/CPAN/authors/id/S/SZ/SZABGAB/SVG-2.63.tar.gz not reachable: 550 ("SVG-2.63.tar.gz: No such file or directory")
gnu/packages/perl.scm:4485:5: perl-svg-2.63: URI http://mirrors.163.com/cpan/authors/id/S/SZ/SZABGAB/SVG-2.63.tar.gz not reachable: 404 ("Not Found")
gnu/packages/perl.scm:4481:2: perl-svg-2.63: URI ftp://cpan.mirror.ac.za/authors/id/S/SZ/SZABGAB/SVG-2.63.tar.gz not reachable: 550 ("Can't check for file existence")
gnu/packages/perl.scm:1622:5: perl-datetime-timezone-1.86: all the source URIs are unreachable:
gnu/packages/perl.scm:1622:5: perl-datetime-timezone-1.86: URI http://cpan.enstimac.fr/authors/id/D/DR/DROLSKY/DateTime-TimeZone-1.86.tar.gz not reachable: 404 ("Not Found")
gnu/packages/perl.scm:1618:2: perl-datetime-timezone-1.86: URI ftp://ftp.ciril.fr/pub/cpan/authors/id/D/DR/DROLSKY/DateTime-TimeZone-1.86.tar.gz not reachable: 550 ("DateTime-TimeZone-1.86.tar.gz: No such file or directory")
gnu/packages/perl.scm:1618:2: perl-datetime-timezone-1.86: URI ftp://artfiles.org/cpan.org/authors/id/D/DR/DROLSKY/DateTime-TimeZone-1.86.tar.gz not reachable: 550 ("DateTime-TimeZone-1.86.tar.gz: No such file or directory")
gnu/packages/perl.scm:1622:5: perl-datetime-timezone-1.86: URI http://www.cpan.org/authors/id/D/DR/DROLSKY/DateTime-TimeZone-1.86.tar.gz not reachable: 404 ("Not Found")
gnu/packages/perl.scm:1618:2: perl-datetime-timezone-1.86: URI ftp://cpan.rinet.ru/pub/mirror/CPAN/authors/id/D/DR/DROLSKY/DateTime-TimeZone-1.86.tar.gz not reachable: 550 ("DateTime-TimeZone-1.86.tar.gz: No such file or directory.")
gnu/packages/perl.scm:1622:5: perl-datetime-timezone-1.86: URI http://cpan.cu.be/authors/id/D/DR/DROLSKY/DateTime-TimeZone-1.86.tar.gz not reachable: 404 ("Not Found")
gnu/packages/perl.scm:1622:5: perl-datetime-timezone-1.86: URI ftp://cpan.inode.at/authors/id/D/DR/DROLSKY/DateTime-TimeZone-1.86.tar.gz unreachable: Protocol not supported
gnu/packages/perl.scm:1618:2: perl-datetime-timezone-1.86: URI ftp://cpan.iht.co.il/authors/id/D/DR/DROLSKY/DateTime-TimeZone-1.86.tar.gz not reachable: 550 ("Could not get file size.")
gnu/packages/perl.scm:1618:2: perl-datetime-timezone-1.86: URI ftp://ftp.osuosl.org/pub/CPAN/authors/id/D/DR/DROLSKY/DateTime-TimeZone-1.86.tar.gz not reachable: 550 ("Could not get file size.")
