From cjfields at illinois.edu Wed Jan 7 13:57:14 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 7 Jan 2009 12:57:14 -0600 Subject: [Bioperl-announce-l] BioPerl 1.6 RC2 is now available Message-ID: <1C84285B-1C49-43F6-8B53-EE011EDAA0BE@illinois.edu> All, I would like to announce the second release candidate for BioPerl 1.6 is available for testing. A quick note on versioning: due to issues with alpha numbered versions on CPAN possibly overwriting a stable release, this release candidate has a VERSION of 1.005009_002 (or 1.005009002). This will be switched to 1.006000 (no alpha) once the release is final. RC2 has been uploaded to CPAN is available under authorname CJFIELDS. From the CPAN shell: cpan[1]> install CJFIELDS/BioPerl-1.5.9_2.tar.gz RC2 can be directly downloaded here: http://bioperl.org/DIST/BioPerl-1.5.9_2.tar.bz2 http://bioperl.org/DIST/BioPerl-1.5.9_2.tar.gz http://bioperl.org/DIST/BioPerl-1.5.9_2.zip Signature file: http://bioperl.org/DIST/SIGNATURES.md5 A preliminary ActiveState PPM is also available and is located in the BioPerl Release Candidate repository; the directions for installation are here: http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows Please feel free to report issues with testing, installation, etc. on the mail list and on this page: http://www.bioperl.org/wiki/Release_1.6_Testing Again, just to note we will be releasing bioperl-run, bioperl-db, bioperl-network, and others separately once the final 1.6 release is complete. Since the last release: Fixed: 1) Some cruft from testing the last release is no longer present. 2) Several warnings and test failures (via CPAN Testers) now fixed. Known Issues: 1) A very recent change in ENSembl data causes one of the Map.t tests to fail; this has already been fixed and will be present in the next (final?) release. 2) Some odd warnings for Bio::Assembly tests are still present, but they are harmless. Nevertheless they will be addressed prior to the next release. 3) Warnings for Bio::Annotation tests can be fixed by an upgrade to the latest Data::Stag (this is NOT a required upgrade). 4) PPM issues; note this is not high on our priority list ATM but I will try to address it for the next release). Enjoy! chris From cjfields at illinois.edu Sun Jan 25 19:22:16 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 25 Jan 2009 18:22:16 -0600 Subject: [Bioperl-announce-l] [ANNOUNCEMENT] BioPerl 1.6.0 Message-ID: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> All, I am proud to announce, on behalf of the BioPerl core developers, that BioPerl 1.6.0 is now available. This is the first BioPerl core release in the 1.6 series and is considered a 'stable' (non-developer) release. The distribution has been uploaded to CPAN and is available under author name CJFIELDS; it should be hitting the various CPAN nodes over the next 24 hours. A direct CPAN link is here: http://search.cpan.org/~cjfields/BioPerl-1.6.0/ The release can also be directly downloaded here: http://bioperl.org/DIST/BioPerl-1.6.0.tar.bz2 http://bioperl.org/DIST/BioPerl-1.6.0.tar.gz http://bioperl.org/DIST/BioPerl-1.6.0.zip Signature file: http://bioperl.org/DIST/SIGNATURES.md5 Please feel free to report issues with testing, installation, etc. on the mail list, on this page: http://www.bioperl.org/wiki/Release_1.6_Testing or via Bugzilla: http://bugzilla.open-bio.org/ We will be releasing BioPerl-run, BioPerl-db, BioPerl-network, and other BioPerl distributions separately in the next few days. These will likely go through a short alpha release cycle depending on any problems that arise. A PPM release for all distributions (including BioPerl core) will also be announced in the near future. Thanks to everyone for chipping in on getting this release out the door! It's been a looooong wait... Enjoy! chris From florent.angly at gmail.com Mon Jan 26 00:06:03 2009 From: florent.angly at gmail.com (Florent Angly) Date: Sun, 25 Jan 2009 21:06:03 -0800 Subject: [Bioperl-announce-l] [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 In-Reply-To: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> References: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> Message-ID: <497D44BB.3080204@gmail.com> Good job! It's very exciting to have a new BioPerl release out there Florent Chris Fields wrote: > All, > > I am proud to announce, on behalf of the BioPerl core developers, that > BioPerl 1.6.0 is now available. This is the first BioPerl core > release in the 1.6 series and is considered a 'stable' (non-developer) > release. The distribution has been uploaded to CPAN and is available > under author name CJFIELDS; it should be hitting the various CPAN > nodes over the next 24 hours. A direct CPAN link is here: > > http://search.cpan.org/~cjfields/BioPerl-1.6.0/ > > The release can also be directly downloaded here: > > http://bioperl.org/DIST/BioPerl-1.6.0.tar.bz2 > http://bioperl.org/DIST/BioPerl-1.6.0.tar.gz > http://bioperl.org/DIST/BioPerl-1.6.0.zip > > Signature file: > http://bioperl.org/DIST/SIGNATURES.md5 > > Please feel free to report issues with testing, installation, etc. on > the mail list, on this