gnu/packages/perl.scm:1618:2: perl-datetime-timezone-1.86: URI ftp://ftp.nara.wide.ad.jp/pub/CPAN/authors/id/D/DR/DROLSKY/DateTime-TimeZone-1.86.tar.gz not reachable: 550 ("DateTime-TimeZone-1.86.tar.gz: No such file or directory")
gnu/packages/perl.scm:1622:5: perl-datetime-timezone-1.86: URI http://mirrors.163.com/cpan/authors/id/D/DR/DROLSKY/DateTime-TimeZone-1.86.tar.gz not reachable: 404 ("Not Found")
gnu/packages/perl.scm:1618:2: perl-datetime-timezone-1.86: URI ftp://cpan.mirror.ac.za/authors/id/D/DR/DROLSKY/DateTime-TimeZone-1.86.tar.gz not reachable: 550 ("Can't check for file existence")
gnu/packages/perl.scm:2731:5: perl-json-maybexs-1.003003: all the source URIs are unreachable:
gnu/packages/perl.scm:2731:5: perl-json-maybexs-1.003003: URI http://cpan.enstimac.fr/authors/id/E/ET/ETHER/JSON-MaybeXS-1.003003.tar.gz not reachable: 404 ("Not Found")
gnu/packages/perl.scm:2727:2: perl-json-maybexs-1.003003: URI ftp://ftp.ciril.fr/pub/cpan/authors/id/E/ET/ETHER/JSON-MaybeXS-1.003003.tar.gz not reachable: 550 ("JSON-MaybeXS-1.003003.tar.gz: No such file or directory")
gnu/packages/perl.scm:2727:2: perl-json-maybexs-1.003003: URI ftp://artfiles.org/cpan.org/authors/id/E/ET/ETHER/JSON-MaybeXS-1.003003.tar.gz not reachable: 550 ("JSON-MaybeXS-1.003003.tar.gz: No such file or directory")
gnu/packages/perl.scm:2731:5: perl-json-maybexs-1.003003: URI http://www.cpan.org/authors/id/E/ET/ETHER/JSON-MaybeXS-1.003003.tar.gz not reachable: 404 ("Not Found")
gnu/packages/perl.scm:2727:2: perl-json-maybexs-1.003003: URI ftp://cpan.rinet.ru/pub/mirror/CPAN/authors/id/E/ET/ETHER/JSON-MaybeXS-1.003003.tar.gz not reachable: 550 ("JSON-MaybeXS-1.003003.tar.gz: No such file or directory.")
gnu/packages/perl.scm:2731:5: perl-json-maybexs-1.003003: URI http://cpan.cu.be/authors/id/E/ET/ETHER/JSON-MaybeXS-1.003003.tar.gz not reachable: 404 ("Not Found")
gnu/packages/perl.scm:2731:5: perl-json-maybexs-1.003003: URI ftp://cpan.inode.at/authors/id/E/ET/ETHER/JSON-MaybeXS-1.003003.tar.gz unreachable: Protocol not supported
gnu/packages/perl.scm:2727:2: perl-json-maybexs-1.003003: URI ftp://cpan.iht.co.il/authors/id/E/ET/ETHER/JSON-MaybeXS-1.003003.tar.gz not reachable: 550 ("Could not get file size.")
gnu/packages/perl.scm:2727:2: perl-json-maybexs-1.003003: URI ftp://ftp.osuosl.org/pub/CPAN/authors/id/E/ET/ETHER/JSON-MaybeXS-1.003003.tar.gz not reachable: 550 ("Could not get file size.")
gnu/packages/perl.scm:2727:2: perl-json-maybexs-1.003003: URI ftp://ftp.nara.wide.ad.jp/pub/CPAN/authors/id/E/ET/ETHER/JSON-MaybeXS-1.003003.tar.gz not reachable: 550 ("JSON-MaybeXS-1.003003.tar.gz: No such file or directory")
gnu/packages/perl.scm:2731:5: perl-json-maybexs-1.003003: URI http://mirrors.163.com/cpan/authors/id/E/ET/ETHER/JSON-MaybeXS-1.003003.tar.gz not reachable: 404 ("Not Found")
gnu/packages/perl.scm:2727:2: perl-json-maybexs-1.003003: URI ftp://cpan.mirror.ac.za/authors/id/E/ET/ETHER/JSON-MaybeXS-1.003003.tar.gz not reachable: 550 ("Can't check for file existence")
gnu/packages/perl.scm:4804:15: perl-test-deep-0.114: URI http://search.cpan.org/~rjbs/Test-Deep-0.114 not reachable: 404 ("Not Found")
gnu/packages/perl.scm:4788:12: perl-test-deep-0.114: all the source URIs are unreachable:
gnu/packages/perl.scm:4788:12: perl-test-deep-0.114: URI http://cpan.enstimac.fr/authors/id/R/RJ/RJBS/Test-Deep-0.114.tar.gz not reachable: 404 ("Not Found")
gnu/packages/perl.scm:4785:2: perl-test-deep-0.114: URI ftp://ftp.ciril.fr/pub/cpan/authors/id/R/RJ/RJBS/Test-Deep-0.114.tar.gz not reachable: 550 ("Test-Deep-0.114.tar.gz: No such file or directory")
gnu/packages/perl.scm:4785:2: perl-test-deep-0.114: URI ftp://artfiles.org/cpan.org/authors/id/R/RJ/RJBS/Test-Deep-0.114.tar.gz not reachable: 550 ("Test-Deep-0.114.tar.gz: No such file or directory")
gnu/packages/perl.scm:4788:12: perl-test-deep-0.114: URI http://www.cpan.org/authors/id/R/RJ/RJBS/Test-Deep-0.114.tar.gz not reachable: 404 ("Not Found")
gnu/packages/perl.scm:4785:2: perl-test-deep-0.114: URI ftp://cpan.rinet.ru/pub/mirror/CPAN/authors/id/R/RJ/RJBS/Test-Deep-0.114.tar.gz not reachable: 550 ("Test-Deep-0.114.tar.gz: No such file or directory.")
gnu/packages/perl.scm:4788:12: perl-test-deep-0.114: URI http://cpan.cu.be/authors/id/R/RJ/RJBS/Test-Deep-0.114.tar.gz not reachable: 404 ("Not Found")
gnu/packages/perl.scm:4788:12: perl-test-deep-0.114: URI ftp://cpan.inode.at/authors/id/R/RJ/RJBS/Test-Deep-0.114.tar.gz unreachable: Protocol not supported
gnu/packages/perl.scm:4785:2: perl-test-deep-0.114: URI ftp://cpan.iht.co.il/authors/id/R/RJ/RJBS/Test-Deep-0.114.tar.gz not reachable: 550 ("Could not get file size.")
gnu/packages/perl.scm:4785:2: perl-test-deep-0.114: URI ftp://ftp.osuosl.org/pub/CPAN/authors/id/R/RJ/RJBS/Test-Deep-0.114.tar.gz not reachable: 550 ("Could not get file size.")
gnu/packages/perl.scm:4785:2: perl-test-deep-0.114: URI ftp://ftp.nara.wide.ad.jp/pub/CPAN/authors/id/R/RJ/RJBS/Test-Deep-0.114.tar.gz not reachable: 550 ("Test-Deep-0.114.tar.gz: No such file or directory")
gnu/packages/perl.scm:4788:12: perl-test-deep-0.114: URI http://mirrors.163.com/cpan/authors/id/R/RJ/RJBS/Test-Deep-0.114.tar.gz not reachable: 404 ("Not Found")
gnu/packages/perl.scm:4785:2: perl-test-deep-0.114: URI ftp://cpan.mirror.ac.za/authors/id/R/RJ/RJBS/Test-Deep-0.114.tar.gz not reachable: 550 ("Can't check for file existence")
^ permalink raw reply [flat|nested] 7+ messages in thread
* Broken URLs
@ 2015-11-13 8:36 Federico Beffa
2015-11-14 10:47 ` Ludovic Courtès
0 siblings, 1 reply; 7+ messages in thread
From: Federico Beffa @ 2015-11-13 8:36 UTC (permalink / raw)
To: ludo, Guix-devel
ludo@gnu.org (Ludovic Courtès) writes:
> As discussed today on IRC, commit bd7e1ff adds a timeout on connection
> attempts made by ‘guix lint’ for the ‘source’ and ‘home-page’ checkers.
>
> Along with the previous commits, it’s allowed me to run a whole-distro
> check with:
>
> guix lint -c source,home-page
>
> It seems to work nicely (it still leaks FDs due to
> <http://bugs.gnu.org/20145> but that’s OK since these are eventually
> GC’d.)
>
> After letting it run for ~20mn, I’ve collected a whole bunch of URL
> issues (below) that I’m sure everyone will rush to fix. :-)
...
> gnu/packages/maths.scm:1645:15: atlas-3.10.2: URI
> http://math-atlas.sourceforge.net/ unreachable: Connection timed out
I can reach this URL without problems.
Regards,
Fede
^ permalink raw reply [flat|nested] 7+ messages in thread
* Re: Broken URLs
2015-11-13 8:36 Broken URLs Federico Beffa
@ 2015-11-14 10:47 ` Ludovic Courtès
2015-11-14 13:10 ` Federico Beffa
0 siblings, 1 reply; 7+ messages in thread
From: Ludovic Courtès @ 2015-11-14 10:47 UTC (permalink / raw)
To: Federico Beffa; +Cc: Guix-devel
Federico Beffa <beffa@ieee.org> skribis:
> ludo@gnu.org (Ludovic Courtès) writes:
[...]
>> gnu/packages/maths.scm:1645:15: atlas-3.10.2: URI
>> http://math-atlas.sourceforge.net/ unreachable: Connection timed out
>
> I can reach this URL without problems.
Yes, works for me too now.
The URL probe is sensitive to latency and transient network issues, so
there can be false positives like this.
Ludo’.