page: > > http://www.bioperl.org/wiki/Release_1.6_Testing > > or via Bugzilla: > > http://bugzilla.open-bio.org/ > > We will be releasing BioPerl-run, BioPerl-db, BioPerl-network, and > other BioPerl distributions separately in the next few days. These > will likely go through a short alpha release cycle depending on any > problems that arise. A PPM release for all distributions (including > BioPerl core) will also be announced in the near future. > > Thanks to everyone for chipping in on getting this release out the > door! It's been a looooong wait... > > Enjoy! > > chris > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From mauricio at open-bio.org Mon Jan 26 10:25:19 2009 From: mauricio at open-bio.org (Mauricio Herrera Cuadra) Date: Mon, 26 Jan 2009 09:25:19 -0600 Subject: [Bioperl-announce-l] [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 In-Reply-To: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> References: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> Message-ID: <497DD5DF.3070900@open-bio.org> Great job Chris et al. Congratulations!! :) Chris Fields wrote: > All, > > I am proud to announce, on behalf of the BioPerl core developers, that > BioPerl 1.6.0 is now available. This is the first BioPerl core release > in the 1.6 series and is considered a 'stable' (non-developer) release. > The distribution has been uploaded to CPAN and is available under author > name CJFIELDS; it should be hitting the various CPAN nodes over the next > 24 hours. A direct CPAN link is here: > > http://search.cpan.org/~cjfields/BioPerl-1.6.0/ > > The release can also be directly downloaded here: > > http://bioperl.org/DIST/BioPerl-1.6.0.tar.bz2 > http://bioperl.org/DIST/BioPerl-1.6.0.tar.gz > http://bioperl.org/DIST/BioPerl-1.6.0.zip > > Signature file: > http://bioperl.org/DIST/SIGNATURES.md5 > > Please feel free to report issues with testing, installation, etc. on > the mail list, on this page: > > http://www.bioperl.org/wiki/Release_1.6_Testing > > or via Bugzilla: > > http://bugzilla.open-bio.org/ > > We will be releasing BioPerl-run, BioPerl-db, BioPerl-network, and other > BioPerl distributions separately in the next few days. These will > likely go through a short alpha release cycle depending on any problems > that arise. A PPM release for all distributions (including BioPerl > core) will also be announced in the near future. > > Thanks to everyone for chipping in on getting this release out the > door! It's been a looooong wait... > > Enjoy! > > chris > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From cjfields at illinois.edu Wed Jan 7 18:57:14 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 7 Jan 2009 12:57:14 -0600 Subject: [Bioperl-announce-l] BioPerl 1.6 RC2 is now available Message-ID: <1C84285B-1C49-43F6-8B53-EE011EDAA0BE@illinois.edu> All, I would like to announce the second release candidate for BioPerl 1.6 is available for testing. A quick note on versioning: due to issues with alpha numbered versions on CPAN possibly overwriting a stable release, this release candidate has a VERSION of 1.005009_002 (or 1.005009002). This will be switched to 1.006000 (no alpha) once the release is final. RC2 has been uploaded to CPAN is available under authorname CJFIELDS. From the CPAN shell: cpan[1]> install CJFIELDS/BioPerl-1.5.9_2.tar.gz RC2 can be directly downloaded here: http://bioperl.org/DIST/BioPerl-1.5.9_2.tar.bz2 http://bioperl.org/DIST/BioPerl-1.5.9_2.tar.gz http://bioperl.org/DIST/BioPerl-1.5.9_2.zip Signature file: http://bioperl.org/DIST/SIGNATURES.md5 A preliminary ActiveState PPM is also available and is located in the BioPerl Release Candidate repository; the directions for installation are here: http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows Please feel free to report issues with testing, installation, etc. on the mail list and on this page: http://www.bioperl.org/wiki/Release_1.6_Testing Again, just to note we will be releasing bioperl-run, bioperl-db, bioperl-network, and others separately once the final 1.6 release is complete. Since the last release: Fixed: 1) Some cruft from testing the last release is no longer present. 2) Several warnings and test failures (via CPAN Testers) now fixed. Known Issues: 1) A very recent change in ENSembl data causes one of the Map.t tests to fail; this has already been fixed and will be present in the next (final?) release. 2) Some odd warnings for Bio::Assembly tests are still present, but they are harmless. Nevertheless they will be addressed prior to the next release. 3) Warnings for Bio::Annotation tests can be fixed by an upgrade to the latest Data::Stag (this is NOT a required upgrade). 