^ permalink raw reply [flat|nested] 7+ messages in thread
* Re: Broken URLs
2015-11-14 10:47 ` Ludovic Courtès
@ 2015-11-14 13:10 ` Federico Beffa
2015-11-14 14:43 ` Ludovic Courtès
0 siblings, 1 reply; 7+ messages in thread
From: Federico Beffa @ 2015-11-14 13:10 UTC (permalink / raw)
To: Ludovic Courtès; +Cc: Guix-devel
On Sat, Nov 14, 2015 at 11:47 AM, Ludovic Courtès <ludo@gnu.org> wrote:
> The URL probe is sensitive to latency and transient network issues, so
> there can be false positives like this.
Of course. The point is that if you are testing 1000s of URL at the
same time, you may be overloading your own bit of network and you may
need to increase the timeout.
Regards,
Fede
^ permalink raw reply [flat|nested] 7+ messages in thread
* Re: Broken URLs
2015-11-14 13:10 ` Federico Beffa
@ 2015-11-14 14:43 ` Ludovic Courtès
0 siblings, 0 replies; 7+ messages in thread
From: Ludovic Courtès @ 2015-11-14 14:43 UTC (permalink / raw)
To: Federico Beffa; +Cc: Guix-devel
Federico Beffa <beffa@ieee.org> skribis:
> On Sat, Nov 14, 2015 at 11:47 AM, Ludovic Courtès <ludo@gnu.org> wrote:
>> The URL probe is sensitive to latency and transient network issues, so
>> there can be false positives like this.
>
> Of course. The point is that if you are testing 1000s of URL at the
> same time, you may be overloading your own bit of network and you may
> need to increase the timeout.
Yeah, possibly. There were only two ETIMEDOUT in the examples I sent;
the other one was for Cook, which is still unreachable.
Ludo’.
^ permalink raw reply [flat|nested] 7+ messages in thread
* Re: Broken URLs
2015-11-12 22:55 Ludovic Courtès
@ 2015-11-20 10:24 ` Ricardo Wurmus
2015-11-20 13:41 ` Ludovic Courtès
0 siblings, 1 reply; 7+ messages in thread
From: Ricardo Wurmus @ 2015-11-20 10:24 UTC (permalink / raw)
To: Ludovic Courtès; +Cc: guix
[-- Attachment #1: Type: text/plain, Size: 2867 bytes --]
Ludovic Courtès <ludo@gnu.org> writes:
> gnu/packages/audio.scm:272:12: calf-0.0.60: all the source URIs are unreachable:
> gnu/packages/audio.scm:272:12: calf-0.0.60: URI http://prdownloads.sourceforge.net/calf/calf/0.0.60/calf-0.0.60.tar.gz not reachable: 404 ("Not Found")
> gnu/packages/audio.scm:272:12: calf-0.0.60: URI http://heanet.dl.sourceforge.net/sourceforge/calf/calf/0.0.60/calf-0.0.60.tar.gz not reachable: 404 ("Not Found")
> gnu/packages/audio.scm:272:12: calf-0.0.60: URI http://surfnet.dl.sourceforge.net/sourceforge/calf/calf/0.0.60/calf-0.0.60.tar.gz unreachable: Network is unreachable
> gnu/packages/audio.scm:272:12: calf-0.0.60: URI http://dfn.dl.sourceforge.net/sourceforge/calf/calf/0.0.60/calf-0.0.60.tar.gz not reachable: 404 ("Not Found")
> gnu/packages/audio.scm:272:12: calf-0.0.60: URI http://mesh.dl.sourceforge.net/sourceforge/calf/calf/0.0.60/calf-0.0.60.tar.gz domain not found: Name or service not known
> gnu/packages/audio.scm:272:12: calf-0.0.60: URI http://ovh.dl.sourceforge.net/sourceforge/calf/calf/0.0.60/calf-0.0.60.tar.gz domain not found: Name or service not known
> gnu/packages/audio.scm:272:12: calf-0.0.60: URI http://osdn.dl.sourceforge.net/sourceforge/calf/calf/0.0.60/calf-0.0.60.tar.gz not reachable: 404 ("Not Found")
This has been fixed in commit 73cea74ddaf98f.
> gnu/packages/bioinformatics.scm:1115:15: edirect-2.50: URI http://www.ncbi.nlm.nih.gov/books/NBK179288 not reachable: 303 ("See Other")
I can reach it, but it seems to redirect to URL + “/”. I’ll add the
trailing slash.
> gnu/packages/bioinformatics.scm:2627:5: sra-tools-2.4.5-5: all the source URIs are unreachable:
> gnu/packages/bioinformatics.scm:2627:5: sra-tools-2.4.5-5: URI https://github.com/ncbi/sra-tools/archive/2.4.5-5.tar.gz not reachable: 404 ("Not Found")
The tarball has been removed. I’ll update it to the latest version.
> gnu/packages/bioinformatics.scm:2419:5: ncbi-vdb-2.4.5-5: all the source URIs are unreachable:
> gnu/packages/bioinformatics.scm:2419:5: ncbi-vdb-2.4.5-5: URI https://github.com/ncbi/ncbi-vdb /archive/2.4.5-5.tar.gz not reachable: 404 ("Not Found")
Same here. The tarball was removed. There are new versions out
already, so I’ll take the opportunity to update it.
> gnu/packages/bioinformatics.scm:2570:12: preseq-1.0.2: all the source URIs are unreachable:
> gnu/packages/bioinformatics.scm:2570:12: preseq-1.0.2: URI http://smithlabresearch.org/downloads/preseq-1.0.2.tar.bz2 not reachable: 404 ("Not Found")
Version 2.0 has been released and the old tarball has been removed. The
location for 2.0 is this:
https://github.com/smithlabcode/preseq/archive/v2.0.tar.gz
Attached are two patches to update our recipe. A new package was added
to deal with the fact that bundled sources have been removed from the
tarball.
[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #2: 0001-gnu-Add-smithlab-cpp.patch --]
[-- Type: text/x-patch, Size: 3049 bytes --]
From 01d547a6eedfb28d19551042f581e588dcc56fb5 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Fri, 20 Nov 2015 11:14:00 +0100
Subject: [PATCH 1/2] gnu: Add smithlab-cpp.
* gnu/packages/bioinformatics.scm (smithlab-cpp): New variable.
---
gnu/packages/bioinformatics.scm | 53 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 53 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index e0c1944..90a3c51 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2662,6 +2662,59 @@ subsequent visualization, annotation and storage of results.")
;; LGPLv2.1+
(license (list license:gpl2 license:lgpl2.1+))))
+(define-public smithlab-cpp
+ (let ((revision "1")
+ (commit "728a097"))
+ (package
+ (name "smithlab-cpp")
+ (version (string-append "0." revision "." commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/smithlabcode/smithlab_cpp.git")
+ (commit commit)))
+ (file-name (string-append name "-" version "-checkout"))
+ (sha256
+ (base32
+ "0d476lmj312xk77kr9fzrv7z1bv96yfyx0w7y62ycmnfbx32ll74"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:modules ((guix build gnu-build-system)
+ (guix build utils)
+ (srfi srfi-26))
+ #:tests? #f ;no "check" target
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'use-samtools-headers
+ (lambda _
+ (substitute* '("SAM.cpp"
+ "SAM.hpp")
+ (("sam.h") "samtools/sam.h"))
+ #t))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (lib (string-append out "/lib"))
+ (include (string-append out "/include/smithlab-cpp")))
+ (mkdir-p lib)
+ (mkdir-p include)
+ (for-each (cut install-file <> lib)
+ (find-files "." "\\.o$"))
+ (for-each (cut install-file <> include)
+ (find-files "." "\\.hpp$")))
+ #t))
+ (delete 'configure))))
+ (inputs
+ `(("samtools" ,samtools-0.1)
+ ("zlib" ,zlib)))
+ (home-page "https://github.com/smithlabcode/smithlab_cpp")
+ (synopsis "C++ helper library for functions used in Smith lab projects")
+ (description
+ "Smithlab CPP is a C++ library that includes functions used in many of
+the Smith lab bioinformatics projects, such as a wrapper around Samtools data
+structures, classes for genomic regions, mapped sequencing reads, etc.")
+ (license license:gpl3+))))
+
(define-public preseq
(package
(name "preseq")
--
2.1.0
[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #3: 0002-gnu-preseq-Update-to-2.0.patch --]
[-- Type: text/x-patch, Size: 7396 bytes --]
From 534d7b73cda92b982f1338b1c9db420767d78066 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Fri, 20 Nov 2015 11:14:48 +0100
Subject: [PATCH 2/2] gnu: preseq: Update to 2.0.
* gnu/packages/bioinformatics.scm (preseq): Update to 2.0.
[source]: Add file-name field, remove patches.
[arguments]: Remove unused build phases, add make flags.
[inputs]: Add smithlab-cpp.
* gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch: Remove file.
* gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch: Remove
file.
* gnu-system.am (dist_patch_DATA): Remove them.