4) PPM issues; note this is not high on our priority list ATM but I will try to address it for the next release). Enjoy! chris From cjfields at illinois.edu Mon Jan 26 00:22:16 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 25 Jan 2009 18:22:16 -0600 Subject: [Bioperl-announce-l] [ANNOUNCEMENT] BioPerl 1.6.0 Message-ID: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> All, I am proud to announce, on behalf of the BioPerl core developers, that BioPerl 1.6.0 is now available. This is the first BioPerl core release in the 1.6 series and is considered a 'stable' (non-developer) release. The distribution has been uploaded to CPAN and is available under author name CJFIELDS; it should be hitting the various CPAN nodes over the next 24 hours. A direct CPAN link is here: http://search.cpan.org/~cjfields/BioPerl-1.6.0/ The release can also be directly downloaded here: http://bioperl.org/DIST/BioPerl-1.6.0.tar.bz2 http://bioperl.org/DIST/BioPerl-1.6.0.tar.gz http://bioperl.org/DIST/BioPerl-1.6.0.zip Signature file: http://bioperl.org/DIST/SIGNATURES.md5 Please feel free to report issues with testing, installation, etc. on the mail list, on this page: http://www.bioperl.org/wiki/Release_1.6_Testing or via Bugzilla: http://bugzilla.open-bio.org/ We will be releasing BioPerl-run, BioPerl-db, BioPerl-network, and other BioPerl distributions separately in the next few days. These will likely go through a short alpha release cycle depending on any problems that arise. A PPM release for all distributions (including BioPerl core) will also be announced in the near future. Thanks to everyone for chipping in on getting this release out the door! It's been a looooong wait... Enjoy! chris From florent.angly at gmail.com Mon Jan 26 05:06:03 2009 From: florent.angly at gmail.com (Florent Angly) Date: Sun, 25 Jan 2009 21:06:03 -0800 Subject: [Bioperl-announce-l] [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 In-Reply-To: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> References: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> Message-ID: <497D44BB.3080204@gmail.com> Good job! It's very exciting to have a new BioPerl release out there Florent Chris Fields wrote: > All, > > I am proud to announce, on behalf of the BioPerl core developers, that > BioPerl 1.6.0 is now available. This is the first BioPerl core > release in the 1.6 series and is considered a 'stable' (non-developer) > release. The distribution has been uploaded to CPAN and is available > under author name CJFIELDS; it should be hitting the various CPAN > nodes over the next 24 hours. A direct CPAN link is here: > > http://search.cpan.org/~cjfields/BioPerl-1.6.0/ > > The release can also be directly downloaded here: > > http://bioperl.org/DIST/BioPerl-1.6.0.tar.bz2 > http://bioperl.org/DIST/BioPerl-1.6.0.tar.gz > http://bioperl.org/DIST/BioPerl-1.6.0.zip > > Signature file: > http://bioperl.org/DIST/SIGNATURES.md5 > > Please feel free to report issues with testing, installation, etc. on > the mail list, on this page: > > http://www.bioperl.org/wiki/Release_1.6_Testing > > or via Bugzilla: > > http://bugzilla.open-bio.org/ > > We will be releasing BioPerl-run, BioPerl-db, BioPerl-network, and > other BioPerl distributions separately in the next few days. These > will likely go through a short alpha release cycle depending on any > problems that arise. A PPM release for all distributions (including > BioPerl core) will also be announced in the near future. > > Thanks to everyone for chipping in on getting this release out the > door! It's been a looooong wait... > > Enjoy! > > chris > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From mauricio at open-bio.org Mon Jan 26 15:25:19 2009 From: mauricio at open-bio.org (Mauricio Herrera Cuadra) Date: Mon, 26 Jan 2009 09:25:19 -0600 Subject: [Bioperl-announce-l] [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 In-Reply-To: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> References: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> Message-ID: <497DD5DF.3070900@open-bio.org> Great job Chris et al. Congratulations!! :) Chris Fields wrote: > All, > > I am proud to announce, on behalf of the BioPerl core developers, that > BioPerl 1.6.0 is now available. This is the first BioPerl core release > in the 1.6 series and is considered a 'stable' (non-developer) release. > The distribution has been uploaded to CPAN and is available under author > name CJFIELDS; it should be hitting the various CPAN nodes over the next > 24 hours. A direct CPAN link is here: > > http://search.cpan.org/~cjfields/BioPerl-1.6.0/ > > The release can also be directly downloaded here: > > http://bioperl.org/DIST/BioPerl-1.6.0.tar.bz2 > http://bioperl.org/DIST/BioPerl-1.6.0.tar.gz > http://bioperl.org/DIST/BioPerl-1.6.0.zip > > Signature file: > http://bioperl.org/DIST/SIGNATURES.md5 > > Please feel free to report issues with testing, installation, etc. on > the mail list, on this page: > > http://www.bioperl.org/wiki/Release_1.6_Testing > > or via Bugzilla: > > http://bugzilla.open-bio.org/ > > We will be releasing BioPerl-run, BioPerl-db, BioPerl-network, and other > BioPerl distributions separately in the next few days. These will > likely go through a short alpha release cycle depending on any problems > that arise. A PPM release for all distributions (including BioPerl > core) will also be announced in the near future. > > Thanks to everyone for chipping in on getting this release out the > door! It's been a looooong wait... > > Enjoy! > > chris > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l >