---
gnu-system.am | 2 -
gnu/packages/bioinformatics.scm | 43 +++++++++-------------
.../patches/preseq-1.0.2-install-to-PREFIX.patch | 37 -------------------
.../patches/preseq-1.0.2-link-with-libbam.patch | 33 -----------------
4 files changed, 18 insertions(+), 97 deletions(-)
delete mode 100644 gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch
delete mode 100644 gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch
diff --git a/gnu-system.am b/gnu-system.am
index 9d41c49..7d9afba 100644
--- a/gnu-system.am
+++ b/gnu-system.am
@@ -625,8 +625,6 @@ dist_patch_DATA = \
gnu/packages/patches/plotutils-libpng-jmpbuf.patch \
gnu/packages/patches/polkit-drop-test.patch \
gnu/packages/patches/portaudio-audacity-compat.patch \
- gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch \
- gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch \
gnu/packages/patches/procps-make-3.82.patch \
gnu/packages/patches/pt-scotch-build-parallelism.patch \
gnu/packages/patches/pulseaudio-fix-mult-test.patch \
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 90a3c51..d66c6ab 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2718,46 +2718,39 @@ structures, classes for genomic regions, mapped sequencing reads, etc.")
(define-public preseq
(package
(name "preseq")
- (version "1.0.2")
+ (version "2.0")
(source (origin
(method url-fetch)
- (uri
- (string-append "http://smithlabresearch.org/downloads/preseq-"
- version ".tar.bz2"))
+ (uri (string-append "https://github.com/smithlabcode/"
+ "preseq/archive/v" version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
(sha256
- (base32 "0r7sw07p6nv8ygvc17gd78lisbw5336v3vhs86b5wv8mw3pwqksc"))
- (patches (list (search-patch "preseq-1.0.2-install-to-PREFIX.patch")
- (search-patch "preseq-1.0.2-link-with-libbam.patch")))
+ (base32 "08r684l50pnxjpvmhzjgqq56yv9rfw90k8vx0nsrnrzk8mf9hsdq"))
(modules '((guix build utils)))
(snippet
;; Remove bundled samtools.
- '(delete-file-recursively "preseq-master/samtools"))))
+ '(delete-file-recursively "samtools"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ;no "check" target
#:phases
(modify-phases %standard-phases
- (add-after
- 'unpack 'enter-dir
- (lambda _
- (chdir "preseq-master")
- #t))
- (add-after
- 'enter-dir 'use-samtools-headers
- (lambda _
- (substitute* '("smithlab_cpp/SAM.cpp"
- "smithlab_cpp/SAM.hpp")
- (("sam.h") "samtools/sam.h"))
- #t))
(delete 'configure))
- #:make-flags (list (string-append "PREFIX="
- (assoc-ref %outputs "out"))
- (string-append "LIBBAM="
- (assoc-ref %build-inputs "samtools")
- "/lib/libbam.a"))))
+ #:make-flags
+ (list (string-append "PREFIX="
+ (assoc-ref %outputs "out"))
+ (string-append "LIBBAM="
+ (assoc-ref %build-inputs "samtools")
+ "/lib/libbam.a")
+ (string-append "SMITHLAB_CPP="
+ (assoc-ref %build-inputs "smithlab-cpp")
+ "/lib")
+ "PROGS=preseq"
+ "INCLUDEDIRS=$(SMITHLAB_CPP)/../include/smithlab-cpp $(SAMTOOLS_DIR)")))
(inputs
`(("gsl" ,gsl)
("samtools" ,samtools-0.1)
+ ("smithlab-cpp" ,smithlab-cpp)
("zlib" ,zlib)))
(home-page "http://smithlabresearch.org/software/preseq/")
(synopsis "Program for analyzing library complexity")
diff --git a/gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch b/gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch
deleted file mode 100644
index f8318ae..0000000
--- a/gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch
+++ /dev/null
@@ -1,37 +0,0 @@
-This patch has been submitted upstream: https://github.com/smithlabcode/preseq/pull/15
-
-From 65387b0d766e6c06a15cf8d8f9183d9a4ba644bb Mon Sep 17 00:00:00 2001
-From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
-Date: Thu, 25 Jun 2015 15:01:53 +0200
-Subject: [PATCH] Install to PREFIX
-
----
- Makefile | 8 ++++++--
- 1 file changed, 6 insertions(+), 2 deletions(-)
-
-diff --git a/Makefile b/Makefile
-index 4d0367a..e334f2f 100644
---- a/preseq-master/Makefile
-+++ b/preseq-master/Makefile
-@@ -22,6 +22,10 @@ ifndef ROOT
- ROOT = $(shell pwd)
- endif
-
-+ifndef PREFIX
-+PREFIX = $(ROOT)
-+endif
-+
- ifndef SMITHLAB_CPP
- SMITHLAB_CPP=$(ROOT)/smithlab_cpp/
- endif
-@@ -91,8 +95,8 @@ endif
- $(CXX) $(CXXFLAGS) -o $@ $^ $(INCLUDEARGS) $(LIBS)
-
- install: $(PROGS)
-- @mkdir -p $(ROOT)/bin
-- @install -m 755 $(PROGS) $(ROOT)/bin
-+ @mkdir -p $(PREFIX)/bin
-+ @install -m 755 $(PROGS) $(PREFIX)/bin
-
- clean:
- @-rm -f $(PROGS) *.o *~
diff --git a/gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch b/gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch
deleted file mode 100644
index 035a3b1..0000000
--- a/gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch
+++ /dev/null
@@ -1,33 +0,0 @@
-This patch has been submitted upstream: https://github.com/smithlabcode/preseq/pull/15
-
-From a937a54d56e8a6ff06237471e568154d1fa5f267 Mon Sep 17 00:00:00 2001
-From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
-Date: Thu, 25 Jun 2015 15:02:35 +0200
-Subject: [PATCH] Link with libbam.a if provided via LIBBAM
-
----
- Makefile | 7 +++++++
- 1 file changed, 7 insertions(+)
-
-diff --git a/Makefile b/Makefile
-index e334f2f..de310e4 100644
---- a/preseq-master/Makefile
-+++ b/preseq-master/Makefile
-@@ -83,10 +83,17 @@ $(PROGS): $(addprefix $(SMITHLAB_CPP)/, \
- preseq: continued_fraction.o load_data_for_complexity.o moment_sequence.o
-
- ifdef SAMTOOLS_DIR
-+ifdef LIBBAM
-+LIBS += -pthread
-+bam2mr preseq: $(addprefix $(SMITHLAB_CPP)/, SAM.o) \
-+ $(LIBBAM)
-+else
- bam2mr preseq: $(addprefix $(SMITHLAB_CPP)/, SAM.o) \
- $(addprefix $(SAMTOOLS_DIR)/, sam.o bam.o bam_import.o bam_pileup.o \
- faidx.o bam_aux.o kstring.o knetfile.o sam_header.o razf.o bgzf.o)
- endif
-+endif # SAMTOOLS_DIR
-+
-
- %.o: %.cpp %.hpp
- $(CXX) $(CXXFLAGS) -c -o $@ $< $(INCLUDEARGS)
--
2.1.0
[-- Attachment #4: Type: text/plain, Size: 414 bytes --]
> gnu/packages/java.scm:139:12: ant-1.9.4: all the source URIs are unreachable:
> gnu/packages/java.scm:139:12: ant-1.9.4: URI https://www.apache.org/dist/ant/source/apache-ant-1.9.4-src.tar.gz not reachable: 404 ("Not Found")
I don’t know why people do this but here again the tarballs have been
removed and replaced with those for version 1.9.6. Here’s another patch
to update our ant package:
[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #5: 0001-gnu-ant-Update-to-1.9.6.patch --]
[-- Type: text/x-patch, Size: 1095 bytes --]
From 212e56286c946b7a34d03819c20faa473cc42a9d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Fri, 20 Nov 2015 11:23:18 +0100
Subject: [PATCH] gnu: ant: Update to 1.9.6.
* gnu/packages/java.scm (ant): Update to 1.9.6.
---
gnu/packages/java.scm | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm
index 6d34460..f00a3d7 100644
--- a/gnu/packages/java.scm
+++ b/gnu/packages/java.scm
@@ -135,7 +135,7 @@ is implemented.")
(define-public ant
(package
(name "ant")
- (version "1.9.4")
+ (version "1.9.6")
(source (origin
(method url-fetch)
(uri (string-append
@@ -143,7 +143,7 @@ is implemented.")
version "-src.tar.gz"))
(sha256
(base32
- "09kf5s1ir0rdrclsy174bsvbdcbajza9fja490w4mmvcpkw3zpak"))))
+ "1396wflczyxjxl603dhxjvd559f289lha9y2f04f71c7hapjl3am"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; no "check" target
--
2.1.0
[-- Attachment #6: Type: text/plain, Size: 436 bytes --]
> gnu/packages/messaging.scm:413:15: python2-nbxmpp-0.5.3: URI http://python-nbxmpp.gajim.org not reachable: 500 ("Internal Server Error")
> gnu/packages/messaging.scm:413:15: python-nbxmpp-0.5.3: URI http://python-nbxmpp.gajim.org not reachable: 500 ("Internal Server Error")
There are some problems with the project’s homepage (self-signed cert
and trac configuration issues), but I don’t see a 500 error.
~~ Ricardo
^ permalink raw reply related [flat|nested] 7+ messages in thread
* Re: Broken URLs
2015-11-20 10:24 ` Ricardo Wurmus
@ 2015-11-20 13:41 ` Ludovic Courtès
0 siblings, 0 replies; 7+ messages in thread
From: Ludovic Courtès @ 2015-11-20 13:41 UTC (permalink / raw)
To: Ricardo Wurmus; +Cc: guix
Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:
> Ludovic Courtès <ludo@gnu.org> writes:
[...]
>> gnu/packages/bioinformatics.scm:2627:5: sra-tools-2.4.5-5: all the source URIs are unreachable:
>> gnu/packages/bioinformatics.scm:2627:5: sra-tools-2.4.5-5: URI https://github.com/ncbi/sra-tools/archive/2.4.5-5.tar.gz not reachable: 404 ("Not Found")
>
> The tarball has been removed. I’ll update it to the latest version.
>
>> gnu/packages/bioinformatics.scm:2419:5: ncbi-vdb-2.4.5-5: all the source URIs are unreachable:
>> gnu/packages/bioinformatics.scm:2419:5: ncbi-vdb-2.4.5-5: URI https://github.com/ncbi/ncbi-vdb /archive/2.4.5-5.tar.gz not reachable: 404 ("Not Found")
>
> Same here. The tarball was removed. There are new versions out
> already, so I’ll take the opportunity to update it.
Aren’t these /archive URLs providing tarballs generated on the fly from
a Git tag?
Looking at <https://github.com/ncbi/ncbi-vdb/releases>, it seems that
this particular tag has been removed.
> From 01d547a6eedfb28d19551042f581e588dcc56fb5 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Fri, 20 Nov 2015 11:14:00 +0100
> Subject: [PATCH 1/2] gnu: Add smithlab-cpp.
>
> * gnu/packages/bioinformatics.scm (smithlab-cpp): New variable.
LGTM.
> From 534d7b73cda92b982f1338b1c9db420767d78066 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Fri, 20 Nov 2015 11:14:48 +0100
> Subject: [PATCH 2/2] gnu: preseq: Update to 2.0.
>
> * gnu/packages/bioinformatics.scm (preseq): Update to 2.0.
> [source]: Add file-name field, remove patches.
> [arguments]: Remove unused build phases, add make flags.
> [inputs]: Add smithlab-cpp.
> * gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch: Remove file.
> * gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch: Remove
> file.
> * gnu-system.am (dist_patch_DATA): Remove them.
LGTM.
>> gnu/packages/java.scm:139:12: ant-1.9.4: all the source URIs are unreachable:
>> gnu/packages/java.scm:139:12: ant-1.9.4: URI https://www.apache.org/dist/ant/source/apache-ant-1.9.4-src.tar.gz not reachable: 404 ("Not Found")
>
> I don’t know why people do this but here again the tarballs have been
> removed and replaced with those for version 1.9.6. Here’s another patch
> to update our ant package:
mirror://apache includes http://archive.apache.org/dist/, which is where
old archives go. Could you use that one instead?
> From 212e56286c946b7a34d03819c20faa473cc42a9d Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Fri, 20 Nov 2015 11:23:18 +0100
> Subject: [PATCH] gnu: ant: Update to 1.9.6.
>
> * gnu/packages/java.scm (ant): Update to 1.9.6.
Upgrading is fine too.
Thank you!
Ludo’.
^ permalink raw reply [flat|nested] 7+ messages in thread
end of thread, other threads:[~2015-11-20 13:41 UTC | newest]
Thread overview: 7+ messages (download: mbox.gz follow: Atom feed
-- links below jump to the message on this page --
2015-11-13 8:36 Broken URLs Federico Beffa
2015-11-14 10:47 ` Ludovic Courtès
2015-11-14 13:10 ` Federico Beffa
2015-11-14 14:43 ` Ludovic Courtès
-- strict thread matches above, loose matches on Subject: below --
2015-11-12 22:55 Ludovic Courtès
2015-11-20 10:24 ` Ricardo Wurmus
2015-11-20 13:41 ` Ludovic Courtès
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